Starting phenix.real_space_refine
on Sat May 10 15:14:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6u_50240/05_2025/9f6u_50240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6u_50240/05_2025/9f6u_50240.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6u_50240/05_2025/9f6u_50240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6u_50240/05_2025/9f6u_50240.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6u_50240/05_2025/9f6u_50240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6u_50240/05_2025/9f6u_50240.cif"
  }
  resolution = 3.6
  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=   0.002 sd=   0.161
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       5      5.49       5
     S      34      5.16       5
     C    4166      2.51       5
     N    1090      2.21       5
     O    1275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6570
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3230
          Classifications: {'peptide': 422}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406}
    Chain: "B"
      Number of atoms: 3280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3280
          Classifications: {'peptide': 423}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 406}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.04, per 1000 atoms: 0.61
  Number of scatterers: 6570
  At special positions: 0
  Unit cell: (98.8, 78, 104, 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      34     16.00
     P       5     15.00
     O    1275      8.00
     N    1090      7.00
     C    4166      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 873.5 milliseconds
  

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1546

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      49.3% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 30
    Processing helix  chain 'A' and resid 44 through 47
    Processing helix  chain 'A' and resid 66 through 69
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 82 through 84
      No H-bonds generated for 'chain 'A' and resid 82 through 84'
    Processing helix  chain 'A' and resid 96 through 102
    Processing helix  chain 'A' and resid 105 through 122
    Processing helix  chain 'A' and resid 141 through 155
    Processing helix  chain 'A' and resid 176 through 192
      removed outlier: 3.505A  pdb=" N   ASN A 180 " --> pdb=" O   VAL A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 217 through 234
      removed outlier: 4.237A  pdb=" N   LEU A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE A 224 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 245 through 254
    Processing helix  chain 'A' and resid 281 through 290
    Processing helix  chain 'A' and resid 291 through 295
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 318 through 331
      removed outlier: 3.942A  pdb=" N   GLU A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 339
    Processing helix  chain 'A' and resid 368 through 382
      removed outlier: 3.899A  pdb=" N   PHE A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 420
    Processing helix  chain 'B' and resid 11 through 29
    Processing helix  chain 'B' and resid 70 through 78
    Processing helix  chain 'B' and resid 85 through 87
      No H-bonds generated for 'chain 'B' and resid 85 through 87'
    Processing helix  chain 'B' and resid 99 through 106
    Processing helix  chain 'B' and resid 110 through 124
      removed outlier: 4.229A  pdb=" N   ASN B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 158
    Processing helix  chain 'B' and resid 179 through 195
    Processing helix  chain 'B' and resid 203 through 213
    Processing helix  chain 'B' and resid 220 through 236
      removed outlier: 3.965A  pdb=" N   HIS B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 241
      removed outlier: 3.603A  pdb=" N   PHE B 241 " --> pdb=" O   SER B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 257
    Processing helix  chain 'B' and resid 284 through 292
      removed outlier: 4.875A  pdb=" N   ASN B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 298
      removed outlier: 6.542A  pdb=" N   ASN B 296 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 330
      removed outlier: 3.865A  pdb=" N   LEU B 330 " --> pdb=" O   THR B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
      removed outlier: 4.123A  pdb=" N   ILE B 374 " --> pdb=" O   GLY B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 397
    Processing helix  chain 'B' and resid 401 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88
