Starting phenix.real_space_refine
on Tue Mar  3 16:59:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dce_30636/03_2026/7dce_30636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dce_30636/03_2026/7dce_30636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_2026/7dce_30636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_2026/7dce_30636.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_2026/7dce_30636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_2026/7dce_30636.map"
  }
  resolution = 3.8
  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=   0.001 sd=   0.011
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
     P       1      5.49       5
     S      28      5.16       5
     C    4602      2.51       5
     N    1161      2.21       5
     O    1310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7102
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1032
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1032
          Classifications: {'peptide': 132}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "X"
      Number of atoms: 2837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2837
          Classifications: {'peptide': 354}
          Link IDs: {'PTRANS': 17, 'TRANS': 336}
    Chain: "H"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1553
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1626
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 207}
    Chain: "X"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 54
          Unusual residues: {'DLP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.82, per 1000 atoms: 0.26
  Number of scatterers: 7102
  At special positions: 0
  Unit cell: (113.295, 70.965, 117.03, 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      28     16.00
     P       1     15.00
     O    1310      8.00
     N    1161      7.00
     C    4602      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 185 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  21 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 139 " - pdb=" SG  CYS H 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  81 " - pdb=" SG  CYS L 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 138 " - pdb=" SG  CYS L 198 " distance=2.03

  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: 0.76
  Conformation dependent library (CDL) restraints added in 292.3 milliseconds
  

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1690

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      40.4% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 153 through 156
    Processing helix  chain 'B' and resid 204 through 209
    Processing helix  chain 'B' and resid 209 through 230
      removed outlier: 3.713A  pdb=" N   LEU B 213 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE B 215 " --> pdb=" O   PRO B 211 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 8 through 41
    Processing helix  chain 'X' and resid 43 through 71
    Processing helix  chain 'X' and resid 83 through 91
    Processing helix  chain 'X' and resid 95 through 112
    Processing helix  chain 'X' and resid 116 through 141
      removed outlier: 3.505A  pdb=" N   LEU X 120 " --> pdb=" O   SER X 116 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA X 121 " --> pdb=" O   GLU X 117 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 141 through 157
    Processing helix  chain 'X' and resid 160 through 188
    Processing helix  chain 'X' and resid 195 through 225
      Proline residue:  X 213  - end of helix
    Processing helix  chain 'X' and resid 228 through 247
    Processing helix  chain 'X' and resid 257 through 270
      removed outlier: 4.160A  pdb=" N   TYR X 261 " --> pdb=" O   SER X 257 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 283 through 306
    Processing helix  chain 'X' and resid 315 through 340
      removed outlier: 3.859A  pdb=" N   LEU X 320 " --> pdb=" O   LEU X 316 " (cutoff:3.500A)
      Proline residue:  X 321  - end of helix
    Processing helix  chain 'X' and resid 348 through 358
      removed outlier: 3.594A  pdb=" N   ASP X 352 " --> pdb=" O   LYS X 348 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 60 through 63
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.603A  pdb=" N   THR H  87 " --> pdb=" O   THR H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 155 through 157
      No H-bonds generated for 'chain 'H' and resid 155 through 157'
    Processing helix  chain 'H' and resid 185 through 190
      removed outlier: 4.389A  pdb=" N   GLY H 189 " --> pdb=" O   SER H 185 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   THR H 190 " --> pdb=" O   SER H 186 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 185 through 190'
    Processing helix  chain 'H' and resid 200 through 203
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'L' and resid 94 through 99
    Processing helix  chain 'L' and resid 125 through 132
      removed outlier: 3.514A  pdb=" N   LYS L 130 " --> pdb=" O   ASP L 126 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   SER L 131 " --> pdb=" O   GLU L 127 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 187 through 193
      removed outlier: 3.593A  pdb=" N   HIS L 193 " --> pdb=" O   ASP L 189 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 107 through 109
    Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 117
      removed outlier: 6.706A  pdb=" N   GLU B 114 " --> pdb=" O   ARG B 201 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   ARG B 203 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE B 116 " --> pdb=" O   ARG B 203 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   GLN B 182 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASP B 136 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 2 through 6
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.811A  pdb=" N   ALA H  32 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   MET H  33 " --> pdb=" O   ILE H  49 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ILE H  49 " --> pdb=" O   MET H  33 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   TRP H  35 " --> pdb=" O   ILE H  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 4.221A  pdb=" N   ILE H 101 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 119 through 123
