Starting phenix.real_space_refine
on Fri Jul 25 08:49:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dce_30636/07_2025/7dce_30636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dce_30636/07_2025/7dce_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2025/7dce_30636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2025/7dce_30636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2025/7dce_30636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2025/7dce_30636.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.64, per 1000 atoms: 0.65
  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: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.98
  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: 2.88

  Time building geometry restraints manager: 2.16 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:             0.480
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.990
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.990
-------------------------------------------------------------------------------
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 : 11.92
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (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
 TRP   0.053   0.004   TRP X 303 
 HIS   0.010   0.003   HIS X 232 
 PHE   0.026   0.003   PHE L 102 
 TYR   0.028   0.003   TYR L  98 
 ARG   0.086   0.003   ARG X 262 

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

*********************** 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  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  117 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8162 (p0)
REVERT: B  123 MET cc_start: 0.9055 (ttp) cc_final: 0.8611 (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: 0.8154 (t80)
REVERT: X   43 TYR cc_start: 0.7301 (p90) cc_final: 0.6745 (p90)
REVERT: X   66 LEU cc_start: 0.9346 (mm) cc_final: 0.9072 (mp)
REVERT: X  103 LEU cc_start: 0.9205 (mt) cc_final: 0.8900 (mt)
REVERT: X  132 MET cc_start: 0.9183 (mmm) cc_final: 0.8786 (mmp)
REVERT: X  145 GLN cc_start: 0.8767 (tp40) cc_final: 0.8462 (tp40)
REVERT: X  209 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8574 (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: 0.6063 (t-100)
REVERT: X  299 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (mp)
REVERT: X  326 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8511 (t)
REVERT: H   28 LEU cc_start: 0.9142 (mt) cc_final: 0.8870 (mp)
REVERT: H   33 MET cc_start: 0.8744 (mmm) cc_final: 0.8376 (mmt)
REVERT: H   86 ASP cc_start: 0.8595 (m-30) cc_final: 0.8263 (m-30)
REVERT: H  139 CYS cc_start: 0.6328 (m) cc_final: 0.6049 (m)
REVERT: H  140 LEU cc_start: 0.9212 (tp) cc_final: 0.8795 (tt)
REVERT: H  143 ASP cc_start: 0.7615 (m-30) cc_final: 0.7188 (m-30)
REVERT: H  144 TYR cc_start: 0.8260 (p90) cc_final: 0.8026 (p90)
REVERT: H  153 TRP cc_start: 0.7771 (m100) cc_final: 0.6836 (m100)
REVERT: L    5 MET cc_start: 0.8959 (mmm) cc_final: 0.8100 (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: 0.7016 (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: 0.1856
  time to fit residues: 63.6068
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  : 0.866 
-------------------------------------------------------------------------------
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 75 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 23 optimal weight:   30.0000
   chunk 45 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 HIS
B 205 HIS
X 105 GLN
** 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 = 0.3870 r_free = 0.3870 target = 0.148714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112488 restraints weight = 12353.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.111850 restraints weight = 9617.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.112477 restraints weight = 9269.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7296  Z= 0.157
  Angle     :  0.726  11.109   9956  Z= 0.359
  Chirality :  0.044   0.154   1133
  Planarity :  0.006   0.060   1234
  Dihedral  :  8.673 117.624   1053
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.56 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.27), residues: 901
  helix:  0.88 (0.28), residues: 315
  sheet:  0.34 (0.31), residues: 252
  loop : -1.67 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP X 259 
 HIS   0.004   0.001   HIS H 163 
 PHE   0.030   0.002   PHE L 213 
 TYR   0.029   0.002   TYR L  33 
 ARG   0.007   0.001   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  412)
  hydrogen bonds       : angle       5.49715 ( 1209)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       0.89469 (   12)
  covalent geometry    : bond        0.00339 ( 7290)
  covalent geometry    : angle       0.72591 ( 9944)