      removed outlier: 8.271A  pdb=" N   VAL A  87 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   VAL A  62 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   GLU A   4 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY A 128 " --> pdb=" O   GLU A   4 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   SER A 134 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   PHE A 161 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   PHE A 129 " --> pdb=" O   PHE A 161 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   PHE A 163 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU A 131 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ILE A 165 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   HIS A 133 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS A 194 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   SER A 195 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ALA A 264 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   VAL A 197 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 10.693A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 13.744A  pdb=" N   ASP A 199 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   PHE A 261 " --> pdb=" O   ASN A 365 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   ASN A 365 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91
      removed outlier: 7.891A  pdb=" N   ILE B  90 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   LEU B  64 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   LEU B  63 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   MET B   7 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   ILE B  65 " --> pdb=" O   MET B   7 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   HIS B   9 " --> pdb=" O   ILE B  65 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   GLU B   4 " --> pdb=" O   GLN B 130 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   PHE B 132 " --> pdb=" O   GLU B   4 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ILE B   6 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   MET B 134 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU B   8 " --> pdb=" O   MET B 134 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   HIS B 136 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   VAL B  10 " --> pdb=" O   HIS B 136 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   GLN B 130 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   TRP B 164 " --> pdb=" O   GLN B 130 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   PHE B 132 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   TYR B 166 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   MET B 134 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   ILE B 168 " --> pdb=" O   MET B 134 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   HIS B 136 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   THR B 198 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ALA B 267 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL B 200 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
      removed outlier: 10.303A  pdb=" N   PHE B 269 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 12.617A  pdb=" N   ASP B 202 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   PHE B 264 " --> pdb=" O   HIS B 368 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   HIS B 368 " --> pdb=" O   PHE B 264 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   SER B 361 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   PHE B 316 " --> pdb=" O   SER B 361 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   SER B 363 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   LEU B 314 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LEU B 365 " --> pdb=" O   CYS B 312 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   CYS B 312 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ASN B 367 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 52

    322 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2006
        1.33 -     1.46: 1582
        1.46 -     1.58: 3047
        1.58 -     1.71: 8
        1.71 -     1.83: 57
  Bond restraints: 6700
  Sorted by residual:
  bond pdb=" CA  HIS B 226 "
       pdb=" C   HIS B 226 "
    ideal  model  delta    sigma   weight residual
    1.524  1.449  0.075 1.24e-02 6.50e+03 3.70e+01
  bond pdb=" CA  PHE B 207 "
       pdb=" C   PHE B 207 "
    ideal  model  delta    sigma   weight residual
    1.524  1.466  0.058 1.24e-02 6.50e+03 2.20e+01
  bond pdb=" CB  ASN A 222 "
       pdb=" CG  ASN A 222 "
    ideal  model  delta    sigma   weight residual
    1.516  1.412  0.104 2.50e-02 1.60e+03 1.72e+01
  bond pdb=" CA  LEU B 206 "