      removed outlier: 6.005A  pdb=" N   TYR H 175 " --> pdb=" O   ASP H 143 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 119 through 123
      removed outlier: 6.005A  pdb=" N   TYR H 175 " --> pdb=" O   ASP H 143 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER H 176 " --> pdb=" O   VAL H 168 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 153
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 8
      removed outlier: 3.502A  pdb=" N   GLN L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 15
      removed outlier: 6.452A  pdb=" N   VAL L  12 " --> pdb=" O   VAL L 109 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   LYS L 111 " --> pdb=" O   VAL L  12 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA L  14 " --> pdb=" O   LYS L 111 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA L  85 " --> pdb=" O   VAL L 108 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 122
      removed outlier: 5.505A  pdb=" N   TYR L 177 " --> pdb=" O   ASN L 142 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 157 through 158
      removed outlier: 3.621A  pdb=" N   LYS L 211 " --> pdb=" O   CYS L 198 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1211
        1.32 -     1.44: 2012
        1.44 -     1.57: 4029
        1.57 -     1.69: 2
        1.69 -     1.82: 36
  Bond restraints: 7290
  Sorted by residual:
  bond pdb=" N   PCA H   1 "
       pdb=" CD  PCA H   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.460 -0.115 2.00e-02 2.50e+03 3.30e+01
  bond pdb=" C4  DLP X 501 "
       pdb=" O4P DLP X 501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.454 -0.045 2.00e-02 2.50e+03 5.05e+00
  bond pdb=" O4P DLP X 501 "
       pdb=" P   DLP X 501 "
    ideal  model  delta    sigma   weight residual
    1.649  1.605  0.044 2.00e-02 2.50e+03 4.76e+00
  bond pdb=" CB  VAL X  49 "
       pdb=" CG2 VAL X  49 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.52e+00
  bond pdb=" CA  ALA X 285 "
       pdb=" C   ALA X 285 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.027 1.29e-02 6.01e+03 4.25e+00
  ... (remaining 7285 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 9618
        2.94 -     5.88: 280
        5.88 -     8.82: 34
        8.82 -    11.76: 9
       11.76 -    14.70: 3
  Bond angle restraints: 9944
  Sorted by residual:
  angle pdb=" N   ALA X 285 "
        pdb=" CA  ALA X 285 "
        pdb=" C   ALA X 285 "
      ideal   model   delta    sigma   weight residual
     111.40  103.05    8.35 1.22e+00 6.72e-01 4.68e+01
  angle pdb=" N   GLY H  98 "
        pdb=" CA  GLY H  98 "
        pdb=" C   GLY H  98 "
      ideal   model   delta    sigma   weight residual
     112.37  100.25   12.12 1.84e+00 2.95e-01 4.34e+01
  angle pdb=" N   TRP X 340 "
        pdb=" CA  TRP X 340 "
        pdb=" C   TRP X 340 "
      ideal   model   delta    sigma   weight residual
     111.24  118.00   -6.76 1.29e+00 6.01e-01 2.74e+01
  angle pdb=" N   ALA H  97 "
        pdb=" CA  ALA H  97 "
        pdb=" C   ALA H  97 "
      ideal   model   delta    sigma   weight residual
     107.23   99.23    8.00 1.67e+00 3.59e-01 2.29e+01
  angle pdb=" N   GLU B 146 "
        pdb=" CA  GLU B 146 "
        pdb=" C   GLU B 146 "
      ideal   model   delta    sigma   weight residual
     108.52  115.60   -7.08 1.52e+00 4.33e-01 2.17e+01
  ... (remaining 9939 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.90: 4016
       24.90 -    49.81: 222
       49.81 -    74.71: 23
       74.71 -    99.62: 9
       99.62 -   124.52: 1
  Dihedral angle restraints: 4271
    sinusoidal: 1635
      harmonic: 2636
  Sorted by residual:
  dihedral pdb=" CB  CYS L  81 "
           pdb=" SG  CYS L  81 "
           pdb=" SG  CYS L 175 "
           pdb=" CB  CYS L 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.28   40.28     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" N   DLP X 501 "
           pdb=" C4  DLP X 501 "
           pdb=" C5  DLP X 501 "
           pdb=" O4P DLP X 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.95  164.43  124.52     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" CB  GLU L 199 "
           pdb=" CG  GLU L 199 "
           pdb=" CD  GLU L 199 "
           pdb=" OE1 GLU L 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.84  -86.84     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 4268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 802
       0.056 -    0.112: 253
       0.112 -    0.168: 61
       0.168 -    0.224: 12
       0.224 -    0.280: 5
  Chirality restraints: 1133
  Sorted by residual:
  chirality pdb=" CA  PRO X 253 "
            pdb=" N   PRO X 253 "
            pdb=" C   PRO X 253 "
            pdb=" CB  PRO X 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  LEU X 236 "
            pdb=" N   LEU X 236 "
            pdb=" C   LEU X 236 "
            pdb=" CB  LEU X 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  TRP X 212 "
            pdb=" N   TRP X 212 "
            pdb=" C   TRP X 212 "
            pdb=" CB  TRP X 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1130 not shown)

  Planarity restraints: 1234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 DLP X 501 "    0.062 2.00e-02 2.50e+03   1.21e-01 1.46e+02
        pdb=" C22 DLP X 501 "   -0.158 2.00e-02 2.50e+03
        pdb=" C23 DLP X 501 "    0.159 2.00e-02 2.50e+03
        pdb=" C24 DLP X 501 "   -0.063 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG X 262 "    0.123 9.50e-02 1.11e+02   7.08e-02 2.67e+01
        pdb=" NE  ARG X 262 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG X 262 "    0.085 2.00e-02 2.50e+03
        pdb=" NH1 ARG X 262 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH2 ARG X 262 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C41 DLP X 501 "    0.044 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" C42 DLP X 501 "   -0.047 2.00e-02 2.50e+03
        pdb=" C43 DLP X 501 "   -0.040 2.00e-02 2.50e+03
        pdb=" C44 DLP X 501 "    0.043 2.00e-02 2.50e+03