*********************** 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
  220 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 189
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  117 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8266 (p0)
REVERT: B  173 ASN cc_start: 0.8998 (t0) cc_final: 0.8762 (t0)
REVERT: B  227 PHE cc_start: 0.8550 (t80) cc_final: 0.8160 (t80)
REVERT: X   43 TYR cc_start: 0.6962 (p90) cc_final: 0.6033 (p90)
REVERT: X  154 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8435 (mp)
REVERT: X  180 ASP cc_start: 0.8758 (m-30) cc_final: 0.8293 (m-30)
REVERT: X  181 TYR cc_start: 0.9531 (t80) cc_final: 0.9099 (t80)
REVERT: X  233 PHE cc_start: 0.8561 (t80) cc_final: 0.8199 (t80)
REVERT: X  259 TRP cc_start: 0.6185 (t60) cc_final: 0.5877 (t-100)
REVERT: H   28 LEU cc_start: 0.9015 (mt) cc_final: 0.8796 (mp)
REVERT: H   86 ASP cc_start: 0.8532 (m-30) cc_final: 0.8265 (m-30)
REVERT: H  141 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9280 (p)
REVERT: H  143 ASP cc_start: 0.7730 (m-30) cc_final: 0.7202 (t70)
REVERT: H  144 TYR cc_start: 0.8418 (p90) cc_final: 0.8093 (p90)
REVERT: H  153 TRP cc_start: 0.7812 (m100) cc_final: 0.7482 (m100)
  outliers start: 31
  outliers final: 19
  residues processed: 206
  average time/residue: 0.1520
  time to fit residues: 43.8437
Evaluate side-chains
  186 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
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  170 SER
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  141 VAL
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 30 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 0 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0070
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.1600

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

Flipped N/Q/H residues before XYZ refinement:
B 117 ASN
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 = 0.3868 r_free = 0.3868 target = 0.148675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.112463 restraints weight = 12326.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.113329 restraints weight = 9777.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.113716 restraints weight = 9439.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2848

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= 0.148
  Angle     :  0.678   8.614   9956  Z= 0.332
  Chirality :  0.043   0.186   1133
  Planarity :  0.005   0.051   1234
  Dihedral  :  7.709 113.196   1029
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.35 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 901
  helix:  2.01 (0.28), residues: 316
  sheet:  0.85 (0.31), residues: 257
  loop : -1.24 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP X 110 
 HIS   0.014   0.001   HIS H 163 
 PHE   0.017   0.001   PHE L 213 
 TYR   0.018   0.001   TYR X 122 
 ARG   0.004   0.000   ARG X 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03902 (  412)
  hydrogen bonds       : angle       4.96956 ( 1209)
  SS BOND              : bond        0.00293 (    6)
  SS BOND              : angle       1.44912 (   12)
  covalent geometry    : bond        0.00336 ( 7290)
  covalent geometry    : angle       0.67636 ( 9944)

*********************** 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
  210 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 176
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  117 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8467 (p0)
REVERT: B  140 TYR cc_start: 0.8863 (m-80) cc_final: 0.8438 (m-10)
REVERT: B  173 ASN cc_start: 0.9023 (t0) cc_final: 0.8778 (t0)
REVERT: B  227 PHE cc_start: 0.8630 (t80) cc_final: 0.8287 (t80)
REVERT: X  167 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7500 (mt)
REVERT: X  182 HIS cc_start: 0.9224 (t-90) cc_final: 0.8466 (t-90)
REVERT: X  242 LEU cc_start: 0.8721 (tt) cc_final: 0.8248 (mm)
REVERT: X  259 TRP cc_start: 0.6107 (t60) cc_final: 0.5853 (t-100)
REVERT: H   28 LEU cc_start: 0.9136 (mt) cc_final: 0.8887 (mp)
REVERT: H   86 ASP cc_start: 0.8670 (m-30) cc_final: 0.8335 (m-30)
REVERT: H  141 VAL cc_start: 0.9519 (OUTLIER) cc_final: 0.9208 (p)
REVERT: H  143 ASP cc_start: 0.7515 (m-30) cc_final: 0.6905 (t70)
REVERT: H  144 TYR cc_start: 0.8529 (p90) cc_final: 0.8254 (p90)
REVERT: H  153 TRP cc_start: 0.7878 (m100) cc_final: 0.7291 (m100)
REVERT: L    5 MET cc_start: 0.8666 (mmm) cc_final: 0.7774 (mmm)
REVERT: L   91 SER cc_start: 0.9401 (t) cc_final: 0.8734 (m)
REVERT: L  141 ASN cc_start: 0.9065 (t0) cc_final: 0.8535 (t0)
  outliers start: 34
  outliers final: 25
  residues processed: 197
  average time/residue: 0.1554
  time to fit residues: 42.4415
Evaluate side-chains
  192 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
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  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  147 THR
Chi-restraints excluded: chain X residue  167 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  297 ILE
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  338 TYR
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  141 VAL
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  180 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    0.0370
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 82 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.3662