       pdb=" C   LEU B 206 "
    ideal  model  delta    sigma   weight residual
    1.524  1.470  0.053 1.29e-02 6.01e+03 1.70e+01
  bond pdb=" CG1 ILE B  38 "
       pdb=" CD1 ILE B  38 "
    ideal  model  delta    sigma   weight residual
    1.513  1.353  0.160 3.90e-02 6.57e+02 1.69e+01
  ... (remaining 6695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 8228
        2.56 -     5.12: 754
        5.12 -     7.68: 76
        7.68 -    10.24: 14
       10.24 -    12.80: 4
  Bond angle restraints: 9076
  Sorted by residual:
  angle pdb=" N   ARG B 335 "
        pdb=" CA  ARG B 335 "
        pdb=" C   ARG B 335 "
      ideal   model   delta    sigma   weight residual
     113.41  103.88    9.53 1.22e+00 6.72e-01 6.10e+01
  angle pdb=" N   GLN B 279 "
        pdb=" CA  GLN B 279 "
        pdb=" C   GLN B 279 "
      ideal   model   delta    sigma   weight residual
     110.35  101.90    8.45 1.36e+00 5.41e-01 3.86e+01
  angle pdb=" N   SER A 395 "
        pdb=" CA  SER A 395 "
        pdb=" C   SER A 395 "
      ideal   model   delta    sigma   weight residual
     110.61  103.29    7.32 1.25e+00 6.40e-01 3.43e+01
  angle pdb=" C   LEU B 245 "
        pdb=" CA  LEU B 245 "
        pdb=" CB  LEU B 245 "
      ideal   model   delta    sigma   weight residual
     116.34  108.69    7.65 1.40e+00 5.10e-01 2.99e+01
  angle pdb=" C   HIS B 226 "
        pdb=" CA  HIS B 226 "
        pdb=" CB  HIS B 226 "
      ideal   model   delta    sigma   weight residual
     110.95  103.00    7.95 1.55e+00 4.16e-01 2.63e+01
  ... (remaining 9071 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 3953
       34.69 -    69.39: 38
       69.39 -   104.08: 4
      104.08 -   138.77: 1
      138.77 -   173.47: 2
  Dihedral angle restraints: 3998
    sinusoidal: 1586
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" C4' GTP B 501 "
           pdb=" C5' GTP B 501 "
           pdb=" O5' GTP B 501 "
           pdb=" PA  GTP B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87   87.41  173.47     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C8  GTP B 501 "
           pdb=" C1' GTP B 501 "
           pdb=" N9  GTP B 501 "
           pdb=" O4' GTP B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59 -100.43 -154.97     1      2.00e+01 2.50e-03 4.57e+01
  dihedral pdb=" O3B GTP B 501 "
           pdb=" O3A GTP B 501 "
           pdb=" PB  GTP B 501 "
           pdb=" PA  GTP B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92 -179.70  110.78     1      2.00e+01 2.50e-03 3.25e+01
  ... (remaining 3995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 567
       0.059 -    0.118: 318
       0.118 -    0.177: 107
       0.177 -    0.236: 22
       0.236 -    0.294: 3
  Chirality restraints: 1017
  Sorted by residual:
  chirality pdb=" C2' GTP B 501 "
            pdb=" C1' GTP B 501 "
            pdb=" C3' GTP B 501 "
            pdb=" O2' GTP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.77    0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CA  ASN A 187 "
            pdb=" N   ASN A 187 "
            pdb=" C   ASN A 187 "
            pdb=" CB  ASN A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  MET A 113 "
            pdb=" N   MET A 113 "
            pdb=" C   MET A 113 "
            pdb=" CB  MET A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1014 not shown)

  Planarity restraints: 1169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 405 "   -0.036 2.00e-02 2.50e+03   2.49e-02 1.09e+01
        pdb=" CG  PHE B 405 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 405 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 405 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 405 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 405 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 405 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  29 "    0.033 2.00e-02 2.50e+03   2.62e-02 1.03e+01
        pdb=" CG  HIS B  29 "   -0.050 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  29 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  29 "    0.008 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  29 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 335 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   ARG B 335 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ARG B 335 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ILE B 336 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1166 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2049
        2.80 -     3.33: 6540
        3.33 -     3.85: 11164
        3.85 -     4.38: 14022
        4.38 -     4.90: 21673
  Nonbonded interactions: 55448