  ... (remaining 1231 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1158
        2.76 -     3.29: 6879
        3.29 -     3.83: 11876
        3.83 -     4.36: 13450
        4.36 -     4.90: 23314
  Nonbonded interactions: 56677
  Sorted by model distance:
  nonbonded pdb=" OG  SER L 125 "
            pdb=" OE1 GLU L 127 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" NE2 HIS X 182 "
            pdb=" OH  TYR X 337 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" NH2 ARG B 184 "
            pdb=" OE1 GLN B 195 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OH  TYR X  37 "
            pdb=" NE2 GLN X 163 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OD1 ASP X  12 "
            pdb=" NH2 ARG X 183 "
     model   vdw
     2.287 3.120
  ... (remaining 56672 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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.310
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
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      :  0.009   0.115   7296  Z= 0.424
  Angle     :  1.213  14.698   9956  Z= 0.666
  Chirality :  0.060   0.280   1133
  Planarity :  0.009   0.121   1234
  Dihedral  : 14.999 124.523   2563
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.44 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 10.07 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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: -3.04 (0.24), residues: 901
  helix: -2.75 (0.24), residues: 309
  sheet: -0.59 (0.29), residues: 259
  loop : -2.24 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.086   0.003   ARG X 262 
 TYR   0.028   0.003   TYR L  98 
 PHE   0.026   0.003   PHE L 102 
 TRP   0.053   0.004   TRP X 303 
 HIS   0.010   0.003   HIS X 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00945 ( 7290)
  covalent geometry    : angle       1.21171 ( 9944)
  SS BOND              : bond        0.00511 (    6)
  SS BOND              : angle       1.78943 (   12)
  hydrogen bonds       : bond        0.13483 (  412)
  hydrogen bonds       : angle       7.97139 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 242
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  117 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8161 (p0)
REVERT: B  123 MET cc_start: 0.9056 (ttp) cc_final: 0.8610 (ttp)
REVERT: B  160 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (p)
REVERT: B  173 ASN cc_start: 0.8943 (t0) cc_final: 0.8709 (t0)
REVERT: B  227 PHE cc_start: 0.8523 (t80) cc_final: 0.8155 (t80)
REVERT: X   43 TYR cc_start: 0.7301 (p90) cc_final: 0.6747 (p90)
REVERT: X   66 LEU cc_start: 0.9346 (mm) cc_final: 0.9074 (mp)
REVERT: X  103 LEU cc_start: 0.9204 (mt) cc_final: 0.8900 (mt)
REVERT: X  145 GLN cc_start: 0.8767 (tp40) cc_final: 0.8461 (tp40)
REVERT: X  209 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8575 (mp)
REVERT: X  233 PHE cc_start: 0.8576 (t80) cc_final: 0.8246 (t80)
REVERT: X  259 TRP cc_start: 0.6462 (t60) cc_final: 0.6062 (t-100)
REVERT: X  299 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: X  326 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8510 (t)
REVERT: H   28 LEU cc_start: 0.9142 (mt) cc_final: 0.8869 (mp)
REVERT: H   33 MET cc_start: 0.8744 (mmm) cc_final: 0.8375 (mmt)
REVERT: H   86 ASP cc_start: 0.8594 (m-30) cc_final: 0.8263 (m-30)
REVERT: H  139 CYS cc_start: 0.6329 (m) cc_final: 0.6067 (m)
REVERT: H  140 LEU cc_start: 0.9212 (tp) cc_final: 0.8792 (tt)
REVERT: H  141 VAL cc_start: 0.9563 (t) cc_final: 0.9312 (p)
REVERT: H  143 ASP cc_start: 0.7615 (m-30) cc_final: 0.7191 (m-30)
REVERT: H  144 TYR cc_start: 0.8259 (p90) cc_final: 0.8020 (p90)
REVERT: H  153 TRP cc_start: 0.7772 (m100) cc_final: 0.6835 (m100)
REVERT: L    5 MET cc_start: 0.8958 (mmm) cc_final: 0.8102 (mmm)
REVERT: L   91 SER cc_start: 0.9447 (t) cc_final: 0.9016 (m)
REVERT: L  129 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7478 (mm)
REVERT: L  180 SER cc_start: 0.7513 (p) cc_final: 0.7017 (p)
REVERT: L  191 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8760 (mm-30)
  outliers start: 25
  outliers final: 11
  residues processed: 258
  average time/residue: 0.0847
  time to fit residues: 29.3803
Evaluate side-chains
  183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  117 ASN
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  220 LEU
Chi-restraints excluded: chain X residue  263 VAL
Chi-restraints excluded: chain X residue  299 LEU
Chi-restraints excluded: chain X residue  326 CYS
Chi-restraints excluded: chain H residue   49 ILE
Chi-restraints excluded: chain H residue  182 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   24 CYS
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   96 ILE
Chi-restraints excluded: chain L residue  129 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 117 ASN
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 HIS
B 205 HIS
** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 306 HIS
X 339 HIS
H 163 HIS
L 128 GLN
L 142 ASN
L 164 GLN
L 214 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.147157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.110770 restraints weight = 12558.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.110296 restraints weight = 9363.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.110839 restraints weight = 10032.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111837 restraints weight = 6181.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.112614 restraints weight = 5271.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7296  Z= 0.179
  Angle     :  0.738  10.884   9956  Z= 0.366
  Chirality :  0.044   0.156   1133
  Planarity :  0.006   0.061   1234
  Dihedral  :  8.688 118.603   1053
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.95 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.43 (0.27), residues: 901
  helix:  0.71 (0.28), residues: 315
  sheet:  0.27 (0.31), residues: 252
  loop : -1.67 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 184 
 TYR   0.029   0.002   TYR L  33 
 PHE   0.028   0.002   PHE L 213 
 TRP   0.016   0.002   TRP X 259 
 HIS   0.004   0.001   HIS H 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7290)