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

Flipped N/Q/H residues before XYZ refinement:
B 115 HIS
B 152 GLN
B 170 HIS
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.148331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.111615 restraints weight = 12594.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.115025 restraints weight = 11666.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.114446 restraints weight = 10212.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7296  Z= 0.152
  Angle     :  0.674  11.448   9956  Z= 0.326
  Chirality :  0.043   0.333   1133
  Planarity :  0.005   0.047   1234
  Dihedral  :  7.461 108.612   1029
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 21.18 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.28), residues: 901
  helix:  2.28 (0.28), residues: 317
  sheet:  1.00 (0.31), residues: 257
  loop : -1.02 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP X 110 
 HIS   0.003   0.001   HIS X 182 
 PHE   0.030   0.001   PHE L 213 
 TYR   0.016   0.002   TYR L 196 
 ARG   0.003   0.000   ARG X 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  412)
  hydrogen bonds       : angle       4.72983 ( 1209)
  SS BOND              : bond        0.00376 (    6)
  SS BOND              : angle       1.21958 (   12)
  covalent geometry    : bond        0.00346 ( 7290)
  covalent geometry    : angle       0.67288 ( 9944)

*********************** 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
  213 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  117 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8271 (p0)
REVERT: B  140 TYR cc_start: 0.8865 (m-80) cc_final: 0.8473 (m-10)
REVERT: B  227 PHE cc_start: 0.8589 (t80) cc_final: 0.8322 (t80)
REVERT: X  114 GLU cc_start: 0.8872 (tp30) cc_final: 0.8394 (tp30)
REVERT: X  167 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7526 (mt)
REVERT: X  237 TRP cc_start: 0.8795 (t60) cc_final: 0.8369 (t60)
REVERT: X  242 LEU cc_start: 0.8680 (tt) cc_final: 0.8234 (mm)
REVERT: X  259 TRP cc_start: 0.6118 (t60) cc_final: 0.5818 (t-100)
REVERT: H   28 LEU cc_start: 0.9136 (mt) cc_final: 0.8805 (mp)
REVERT: H   86 ASP cc_start: 0.8722 (m-30) cc_final: 0.8367 (m-30)
REVERT: H  143 ASP cc_start: 0.7362 (m-30) cc_final: 0.6957 (t70)
REVERT: L  141 ASN cc_start: 0.9095 (t0) cc_final: 0.8604 (t0)
  outliers start: 37
  outliers final: 26
  residues processed: 196
  average time/residue: 0.1638
  time to fit residues: 44.4699
Evaluate side-chains
  186 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
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  143 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain X residue   17 VAL
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  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  297 ILE
Chi-restraints excluded: chain X residue  314 ILE
Chi-restraints excluded: chain X residue  338 TYR
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 L residue   75 THR
Chi-restraints excluded: chain L residue  167 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 53 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN
B 173 ASN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.112367 restraints weight = 12313.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112304 restraints weight = 10699.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112799 restraints weight = 10494.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7296  Z= 0.124
  Angle     :  0.644   9.585   9956  Z= 0.311
  Chirality :  0.041   0.261   1133
  Planarity :  0.005   0.049   1234
  Dihedral  :  7.208 103.369   1028
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.05 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.28), residues: 901
  helix:  2.53 (0.28), residues: 318
  sheet:  1.21 (0.31), residues: 260
  loop : -0.92 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H 153 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.017   0.001   PHE L 122 
 TYR   0.022   0.002   TYR H 144 
 ARG   0.003   0.000   ARG X 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (  412)
  hydrogen bonds       : angle       4.54719 ( 1209)
  SS BOND              : bond        0.00280 (    6)
  SS BOND              : angle       1.08800 (   12)
  covalent geometry    : bond        0.00287 ( 7290)
  covalent geometry    : angle       0.64285 ( 9944)