  Sorted by model distance:
  nonbonded pdb=" CD1 ILE A  73 "
            pdb=" CE2 PHE A  77 "
     model   vdw
     2.278 3.760
  nonbonded pdb=" O   GLU B 180 "
            pdb=" N   ASN B 183 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   GLU B 180 "
            pdb=" N   TYR B 182 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" N   ASP A 292 "
            pdb=" OD1 ASP A 292 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   ASN A  15 "
            pdb=" CZ  PHE A  77 "
     model   vdw
     2.387 3.340
  ... (remaining 55443 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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     17.460
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5574
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      :  0.018   0.160   6700  Z= 1.017
  Angle     :  1.564  12.804   9076  Z= 0.986
  Chirality :  0.077   0.294   1017
  Planarity :  0.008   0.041   1169
  Dihedral  : 11.743 173.466   2452
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.11 (0.27), residues: 841
  helix: -0.31 (0.25), residues: 340
  sheet:  1.75 (0.45), residues: 120
  loop : -0.32 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.006   TRP A 338 
 HIS   0.013   0.003   HIS B  29 
 PHE   0.052   0.006   PHE B 405 
 TYR   0.025   0.005   TYR A 191 
 ARG   0.007   0.001   ARG B 409 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18516 (  322)
  hydrogen bonds       : angle       7.46819 (  924)
  covalent geometry    : bond        0.01835 ( 6700)
  covalent geometry    : angle       1.56426 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.8079 (mmm) cc_final: 0.7790 (mpp)
REVERT: A  220 ASP cc_start: 0.6986 (m-30) cc_final: 0.6411 (t0)
REVERT: A  305 ARG cc_start: 0.7759 (mmt-90) cc_final: 0.6294 (mtp85)
REVERT: A  372 PHE cc_start: 0.6050 (m-80) cc_final: 0.5713 (m-10)
REVERT: B  121 LYS cc_start: 0.8653 (mttt) cc_final: 0.8276 (mtmt)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.2111
  time to fit residues: 74.0323
Evaluate side-chains
  146 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 180 ASN
** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 GLN
B  24 GLN
B 230 GLN
B 255 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.215072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.183734 restraints weight = 7421.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.189572 restraints weight = 4201.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.193970 restraints weight = 2816.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6063
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6700  Z= 0.193
  Angle     :  0.775  13.538   9076  Z= 0.409
  Chirality :  0.049   0.193   1017
  Planarity :  0.005   0.063   1169
  Dihedral  : 11.077 152.662    919
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  :  9.83 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.06 (0.27), residues: 841
  helix:  0.29 (0.25), residues: 354
  sheet:  1.45 (0.45), residues: 116
  loop : -0.78 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 394 
 HIS   0.003   0.001   HIS B 204 
 PHE   0.023   0.003   PHE B 405 
 TYR   0.030   0.002   TYR A 179 
 ARG   0.007   0.001   ARG B 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06640 (  322)
  hydrogen bonds       : angle       5.39343 (  924)
  covalent geometry    : bond        0.00419 ( 6700)
  covalent geometry    : angle       0.77488 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.7754 (tpp) cc_final: 0.7499 (tpt)
REVERT: A  201 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6998 (mt-10)
REVERT: A  220 ASP cc_start: 0.6732 (m-30) cc_final: 0.6027 (t0)
REVERT: A  380 ASP cc_start: 0.7023 (t0) cc_final: 0.6806 (t0)
REVERT: A  386 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7262 (pttp)
REVERT: B    3 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7211 (ptp90)
REVERT: B  121 LYS cc_start: 0.8087 (mttt) cc_final: 0.7741 (mtmt)
  outliers start: 26
  outliers final: 15
  residues processed: 173
  average time/residue: 0.1862
  time to fit residues: 42.3848
Evaluate side-chains
  145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  400 LYS
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  329 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 ASN
B  77 ASN
B 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.210595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.177815 restraints weight = 7280.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.183621 restraints weight = 4243.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.187844 restraints weight = 2869.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6266