  covalent geometry    : angle       0.73702 ( 9944)
  SS BOND              : bond        0.00282 (    6)
  SS BOND              : angle       1.12490 (   12)
  hydrogen bonds       : bond        0.04740 (  412)
  hydrogen bonds       : angle       5.58574 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  117 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8501 (p0)
REVERT: B  173 ASN cc_start: 0.9016 (t0) cc_final: 0.8777 (t0)
REVERT: B  227 PHE cc_start: 0.8561 (t80) cc_final: 0.8193 (t80)
REVERT: X  154 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8493 (mp)
REVERT: X  180 ASP cc_start: 0.8807 (m-30) cc_final: 0.8587 (m-30)
REVERT: X  181 TYR cc_start: 0.9470 (t80) cc_final: 0.9135 (t80)
REVERT: X  182 HIS cc_start: 0.9201 (t-90) cc_final: 0.8515 (t-90)
REVERT: X  259 TRP cc_start: 0.6239 (t60) cc_final: 0.5894 (t-100)
REVERT: X  347 TRP cc_start: 0.6963 (t-100) cc_final: 0.6744 (t-100)
REVERT: H   28 LEU cc_start: 0.9067 (mt) cc_final: 0.8841 (mp)
REVERT: H   86 ASP cc_start: 0.8544 (m-30) cc_final: 0.8232 (m-30)
REVERT: H  141 VAL cc_start: 0.9482 (t) cc_final: 0.9209 (p)
REVERT: H  143 ASP cc_start: 0.7737 (m-30) cc_final: 0.7160 (t70)
REVERT: H  144 TYR cc_start: 0.8419 (p90) cc_final: 0.8039 (p90)
REVERT: H  153 TRP cc_start: 0.7889 (m100) cc_final: 0.7530 (m100)
REVERT: L  106 THR cc_start: 0.9409 (m) cc_final: 0.9209 (p)
  outliers start: 30
  outliers final: 21
  residues processed: 203
  average time/residue: 0.0680
  time to fit residues: 19.7285
Evaluate side-chains
  183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  117 ASN
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  154 LEU
Chi-restraints excluded: chain X residue  167 ILE
Chi-restraints excluded: chain X residue  170 SER
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  163 HIS
Chi-restraints excluded: chain H residue  203 ASN
Chi-restraints excluded: chain L residue  167 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 115 HIS
X 247 GLN
X 288 HIS
H 163 HIS
L  23 ASN
L 142 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.146094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.109617 restraints weight = 12406.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108776 restraints weight = 9745.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.109973 restraints weight = 7852.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112772 restraints weight = 5778.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113011 restraints weight = 4584.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7296  Z= 0.192
  Angle     :  0.693   8.698   9956  Z= 0.344
  Chirality :  0.043   0.170   1133
  Planarity :  0.005   0.052   1234
  Dihedral  :  8.008 115.207   1031
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 19.08 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.61 (0.28), residues: 901
  helix:  1.85 (0.28), residues: 316
  sheet:  0.68 (0.31), residues: 257
  loop : -1.30 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X 158 
 TYR   0.017   0.002   TYR X 122 
 PHE   0.018   0.002   PHE L 213 
 TRP   0.015   0.001   TRP X 110 
 HIS   0.011   0.001   HIS H 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7290)
  covalent geometry    : angle       0.69099 ( 9944)
  SS BOND              : bond        0.00642 (    6)
  SS BOND              : angle       1.49547 (   12)
  hydrogen bonds       : bond        0.04028 (  412)
  hydrogen bonds       : angle       5.08450 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 176
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  140 TYR cc_start: 0.8886 (m-80) cc_final: 0.8506 (m-10)
REVERT: B  173 ASN cc_start: 0.9114 (t0) cc_final: 0.8885 (t0)
REVERT: B  227 PHE cc_start: 0.8660 (t80) cc_final: 0.8279 (t80)
REVERT: X  181 TYR cc_start: 0.9450 (t80) cc_final: 0.9188 (t80)
REVERT: X  237 TRP cc_start: 0.8777 (t60) cc_final: 0.8305 (t60)
REVERT: X  242 LEU cc_start: 0.8788 (tt) cc_final: 0.8301 (mm)
REVERT: X  259 TRP cc_start: 0.6226 (t60) cc_final: 0.5900 (t-100)
REVERT: H   28 LEU cc_start: 0.9191 (mt) cc_final: 0.8951 (mp)
REVERT: H   86 ASP cc_start: 0.8624 (m-30) cc_final: 0.8282 (m-30)
REVERT: H  141 VAL cc_start: 0.9502 (t) cc_final: 0.9216 (p)
REVERT: H  143 ASP cc_start: 0.7585 (m-30) cc_final: 0.6932 (t70)
REVERT: H  144 TYR cc_start: 0.8586 (p90) cc_final: 0.8287 (p90)
REVERT: H  153 TRP cc_start: 0.8089 (m100) cc_final: 0.7165 (m100)
REVERT: H  162 VAL cc_start: 0.9161 (p) cc_final: 0.8948 (m)
REVERT: L  106 THR cc_start: 0.9449 (m) cc_final: 0.9229 (p)
REVERT: L  112 ARG cc_start: 0.8058 (ttp-170) cc_final: 0.7855 (ttp-170)
REVERT: L  141 ASN cc_start: 0.9129 (t0) cc_final: 0.8571 (t0)
REVERT: L  149 LYS cc_start: 0.8429 (tptt) cc_final: 0.8203 (tptp)
  outliers start: 38
  outliers final: 30
  residues processed: 201
  average time/residue: 0.0688
  time to fit residues: 19.6188
Evaluate side-chains
  193 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  167 ILE
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  174 ILE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  252 MET
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  297 ILE
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue  167 VAL
Chi-restraints excluded: chain L residue  171 ASP
Chi-restraints excluded: chain L residue  180 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 86 optimal weight:   30.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN
L 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.141347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.093971 restraints weight = 12743.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097218 restraints weight = 7508.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.099388 restraints weight = 5542.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.100491 restraints weight = 4631.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.101379 restraints weight = 4193.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   7296  Z= 0.305
  Angle     :  0.749   7.533   9956  Z= 0.374
  Chirality :  0.044   0.168   1133
  Planarity :  0.005   0.050   1234