*********************** 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
  209 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 177
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  140 TYR cc_start: 0.8909 (m-80) cc_final: 0.8492 (m-10)
REVERT: B  176 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8029 (mmm)
REVERT: B  227 PHE cc_start: 0.8631 (t80) cc_final: 0.8402 (t80)
REVERT: B  230 GLU cc_start: 0.7832 (mm-30) cc_final: 0.6934 (tt0)
REVERT: X  114 GLU cc_start: 0.8870 (tp30) cc_final: 0.8459 (tp30)
REVERT: X  180 ASP cc_start: 0.8491 (m-30) cc_final: 0.7993 (m-30)
REVERT: X  237 TRP cc_start: 0.8809 (t60) cc_final: 0.8297 (t60)
REVERT: X  242 LEU cc_start: 0.8585 (tt) cc_final: 0.8126 (mm)
REVERT: H   28 LEU cc_start: 0.9081 (mt) cc_final: 0.8732 (mp)
REVERT: H   86 ASP cc_start: 0.8884 (m-30) cc_final: 0.8533 (m-30)
REVERT: H  143 ASP cc_start: 0.7536 (m-30) cc_final: 0.6947 (t70)
REVERT: L  141 ASN cc_start: 0.8990 (t0) cc_final: 0.8574 (t0)
  outliers start: 32
  outliers final: 25
  residues processed: 194
  average time/residue: 0.1658
  time to fit residues: 44.4698
Evaluate side-chains
  191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  195 GLN
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   27 LEU
Chi-restraints excluded: chain X residue  138 THR
Chi-restraints excluded: chain X residue  147 THR
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  338 TYR
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 L residue   66 SER
Chi-restraints excluded: chain L residue   91 SER
Chi-restraints excluded: chain L residue  167 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0170
   chunk 48 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.7624

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN
X  92 GLN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.108264 restraints weight = 12645.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106866 restraints weight = 11438.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107329 restraints weight = 11122.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7296  Z= 0.247
  Angle     :  0.703   9.284   9956  Z= 0.347
  Chirality :  0.043   0.188   1133
  Planarity :  0.005   0.046   1234
  Dihedral  :  7.438 104.796   1026
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 21.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.28), residues: 901
  helix:  2.22 (0.28), residues: 323
  sheet:  1.14 (0.31), residues: 258
  loop : -0.83 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 153 
 HIS   0.003   0.001   HIS B 170 
 PHE   0.018   0.002   PHE H  91 
 TYR   0.022   0.002   TYR H 144 
 ARG   0.003   0.001   ARG X 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  412)
  hydrogen bonds       : angle       4.71906 ( 1209)
  SS BOND              : bond        0.00341 (    6)
  SS BOND              : angle       1.30064 (   12)
  covalent geometry    : bond        0.00566 ( 7290)
  covalent geometry    : angle       0.70209 ( 9944)

*********************** 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
  214 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 163
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  176 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8076 (mmm)
REVERT: X  237 TRP cc_start: 0.8959 (t60) cc_final: 0.8719 (t60)
REVERT: X  242 LEU cc_start: 0.8708 (tt) cc_final: 0.8239 (mm)
REVERT: H   28 LEU cc_start: 0.9217 (mt) cc_final: 0.8829 (mp)
REVERT: H   86 ASP cc_start: 0.8817 (m-30) cc_final: 0.8434 (m-30)
REVERT: H  143 ASP cc_start: 0.7675 (m-30) cc_final: 0.6954 (t70)
REVERT: L  141 ASN cc_start: 0.8964 (t0) cc_final: 0.8629 (t0)
  outliers start: 51
  outliers final: 42
  residues processed: 196
  average time/residue: 0.1716
  time to fit residues: 47.1829
Evaluate side-chains
  196 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 153
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain X residue   17 VAL
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  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  260 LEU
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   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 L residue    4 VAL
Chi-restraints excluded: chain L residue    6 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   96 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.0770
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
H  34 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 = 0.147491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.110745 restraints weight = 12538.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.114139 restraints weight = 11254.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.113897 restraints weight = 9065.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7296  Z= 0.131
  Angle     :  0.668  10.287   9956  Z= 0.321
  Chirality :  0.042   0.199   1133
  Planarity :  0.004   0.045   1234
  Dihedral  :  7.215 101.204   1026
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 24.31 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.28), residues: 901
  helix:  2.58 (0.27), residues: 318
  sheet:  1.37 (0.32), residues: 250
  loop : -0.88 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP X 110 
 HIS   0.004   0.001   HIS X 182 
 PHE   0.018   0.001   PHE L 122 
 TYR   0.021   0.001   TYR H 144 
 ARG   0.003   0.000   ARG B 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  412)
  hydrogen bonds       : angle       4.57131 ( 1209)
  SS BOND              : bond        0.00313 (    6)
  SS BOND              : angle       1.02017 (   12)
  covalent geometry    : bond        0.00300 ( 7290)
  covalent geometry    : angle       0.66726 ( 9944)