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6700  Z= 0.211
  Angle     :  0.724   9.361   9076  Z= 0.380
  Chirality :  0.048   0.166   1017
  Planarity :  0.005   0.054   1169
  Dihedral  : 10.831 156.299    919
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 12.11 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.35 (0.27), residues: 841
  helix:  0.26 (0.25), residues: 361
  sheet:  0.99 (0.46), residues: 120
  loop : -1.13 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 260 
 PHE   0.023   0.003   PHE B 382 
 TYR   0.031   0.002   TYR B 348 
 ARG   0.006   0.001   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05913 (  322)
  hydrogen bonds       : angle       5.24427 (  924)
  covalent geometry    : bond        0.00476 ( 6700)
  covalent geometry    : angle       0.72446 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7990 (m) cc_final: 0.7233 (p)
REVERT: A  177 GLU cc_start: 0.8006 (pp20) cc_final: 0.7650 (pm20)
REVERT: A  180 ASN cc_start: 0.7270 (m-40) cc_final: 0.7012 (m110)
REVERT: A  201 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7105 (mt-10)
REVERT: A  204 PHE cc_start: 0.7634 (t80) cc_final: 0.7382 (t80)
REVERT: A  220 ASP cc_start: 0.6772 (m-30) cc_final: 0.6029 (t0)
REVERT: A  386 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7359 (pttp)
REVERT: B  121 LYS cc_start: 0.8175 (mttt) cc_final: 0.7927 (mttp)
REVERT: B  266 MET cc_start: 0.6205 (mtp) cc_final: 0.5984 (mtm)
REVERT: B  280 TYR cc_start: 0.4698 (m-10) cc_final: 0.4288 (m-10)
REVERT: B  329 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7033 (mt)
REVERT: B  379 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5946 (mt)
  outliers start: 28
  outliers final: 19
  residues processed: 164
  average time/residue: 0.1613
  time to fit residues: 36.0551
Evaluate side-chains
  150 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  400 LYS
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0030
   chunk 69 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 78 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.215849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.182441 restraints weight = 7654.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.188655 restraints weight = 4428.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.193114 restraints weight = 2987.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6196
moved from start:          0.5348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6700  Z= 0.139
  Angle     :  0.630   9.279   9076  Z= 0.327
  Chirality :  0.044   0.159   1017
  Planarity :  0.004   0.048   1169
  Dihedral  : 10.645 158.987    919
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.25 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.23 (0.28), residues: 841
  helix:  0.46 (0.25), residues: 369
  sheet:  0.90 (0.47), residues: 120
  loop : -1.16 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  22 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.026   0.002   PHE A 372 
 TYR   0.019   0.002   TYR A 179 
 ARG   0.003   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04988 (  322)
  hydrogen bonds       : angle       4.98770 (  924)
  covalent geometry    : bond        0.00297 ( 6700)
  covalent geometry    : angle       0.62976 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7776 (m) cc_final: 0.7122 (p)
REVERT: A  177 GLU cc_start: 0.7986 (pp20) cc_final: 0.7655 (pm20)
REVERT: A  180 ASN cc_start: 0.7245 (m-40) cc_final: 0.6866 (m110)
REVERT: A  183 MET cc_start: 0.8126 (mmm) cc_final: 0.7843 (tpt)
REVERT: A  201 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6996 (mt-10)
REVERT: A  204 PHE cc_start: 0.7474 (t80) cc_final: 0.7026 (t80)
REVERT: A  220 ASP cc_start: 0.6621 (m-30) cc_final: 0.5887 (t0)
REVERT: A  386 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7092 (pttp)
REVERT: A  391 TRP cc_start: 0.6644 (m100) cc_final: 0.6252 (m-10)
REVERT: A  418 LYS cc_start: 0.8112 (tppt) cc_final: 0.7663 (tppt)
REVERT: B  121 LYS cc_start: 0.8171 (mttt) cc_final: 0.7766 (mtmt)
REVERT: B  249 MET cc_start: 0.5281 (mtm) cc_final: 0.5039 (mtm)
REVERT: B  266 MET cc_start: 0.6163 (mtp) cc_final: 0.5934 (mtm)
REVERT: B  420 LYS cc_start: 0.8159 (tppt) cc_final: 0.7933 (tppt)
  outliers start: 22
  outliers final: 15
  residues processed: 154
  average time/residue: 0.1623
  time to fit residues: 34.0739
Evaluate side-chains
  144 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  368 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0870
   chunk 72 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