  Dihedral  :  8.148 115.392   1029
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 19.87 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.74 (0.28), residues: 901
  helix:  1.88 (0.28), residues: 316
  sheet:  0.88 (0.32), residues: 257
  loop : -1.25 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG X 284 
 TYR   0.030   0.002   TYR L  33 
 PHE   0.018   0.002   PHE H  91 
 TRP   0.015   0.002   TRP H 153 
 HIS   0.003   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00694 ( 7290)
  covalent geometry    : angle       0.74785 ( 9944)
  SS BOND              : bond        0.00455 (    6)
  SS BOND              : angle       1.44998 (   12)
  hydrogen bonds       : bond        0.04107 (  412)
  hydrogen bonds       : angle       5.09941 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 165
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  123 MET cc_start: 0.9138 (ttp) cc_final: 0.8852 (ttp)
REVERT: B  227 PHE cc_start: 0.8769 (t80) cc_final: 0.8484 (t80)
REVERT: X  181 TYR cc_start: 0.9471 (t80) cc_final: 0.9248 (t80)
REVERT: X  237 TRP cc_start: 0.8945 (t60) cc_final: 0.8718 (t60)
REVERT: X  252 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8059 (ptm)
REVERT: X  259 TRP cc_start: 0.6430 (t60) cc_final: 0.6006 (t-100)
REVERT: H   28 LEU cc_start: 0.9249 (mt) cc_final: 0.8872 (mp)
REVERT: H   57 TYR cc_start: 0.9059 (m-80) cc_final: 0.8834 (m-80)
REVERT: H   86 ASP cc_start: 0.8671 (m-30) cc_final: 0.8429 (m-30)
REVERT: H  141 VAL cc_start: 0.9632 (t) cc_final: 0.9272 (p)
REVERT: H  143 ASP cc_start: 0.7698 (m-30) cc_final: 0.6956 (t70)
REVERT: L  112 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7846 (ttp-170)
REVERT: L  141 ASN cc_start: 0.9281 (t0) cc_final: 0.8816 (t0)
REVERT: L  149 LYS cc_start: 0.8622 (tptt) cc_final: 0.8360 (tptp)
  outliers start: 53
  outliers final: 41
  residues processed: 200
  average time/residue: 0.0741
  time to fit residues: 20.7126
Evaluate side-chains
  194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 152
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   62 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  167 ILE
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  174 ILE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  252 MET
Chi-restraints excluded: chain X residue  272 SER
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  297 ILE
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  167 VAL
Chi-restraints excluded: chain L residue  171 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0370
   chunk 59 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    2.8066

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

Flipped N/Q/H residues before XYZ refinement:
B 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.141790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.094729 restraints weight = 12698.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.098096 restraints weight = 7393.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.100303 restraints weight = 5428.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.101307 restraints weight = 4525.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.102166 restraints weight = 4108.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7296  Z= 0.245
  Angle     :  0.716  10.258   9956  Z= 0.353
  Chirality :  0.044   0.332   1133
  Planarity :  0.005   0.048   1234
  Dihedral  :  8.112 114.634   1029
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  7.45 %
    Allowed  : 20.65 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.98 (0.28), residues: 901
  helix:  2.00 (0.28), residues: 322
  sheet:  1.09 (0.32), residues: 246
  loop : -1.08 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 158 
 TYR   0.023   0.002   TYR L  33 
 PHE   0.016   0.002   PHE L 122 
 TRP   0.014   0.001   TRP B 210 
 HIS   0.004   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 7290)
  covalent geometry    : angle       0.71531 ( 9944)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       1.14621 (   12)
  hydrogen bonds       : bond        0.03870 (  412)
  hydrogen bonds       : angle       4.93914 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 164
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 ARG cc_start: 0.8091 (ptm160) cc_final: 0.7752 (ptm160)
REVERT: B  203 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7510 (mtm110)
REVERT: B  227 PHE cc_start: 0.8799 (t80) cc_final: 0.8586 (t80)
REVERT: X  237 TRP cc_start: 0.8952 (t60) cc_final: 0.8678 (t60)
REVERT: X  242 LEU cc_start: 0.8718 (tt) cc_final: 0.8219 (mm)
REVERT: X  252 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8099 (ptm)
REVERT: X  259 TRP cc_start: 0.6305 (t60) cc_final: 0.5908 (t-100)
REVERT: H   28 LEU cc_start: 0.9214 (mt) cc_final: 0.8843 (mp)
REVERT: H   86 ASP cc_start: 0.8653 (m-30) cc_final: 0.8343 (m-30)
REVERT: H  141 VAL cc_start: 0.9657 (t) cc_final: 0.9446 (m)
REVERT: H  143 ASP cc_start: 0.7737 (m-30) cc_final: 0.6882 (t70)
REVERT: L  112 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7817 (ttp-170)
REVERT: L  141 ASN cc_start: 0.9126 (t0) cc_final: 0.8733 (t0)
REVERT: L  149 LYS cc_start: 0.8635 (tptt) cc_final: 0.8353 (tptp)
  outliers start: 57
  outliers final: 44
  residues processed: 200
  average time/residue: 0.0721
  time to fit residues: 20.0573
Evaluate side-chains
  203 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 157
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   91 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  167 ILE
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  174 ILE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  252 MET
Chi-restraints excluded: chain X residue  272 SER
Chi-restraints excluded: chain X residue  287 ILE
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  297 ILE
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   49 ILE
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  167 VAL
Chi-restraints excluded: chain L residue  171 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0370
   chunk 76 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0040