*********************** 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
  198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 161
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  177 GLU cc_start: 0.8749 (mp0) cc_final: 0.8492 (mp0)
REVERT: B  230 GLU cc_start: 0.7797 (mm-30) cc_final: 0.6913 (tt0)
REVERT: X  237 TRP cc_start: 0.8875 (t60) cc_final: 0.8599 (t60)
REVERT: X  242 LEU cc_start: 0.8635 (tt) cc_final: 0.8193 (mm)
REVERT: H   28 LEU cc_start: 0.9093 (mt) cc_final: 0.8749 (mp)
REVERT: H   86 ASP cc_start: 0.8894 (m-30) cc_final: 0.8607 (m-30)
REVERT: H  143 ASP cc_start: 0.7325 (m-30) cc_final: 0.6856 (t70)
REVERT: L   98 TYR cc_start: 0.8847 (m-10) cc_final: 0.8580 (m-10)
  outliers start: 37
  outliers final: 27
  residues processed: 184
  average time/residue: 0.1706
  time to fit residues: 43.2760
Evaluate side-chains
  181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  143 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  163 SER
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  147 THR
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  338 TYR
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  123 LEU
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  137 VAL
Chi-restraints excluded: chain L residue  167 VAL
Chi-restraints excluded: chain L residue  180 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 53 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
L  23 ASN
L  28 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.141200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.103929 restraints weight = 12660.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.106351 restraints weight = 12133.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.106676 restraints weight = 9072.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058   7296  Z= 0.375
  Angle     :  0.816  10.386   9956  Z= 0.404
  Chirality :  0.046   0.248   1133
  Planarity :  0.005   0.048   1234
  Dihedral  :  7.741 108.484   1026
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 22.09 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.28), residues: 901
  helix:  2.02 (0.27), residues: 322
  sheet:  1.12 (0.31), residues: 252
  loop : -0.89 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP X 347 
 HIS   0.005   0.001   HIS B 170 
 PHE   0.022   0.002   PHE H  91 
 TYR   0.035   0.003   TYR H 144 
 ARG   0.004   0.001   ARG X 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  412)
  hydrogen bonds       : angle       5.08698 ( 1209)
  SS BOND              : bond        0.00467 (    6)
  SS BOND              : angle       1.55595 (   12)
  covalent geometry    : bond        0.00860 ( 7290)
  covalent geometry    : angle       0.81488 ( 9944)

*********************** 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
  204 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 154
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  177 GLU cc_start: 0.8863 (mp0) cc_final: 0.8595 (mp0)
REVERT: X  237 TRP cc_start: 0.9021 (t60) cc_final: 0.8769 (t60)
REVERT: X  286 ILE cc_start: 0.8554 (pt) cc_final: 0.8201 (mm)
REVERT: H   86 ASP cc_start: 0.8781 (m-30) cc_final: 0.8466 (m-30)
REVERT: L  146 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7751 (tmm-80)
  outliers start: 50
  outliers final: 45
  residues processed: 187
  average time/residue: 0.1624
  time to fit residues: 42.1720
Evaluate side-chains
  192 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 147
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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  135 THR
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  210 TRP
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain X residue   17 VAL
Chi-restraints excluded: chain X residue   91 LEU
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  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   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  109 THR
Chi-restraints excluded: chain H residue  123 LEU
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue    6 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   96 ILE
Chi-restraints excluded: chain L residue  137 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 87 optimal weight:   40.0000
   chunk 17 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.147717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.110830 restraints weight = 12647.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113784 restraints weight = 11930.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.113605 restraints weight = 9535.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7296  Z= 0.141
  Angle     :  0.718  11.566   9956  Z= 0.339
  Chirality :  0.042   0.251   1133
  Planarity :  0.005   0.046   1234
  Dihedral  :  7.402 104.763   1026
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.58 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.28), residues: 901
  helix:  2.55 (0.27), residues: 316
  sheet:  1.35 (0.32), residues: 243
  loop : -0.77 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP X 110 
 HIS   0.004   0.001   HIS X 182 
 PHE   0.021   0.001   PHE L 122 
 TYR   0.023   0.002   TYR H 144 
 ARG   0.002   0.000   ARG X 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  412)
  hydrogen bonds       : angle       4.67833 ( 1209)
  SS BOND              : bond        0.00381 (    6)
  SS BOND              : angle       1.01365 (   12)
  covalent geometry    : bond        0.00327 ( 7290)
  covalent geometry    : angle       0.71761 ( 9944)