B  77 ASN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.213027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.179535 restraints weight = 7560.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.185491 restraints weight = 4442.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.189695 restraints weight = 3037.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6259
moved from start:          0.5703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6700  Z= 0.149
  Angle     :  0.637   8.331   9076  Z= 0.330
  Chirality :  0.045   0.162   1017
  Planarity :  0.004   0.040   1169
  Dihedral  : 10.500 159.906    919
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 14.53 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.22 (0.28), residues: 841
  helix:  0.65 (0.26), residues: 359
  sheet:  0.83 (0.48), residues: 120
  loop : -1.29 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  22 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.024   0.002   PHE A 379 
 TYR   0.019   0.002   TYR A 179 
 ARG   0.004   0.001   ARG B   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05007 (  322)
  hydrogen bonds       : angle       4.91212 (  924)
  covalent geometry    : bond        0.00328 ( 6700)
  covalent geometry    : angle       0.63741 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 GLU cc_start: 0.8002 (pp20) cc_final: 0.7643 (pm20)
REVERT: A  180 ASN cc_start: 0.7453 (m-40) cc_final: 0.7102 (m110)
REVERT: A  204 PHE cc_start: 0.7503 (t80) cc_final: 0.6994 (t80)
REVERT: A  391 TRP cc_start: 0.6593 (m100) cc_final: 0.6299 (m-10)
REVERT: A  397 PHE cc_start: 0.4962 (m-80) cc_final: 0.4368 (m-10)
REVERT: A  418 LYS cc_start: 0.8116 (tppt) cc_final: 0.7884 (tppt)
REVERT: B  121 LYS cc_start: 0.8132 (mttt) cc_final: 0.7751 (mtmt)
REVERT: B  266 MET cc_start: 0.6430 (mtp) cc_final: 0.6032 (mtm)
  outliers start: 26
  outliers final: 20
  residues processed: 154
  average time/residue: 0.1605
  time to fit residues: 34.4581
Evaluate side-chains
  150 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0000
   chunk 5 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
B  77 ASN
** B 130 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 = 0.4545 r_free = 0.4545 target = 0.215312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.182552 restraints weight = 7270.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.188633 restraints weight = 4200.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.192950 restraints weight = 2825.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.5996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6700  Z= 0.134
  Angle     :  0.639   7.852   9076  Z= 0.325
  Chirality :  0.044   0.156   1017
  Planarity :  0.004   0.039   1169
  Dihedral  : 10.397 160.810    919
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.81 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.24 (0.28), residues: 841
  helix:  0.69 (0.26), residues: 362
  sheet:  0.82 (0.48), residues: 120
  loop : -1.39 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  22 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.025   0.002   PHE A 379 
 TYR   0.019   0.002   TYR B 104 
 ARG   0.003   0.000   ARG B   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04697 (  322)
  hydrogen bonds       : angle       4.86640 (  924)
  covalent geometry    : bond        0.00294 ( 6700)
  covalent geometry    : angle       0.63901 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 GLU cc_start: 0.7960 (pp20) cc_final: 0.7424 (pt0)
REVERT: A  180 ASN cc_start: 0.7246 (m-40) cc_final: 0.6869 (m110)
REVERT: A  204 PHE cc_start: 0.7414 (t80) cc_final: 0.6989 (t80)
REVERT: A  220 ASP cc_start: 0.6526 (m-30) cc_final: 0.5939 (t0)
REVERT: A  391 TRP cc_start: 0.6484 (m100) cc_final: 0.6245 (m-10)
REVERT: B   43 LYS cc_start: 0.6454 (tptt) cc_final: 0.6218 (tptt)
REVERT: B  121 LYS cc_start: 0.8105 (mttt) cc_final: 0.7803 (mtmt)
REVERT: B  344 THR cc_start: 0.6548 (p) cc_final: 0.6261 (m)
REVERT: B  420 LYS cc_start: 0.8088 (tppt) cc_final: 0.7866 (tppt)
  outliers start: 26
  outliers final: 24
  residues processed: 155
  average time/residue: 0.1576
  time to fit residues: 34.1047
Evaluate side-chains
  152 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  400 LYS
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  287 ASN
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 ASN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.198698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.165708 restraints weight = 7879.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.171110 restraints weight = 4659.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.174752 restraints weight = 3218.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6381