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 83 optimal weight:   30.0000
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5270

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

Flipped N/Q/H residues before XYZ refinement:
B 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.147616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.110887 restraints weight = 12626.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111344 restraints weight = 10378.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112926 restraints weight = 7476.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113758 restraints weight = 5784.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114337 restraints weight = 5445.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7296  Z= 0.119
  Angle     :  0.665  11.756   9956  Z= 0.317
  Chirality :  0.042   0.324   1133
  Planarity :  0.004   0.046   1234
  Dihedral  :  7.730 109.146   1029
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 24.05 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.34 (0.28), residues: 901
  helix:  2.52 (0.28), residues: 316
  sheet:  1.25 (0.33), residues: 234
  loop : -0.96 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 106 
 TYR   0.028   0.002   TYR L  33 
 PHE   0.019   0.001   PHE L 122 
 TRP   0.014   0.001   TRP X 110 
 HIS   0.003   0.001   HIS X 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7290)
  covalent geometry    : angle       0.66446 ( 9944)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       0.84743 (   12)
  hydrogen bonds       : bond        0.03417 (  412)
  hydrogen bonds       : angle       4.60651 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 173
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7785 (ptm160)
REVERT: B  230 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6842 (tt0)
REVERT: X  114 GLU cc_start: 0.8854 (tp30) cc_final: 0.8420 (tp30)
REVERT: X  180 ASP cc_start: 0.8838 (m-30) cc_final: 0.8466 (m-30)
REVERT: X  237 TRP cc_start: 0.8861 (t60) cc_final: 0.8585 (t60)
REVERT: X  242 LEU cc_start: 0.8698 (tt) cc_final: 0.8235 (mm)
REVERT: X  278 GLU cc_start: 0.6946 (mp0) cc_final: 0.6727 (mp0)
REVERT: H   28 LEU cc_start: 0.9079 (mt) cc_final: 0.8717 (mp)
REVERT: H   57 TYR cc_start: 0.8931 (m-80) cc_final: 0.8723 (m-80)
REVERT: H   86 ASP cc_start: 0.8822 (m-30) cc_final: 0.8566 (m-30)
REVERT: H  143 ASP cc_start: 0.7322 (m-30) cc_final: 0.6827 (t70)
REVERT: L  112 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7646 (ttp-170)
REVERT: L  141 ASN cc_start: 0.8882 (t0) cc_final: 0.8623 (t0)
REVERT: L  149 LYS cc_start: 0.8524 (tptt) cc_final: 0.8278 (tptp)
  outliers start: 34
  outliers final: 23
  residues processed: 193
  average time/residue: 0.0788
  time to fit residues: 20.9105
Evaluate side-chains
  182 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 159
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   91 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  150 LEU
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  335 LEU
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   21 CYS
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 87 optimal weight:   50.0000
   chunk 18 optimal weight:    6.9990
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  92 GLN
** H  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
L  23 ASN
L  71 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.142008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.105119 restraints weight = 12670.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104646 restraints weight = 11914.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106842 restraints weight = 8448.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.107216 restraints weight = 6164.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.108165 restraints weight = 5799.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7296  Z= 0.278
  Angle     :  0.727  12.412   9956  Z= 0.356
  Chirality :  0.044   0.359   1133
  Planarity :  0.005   0.047   1234
  Dihedral  :  7.868 111.590   1028
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 23.79 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.22 (0.28), residues: 901
  helix:  2.24 (0.27), residues: 321
  sheet:  1.24 (0.33), residues: 236
  loop : -0.94 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 203 
 TYR   0.028   0.002   TYR H 144 
 PHE   0.017   0.002   PHE L 122 
 TRP   0.018   0.002   TRP X 347 
 HIS   0.004   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 ( 7290)
  covalent geometry    : angle       0.72583 ( 9944)
  SS BOND              : bond        0.00371 (    6)
  SS BOND              : angle       1.27037 (   12)
  hydrogen bonds       : bond        0.03730 (  412)
  hydrogen bonds       : angle       4.81710 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 153
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 ARG cc_start: 0.8353 (ptm160) cc_final: 0.8101 (ptm160)
REVERT: X   26 ASP cc_start: 0.8476 (t0) cc_final: 0.8232 (t0)
REVERT: X  114 GLU cc_start: 0.8903 (tp30) cc_final: 0.8509 (tp30)
REVERT: X  181 TYR cc_start: 0.9553 (t80) cc_final: 0.9248 (t80)
REVERT: X  205 LEU cc_start: 0.9166 (tp) cc_final: 0.8913 (tp)
REVERT: X  237 TRP cc_start: 0.8990 (t60) cc_final: 0.8744 (t60)
REVERT: X  286 ILE cc_start: 0.8551 (pt) cc_final: 0.8178 (mm)
REVERT: H   28 LEU cc_start: 0.9208 (mt) cc_final: 0.8780 (mp)
REVERT: H   86 ASP cc_start: 0.8808 (m-30) cc_final: 0.8392 (m-30)
REVERT: H  141 VAL cc_start: 0.9584 (t) cc_final: 0.9360 (m)
REVERT: H  143 ASP cc_start: 0.7489 (m-30) cc_final: 0.6848 (t70)
REVERT: L  141 ASN cc_start: 0.8890 (t0) cc_final: 0.8539 (t0)
REVERT: L  146 ARG cc_start: 0.8094 (tmm-80) cc_final: 0.7723 (tmm-80)
REVERT: L  149 LYS cc_start: 0.8557 (tptt) cc_final: 0.8299 (tptp)
  outliers start: 44
  outliers final: 37
  residues processed: 179
  average time/residue: 0.0782
  time to fit residues: 19.3523
Evaluate side-chains
  188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   91 LEU
Chi-restraints excluded: chain X residue  126 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  167 ILE