*********************** 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
  184 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  114 GLU cc_start: 0.8795 (tp30) cc_final: 0.8458 (tp30)
REVERT: X  242 LEU cc_start: 0.8780 (tt) cc_final: 0.8368 (mm)
REVERT: H   86 ASP cc_start: 0.8823 (m-30) cc_final: 0.8480 (m-30)
REVERT: L  146 ARG cc_start: 0.8077 (tmm-80) cc_final: 0.7648 (tmm-80)
REVERT: L  190 TYR cc_start: 0.7905 (t80) cc_final: 0.7606 (t80)
  outliers start: 32
  outliers final: 27
  residues processed: 173
  average time/residue: 0.1674
  time to fit residues: 40.1804
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  163 SER
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  138 THR
Chi-restraints excluded: chain X residue  147 THR
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  338 TYR
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  109 THR
Chi-restraints excluded: chain H residue  123 LEU
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  180 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  23 ASN
L  28 GLN
L  71 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.144849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.107966 restraints weight = 12766.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.109842 restraints weight = 11754.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110092 restraints weight = 9471.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7296  Z= 0.205
  Angle     :  0.735  11.888   9956  Z= 0.353
  Chirality :  0.043   0.279   1133
  Planarity :  0.005   0.047   1234
  Dihedral  :  7.439 105.917   1026
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.36 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.28), residues: 901
  helix:  2.34 (0.27), residues: 321
  sheet:  1.43 (0.33), residues: 242
  loop : -0.77 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP X 110 
 HIS   0.004   0.001   HIS X 182 
 PHE   0.019   0.001   PHE L 122 
 TYR   0.030   0.002   TYR H 144 
 ARG   0.003   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  412)
  hydrogen bonds       : angle       4.73012 ( 1209)
  SS BOND              : bond        0.00331 (    6)
  SS BOND              : angle       1.15927 (   12)
  covalent geometry    : bond        0.00479 ( 7290)
  covalent geometry    : angle       0.73419 ( 9944)

********************** 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
  179 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 1.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  242 LEU cc_start: 0.8800 (tt) cc_final: 0.8411 (mm)
REVERT: X  286 ILE cc_start: 0.8541 (pt) cc_final: 0.8154 (mm)
REVERT: H   86 ASP cc_start: 0.8864 (m-30) cc_final: 0.8501 (m-30)
REVERT: L  141 ASN cc_start: 0.8769 (t0) cc_final: 0.8439 (t0)
REVERT: L  146 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7702 (tmm-80)
REVERT: L  190 TYR cc_start: 0.7971 (t80) cc_final: 0.7649 (t80)
  outliers start: 31
  outliers final: 30
  residues processed: 168
  average time/residue: 0.1887
  time to fit residues: 43.5277
Evaluate side-chains
  178 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
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  135 THR
Chi-restraints excluded: chain B residue  162 SER
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 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  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  338 TYR
Chi-restraints excluded: chain H residue   28 LEU
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  109 THR
Chi-restraints excluded: chain H residue  123 LEU
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   96 ILE
Chi-restraints excluded: chain L residue  167 VAL
Chi-restraints excluded: chain L residue  180 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 86 optimal weight:   30.0000
   chunk 29 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 142 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 = 0.3805 r_free = 0.3805 target = 0.143023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.105653 restraints weight = 12635.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104815 restraints weight = 12140.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.105896 restraints weight = 11362.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   7296  Z= 0.277
  Angle     :  0.788  11.811   9956  Z= 0.379
  Chirality :  0.045   0.282   1133
  Planarity :  0.005   0.046   1234
  Dihedral  :  7.623 109.359   1026
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 24.58 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.28), residues: 901
  helix:  2.13 (0.27), residues: 322
  sheet:  1.23 (0.31), residues: 253
  loop : -0.85 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP X 110 
 HIS   0.005   0.001   HIS B 170 
 PHE   0.019   0.002   PHE L 122 
 TYR   0.031   0.002   TYR H 144 
 ARG   0.007   0.001   ARG H   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  412)
  hydrogen bonds       : angle       4.89243 ( 1209)
  SS BOND              : bond        0.00375 (    6)
  SS BOND              : angle       1.26944 (   12)
  covalent geometry    : bond        0.00640 ( 7290)
  covalent geometry    : angle       0.78711 ( 9944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2432.49 seconds
wall clock time: 43 minutes 42.15 seconds (2622.15 seconds total)