moved from start:          0.6287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6700  Z= 0.216
  Angle     :  0.720   8.171   9076  Z= 0.371
  Chirality :  0.047   0.166   1017
  Planarity :  0.004   0.040   1169
  Dihedral  : 10.481 162.016    919
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 15.53 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.66 (0.28), residues: 841
  helix:  0.35 (0.26), residues: 360
  sheet:  0.65 (0.48), residues: 121
  loop : -1.65 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 338 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.030   0.003   PHE A 379 
 TYR   0.022   0.002   TYR A 179 
 ARG   0.004   0.001   ARG B 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05305 (  322)
  hydrogen bonds       : angle       5.11261 (  924)
  covalent geometry    : bond        0.00484 ( 6700)
  covalent geometry    : angle       0.72022 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 GLU cc_start: 0.8200 (pp20) cc_final: 0.7907 (pt0)
REVERT: A  183 MET cc_start: 0.8012 (mmm) cc_final: 0.7746 (tpt)
REVERT: A  220 ASP cc_start: 0.6670 (m-30) cc_final: 0.5966 (t0)
REVERT: A  391 TRP cc_start: 0.6627 (m100) cc_final: 0.6394 (m-10)
REVERT: B   43 LYS cc_start: 0.6687 (tptt) cc_final: 0.6370 (tptt)
REVERT: B  121 LYS cc_start: 0.8242 (mttt) cc_final: 0.7884 (mttp)
  outliers start: 34
  outliers final: 31
  residues processed: 155
  average time/residue: 0.1587
  time to fit residues: 34.1859
Evaluate side-chains
  153 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  400 LYS
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  287 ASN
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0570
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.212203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.179443 restraints weight = 7433.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.185327 restraints weight = 4313.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.189590 restraints weight = 2919.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6286
moved from start:          0.6532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6700  Z= 0.140
  Angle     :  0.669   9.683   9076  Z= 0.341
  Chirality :  0.045   0.146   1017
  Planarity :  0.004   0.060   1169
  Dihedral  : 10.395 163.768    919
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.38 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.54 (0.28), residues: 841
  helix:  0.51 (0.26), residues: 367
  sheet:  0.54 (0.48), residues: 120
  loop : -1.62 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.031   0.002   PHE A  97 
 TYR   0.022   0.002   TYR A 155 
 ARG   0.003   0.000   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  322)
  hydrogen bonds       : angle       4.93837 (  924)
  covalent geometry    : bond        0.00303 ( 6700)
  covalent geometry    : angle       0.66885 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7842 (m) cc_final: 0.7359 (p)
REVERT: A  177 GLU cc_start: 0.8082 (pp20) cc_final: 0.7689 (pt0)
REVERT: A  220 ASP cc_start: 0.6661 (m-30) cc_final: 0.6035 (t0)
REVERT: A  361 MET cc_start: 0.7258 (tmm) cc_final: 0.6950 (tmm)
REVERT: B   43 LYS cc_start: 0.6478 (tptt) cc_final: 0.6151 (tptt)
REVERT: B  121 LYS cc_start: 0.8120 (mttt) cc_final: 0.7796 (mttp)
REVERT: B  268 SER cc_start: 0.6263 (t) cc_final: 0.5887 (p)
REVERT: B  280 TYR cc_start: 0.5060 (m-10) cc_final: 0.4807 (m-10)
  outliers start: 26
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1466
  time to fit residues: 30.4366
Evaluate side-chains
  148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.2980
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   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 130 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 = 0.4521 r_free = 0.4521 target = 0.212650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.179572 restraints weight = 7508.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.185343 restraints weight = 4364.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.189828 restraints weight = 2943.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6281
moved from start:          0.6725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6700  Z= 0.144
  Angle     :  0.689  10.676   9076  Z= 0.356
  Chirality :  0.046   0.176   1017
  Planarity :  0.004   0.050   1169
  Dihedral  : 10.320 163.316    919
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.38 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.61 (0.28), residues: 841