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  174 ILE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  287 ILE
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  297 ILE
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   21 CYS
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  167 VAL
Chi-restraints excluded: chain L residue  171 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    0.3980
   chunk 20 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:   30.0000
   chunk 49 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 83 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.145373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.107894 restraints weight = 12724.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109790 restraints weight = 10116.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.109907 restraints weight = 9343.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112337 restraints weight = 6190.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.112469 restraints weight = 4694.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7296  Z= 0.162
  Angle     :  0.705  12.878   9956  Z= 0.338
  Chirality :  0.043   0.357   1133
  Planarity :  0.005   0.047   1234
  Dihedral  :  7.736 109.038   1028
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 24.05 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.39 (0.28), residues: 901
  helix:  2.39 (0.27), residues: 321
  sheet:  1.38 (0.33), residues: 234
  loop : -0.87 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 203 
 TYR   0.025   0.002   TYR L  98 
 PHE   0.024   0.001   PHE L 122 
 TRP   0.023   0.001   TRP X 347 
 HIS   0.004   0.001   HIS X 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7290)
  covalent geometry    : angle       0.70436 ( 9944)
  SS BOND              : bond        0.00370 (    6)
  SS BOND              : angle       1.18182 (   12)
  hydrogen bonds       : bond        0.03538 (  412)
  hydrogen bonds       : angle       4.69596 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  106 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7519 (ttp80)
REVERT: B  201 ARG cc_start: 0.8199 (ptm160) cc_final: 0.7879 (ptm160)
REVERT: B  230 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6859 (tt0)
REVERT: X  114 GLU cc_start: 0.8854 (tp30) cc_final: 0.8545 (tp30)
REVERT: X  181 TYR cc_start: 0.9506 (t80) cc_final: 0.9178 (t80)
REVERT: X  205 LEU cc_start: 0.9080 (tp) cc_final: 0.8847 (tp)
REVERT: X  237 TRP cc_start: 0.8948 (t60) cc_final: 0.8686 (t60)
REVERT: X  242 LEU cc_start: 0.8787 (tt) cc_final: 0.8309 (mm)
REVERT: X  286 ILE cc_start: 0.8507 (pt) cc_final: 0.8131 (mm)
REVERT: H   28 LEU cc_start: 0.9121 (mt) cc_final: 0.8711 (mp)
REVERT: H   86 ASP cc_start: 0.8873 (m-30) cc_final: 0.8544 (m-30)
REVERT: H  143 ASP cc_start: 0.7391 (m-30) cc_final: 0.6854 (t70)
REVERT: L  141 ASN cc_start: 0.8846 (t0) cc_final: 0.8522 (t0)
REVERT: L  146 ARG cc_start: 0.8082 (tmm-80) cc_final: 0.7730 (tmm-80)
  outliers start: 42
  outliers final: 37
  residues processed: 186
  average time/residue: 0.0711
  time to fit residues: 18.4658
Evaluate side-chains
  194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  227 PHE
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   91 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  150 LEU
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  335 LEU
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   21 CYS
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue  167 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 72 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   overall best weight:    2.4984

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  34 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.143027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.106344 restraints weight = 12685.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.108265 restraints weight = 11778.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108348 restraints weight = 10311.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109125 restraints weight = 6315.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.111297 restraints weight = 5489.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7296  Z= 0.230
  Angle     :  0.752  12.614   9956  Z= 0.362
  Chirality :  0.044   0.363   1133
  Planarity :  0.005   0.047   1234
  Dihedral  :  7.799 109.933   1028
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 24.58 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.32 (0.28), residues: 901
  helix:  2.30 (0.27), residues: 321
  sheet:  1.34 (0.33), residues: 234
  loop : -0.88 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 203 
 TYR   0.029   0.002   TYR L  98 
 PHE   0.019   0.002   PHE L 122 
 TRP   0.019   0.002   TRP X 347 
 HIS   0.003   0.001   HIS X 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 7290)
  covalent geometry    : angle       0.75131 ( 9944)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       1.19309 (   12)
  hydrogen bonds       : bond        0.03678 (  412)
  hydrogen bonds       : angle       4.77884 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  106 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7592 (ttp80)
REVERT: B  201 ARG cc_start: 0.8208 (ptm160) cc_final: 0.7934 (ptm160)
REVERT: B  230 GLU cc_start: 0.7618 (mm-30) cc_final: 0.6860 (tt0)
REVERT: X  114 GLU cc_start: 0.8889 (tp30) cc_final: 0.8617 (tp30)
REVERT: X  181 TYR cc_start: 0.9523 (t80) cc_final: 0.9255 (t80)
REVERT: X  205 LEU cc_start: 0.9116 (tp) cc_final: 0.8871 (tp)
REVERT: X  237 TRP cc_start: 0.8972 (t60) cc_final: 0.8696 (t60)
REVERT: X  242 LEU cc_start: 0.8817 (tt) cc_final: 0.8375 (mm)
REVERT: X  286 ILE cc_start: 0.8482 (pt) cc_final: 0.8136 (mm)
REVERT: H   28 LEU cc_start: 0.9161 (mt) cc_final: 0.8747 (mp)
REVERT: H   86 ASP cc_start: 0.8835 (m-30) cc_final: 0.8493 (m-30)
REVERT: H  141 VAL cc_start: 0.9577 (t) cc_final: 0.9349 (m)
REVERT: H  143 ASP cc_start: 0.7339 (m-30) cc_final: 0.6804 (t70)
REVERT: L  141 ASN cc_start: 0.8857 (t0) cc_final: 0.8501 (t0)
REVERT: L  146 ARG cc_start: 0.8179 (tmm-80) cc_final: 0.7857 (tmm-80)
REVERT: L  190 TYR cc_start: 0.7890 (t80) cc_final: 0.7574 (t80)
  outliers start: 44
  outliers final: 40
  residues processed: 180
  average time/residue: 0.0781
  time to fit residues: 19.5270
Evaluate side-chains
  191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   91 LEU
Chi-restraints excluded: chain X residue  126 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  174 ILE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  302 THR
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  335 LEU
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   21 CYS
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   96 ILE
Chi-restraints excluded: chain L residue  113 THR
Chi-restraints excluded: chain L residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 83 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN
X  92 GLN
** H  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.110383 restraints weight = 12680.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.110002 restraints weight = 9558.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110476 restraints weight = 10350.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111761 restraints weight = 6401.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112392 restraints weight = 5420.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7296  Z= 0.133
  Angle     :  0.719  12.410   9956  Z= 0.338
  Chirality :  0.043   0.354   1133
  Planarity :  0.005   0.045   1234
  Dihedral  :  7.597 105.652   1028
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.27 %
    Favored  : 69.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.49 (0.29), residues: 901
  helix:  2.46 (0.28), residues: 322
  sheet:  1.44 (0.33), residues: 233
  loop : -0.81 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 203 
 TYR   0.024   0.002   TYR H 144 
 PHE   0.017   0.001   PHE L 122 
 TRP   0.020   0.001   TRP X 110 
 HIS   0.003   0.001   HIS X 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7290)
  covalent geometry    : angle       0.71910 ( 9944)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       0.95684 (   12)
  hydrogen bonds       : bond        0.03370 (  412)
  hydrogen bonds       : angle       4.58949 ( 1209)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  201 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7900 (ptm160)
REVERT: B  230 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6865 (tt0)
REVERT: X  114 GLU cc_start: 0.8900 (tp30) cc_final: 0.8604 (tp30)
REVERT: X  180 ASP cc_start: 0.8858 (m-30) cc_final: 0.8513 (m-30)
REVERT: X  181 TYR cc_start: 0.9406 (t80) cc_final: 0.9050 (t80)
REVERT: X  205 LEU cc_start: 0.9085 (tp) cc_final: 0.8838 (tp)
REVERT: X  242 LEU cc_start: 0.8713 (tt) cc_final: 0.8247 (mm)
REVERT: X  286 ILE cc_start: 0.8438 (pt) cc_final: 0.8039 (mm)
REVERT: H   28 LEU cc_start: 0.9065 (mt) cc_final: 0.8654 (mp)
REVERT: H   45 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7766 (mt-10)
REVERT: H   86 ASP cc_start: 0.8816 (m-30) cc_final: 0.8602 (m-30)
REVERT: H  106 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8649 (p)
REVERT: H  143 ASP cc_start: 0.7452 (m-30) cc_final: 0.6892 (t70)
REVERT: L    5 MET cc_start: 0.8842 (mmm) cc_final: 0.7812 (mmm)
REVERT: L  141 ASN cc_start: 0.8738 (t0) cc_final: 0.8399 (t0)
REVERT: L  146 ARG cc_start: 0.8167 (tmm-80) cc_final: 0.7848 (tmm-80)
REVERT: L  190 TYR cc_start: 0.8018 (t80) cc_final: 0.7724 (t80)
  outliers start: 33
  outliers final: 29
  residues processed: 187
  average time/residue: 0.0741
  time to fit residues: 19.3611
Evaluate side-chains
  187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   30 ASP
Chi-restraints excluded: chain X residue   91 LEU
Chi-restraints excluded: chain X residue  150 LEU
Chi-restraints excluded: chain X residue  171 PHE
Chi-restraints excluded: chain X residue  204 PHE
Chi-restraints excluded: chain X residue  209 LEU
Chi-restraints excluded: chain X residue  229 VAL
Chi-restraints excluded: chain X residue  236 LEU
Chi-restraints excluded: chain X residue  294 SER
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  335 LEU
Chi-restraints excluded: chain X residue  338 TYR
Chi-restraints excluded: chain H residue   21 CYS
Chi-restraints excluded: chain H residue   79 ILE
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue  106 THR
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain H residue  141 VAL
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    8.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  34 ASN ** 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 = 0.3814 r_free = 0.3814 target = 0.143832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.106932 restraints weight = 12722.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.107328 restraints weight = 11517.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.107744 restraints weight = 10754.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.108775 restraints weight = 6556.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.111030 restraints weight = 5641.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7296  Z= 0.220
  Angle     :  0.748  12.130   9956  Z= 0.361
  Chirality :  0.044   0.348   1133
  Planarity :  0.005   0.046   1234
  Dihedral  :  7.649 106.651   1028
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 25.75 %
    Favored  : 69.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.46 (0.28), residues: 901
  helix:  2.39 (0.28), residues: 321
  sheet:  1.46 (0.33), residues: 233
  loop : -0.80 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 106 
 TYR   0.031   0.002   TYR H 144 
 PHE   0.019   0.002   PHE L 122 
 TRP   0.019   0.002   TRP X 110 
 HIS   0.003   0.001   HIS X 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 7290)
  covalent geometry    : angle       0.74690 ( 9944)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       1.22889 (   12)
  hydrogen bonds       : bond        0.03611 (  412)
  hydrogen bonds       : angle       4.70304 ( 1209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1202.83 seconds
wall clock time: 21 minutes 32.39 seconds (1292.39 seconds total)