  helix:  0.55 (0.26), residues: 365
  sheet:  0.28 (0.47), residues: 124
  loop : -1.69 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.033   0.002   PHE A 379 
 TYR   0.026   0.002   TYR A 155 
 ARG   0.003   0.000   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 (  322)
  hydrogen bonds       : angle       4.83354 (  924)
  covalent geometry    : bond        0.00316 ( 6700)
  covalent geometry    : angle       0.68864 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7898 (m) cc_final: 0.7420 (p)
REVERT: A  180 ASN cc_start: 0.6732 (m-40) cc_final: 0.6229 (m110)
REVERT: A  220 ASP cc_start: 0.6513 (m-30) cc_final: 0.5956 (t0)
REVERT: B   43 LYS cc_start: 0.6440 (tptt) cc_final: 0.6103 (tptt)
REVERT: B  121 LYS cc_start: 0.8042 (mttt) cc_final: 0.7785 (mttp)
REVERT: B  268 SER cc_start: 0.6408 (t) cc_final: 0.5886 (p)
REVERT: B  280 TYR cc_start: 0.4936 (m-10) cc_final: 0.4702 (m-10)
  outliers start: 27
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1607
  time to fit residues: 32.9421
Evaluate side-chains
  146 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 77 optimal weight:    0.0020
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0980
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
A 215 ASN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.216697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.183561 restraints weight = 7530.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.189657 restraints weight = 4377.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.193979 restraints weight = 2958.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.6928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6700  Z= 0.137
  Angle     :  0.702  12.505   9076  Z= 0.366
  Chirality :  0.046   0.315   1017
  Planarity :  0.004   0.052   1169
  Dihedral  : 10.260 163.679    919
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.37 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.53 (0.28), residues: 841
  helix:  0.71 (0.27), residues: 359
  sheet:  0.26 (0.48), residues: 124
  loop : -1.69 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.033   0.002   PHE A 379 
 TYR   0.031   0.002   TYR A 155 
 ARG   0.003   0.000   ARG B   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04368 (  322)
  hydrogen bonds       : angle       4.80232 (  924)
  covalent geometry    : bond        0.00295 ( 6700)
  covalent geometry    : angle       0.70225 ( 9076)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7876 (m) cc_final: 0.7338 (p)
REVERT: A  180 ASN cc_start: 0.6578 (m-40) cc_final: 0.6157 (m110)
REVERT: A  386 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7086 (pttm)
REVERT: B   43 LYS cc_start: 0.6363 (tptt) cc_final: 0.6057 (tptt)
REVERT: B  121 LYS cc_start: 0.8105 (mttt) cc_final: 0.7855 (mttp)
REVERT: B  268 SER cc_start: 0.6181 (t) cc_final: 0.5784 (p)
REVERT: B  350 MET cc_start: 0.7006 (mmt) cc_final: 0.6774 (mmm)
  outliers start: 24
  outliers final: 18
  residues processed: 145
  average time/residue: 0.1482
  time to fit residues: 29.7234
Evaluate side-chains
  142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:    0.0370
   chunk 70 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 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 = 0.4498 r_free = 0.4498 target = 0.206744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.173759 restraints weight = 8032.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.179459 restraints weight = 4665.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.183412 restraints weight = 3195.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6212
moved from start:          0.6921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.185   6700  Z= 0.284
  Angle     :  1.109  59.195   9076  Z= 0.638
  Chirality :  0.064   1.358   1017
  Planarity :  0.005   0.079   1169
  Dihedral  : 10.284 163.694    919
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.23 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.54 (0.28), residues: 841
  helix:  0.72 (0.27), residues: 359
  sheet:  0.26 (0.48), residues: 124
  loop : -1.73 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 338 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.030   0.002   PHE A 379 
 TYR   0.026   0.003   TYR A 179 
 ARG   0.002   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04385 (  322)
  hydrogen bonds       : angle       4.79836 (  924)
  covalent geometry    : bond        0.00565 ( 6700)
  covalent geometry    : angle       1.10923 ( 9076)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2460.87 seconds
wall clock time: 43 minutes 38.01 seconds (2618.01 seconds total)