Starting phenix.real_space_refine
on Sun Apr 27 20:22:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6u_50240/04_2025/9f6u_50240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6u_50240/04_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_50240/04_2025/9f6u_50240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6u_50240/04_2025/9f6u_50240.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6u_50240/04_2025/9f6u_50240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6u_50240/04_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-5669/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: 4.30, per 1000 atoms: 0.65
  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: 1.84
  Conformation dependent library (CDL) restraints added in 936.9 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: 0.76
  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: 1.85

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 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:             0.270
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.110
-------------------------------------------------------------------------------
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  : 0.682 
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: 0.2127
  time to fit residues: 74.6241
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  : 0.741 
-------------------------------------------------------------------------------
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 = 31)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.189571 restraints weight = 4201.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.193962 restraints weight = 2816.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6050
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  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.7764 (tpp) cc_final: 0.7507 (tpt)
REVERT: A  201 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6988 (mt-10)
REVERT: A  220 ASP cc_start: 0.6757 (m-30) cc_final: 0.6026 (t0)
REVERT: A  380 ASP cc_start: 0.7064 (t0) cc_final: 0.6848 (t0)
REVERT: A  386 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7261 (pttp)
REVERT: B    3 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7214 (ptp90)
REVERT: B  121 LYS cc_start: 0.8116 (mttt) cc_final: 0.7747 (mtmt)
REVERT: B  249 MET cc_start: 0.5478 (mtm) cc_final: 0.5277 (mtm)
  outliers start: 26
  outliers final: 15
  residues processed: 173
  average time/residue: 0.1910
  time to fit residues: 43.5668
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  : 0.784 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 = 0.4485 r_free = 0.4485 target = 0.207508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.174648 restraints weight = 7369.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.180225 restraints weight = 4299.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.184386 restraints weight = 2928.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6324
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6700  Z= 0.229
  Angle     :  0.751   9.904   9076  Z= 0.394
  Chirality :  0.049   0.171   1017
  Planarity :  0.005   0.056   1169
  Dihedral  : 10.843 158.467    919
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 12.25 %
    Favored  : 83.48 %
  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: -0.48 (0.27), residues: 841
  helix:  0.16 (0.25), residues: 363
  sheet:  0.95 (0.46), residues: 120
  loop : -1.21 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 338 
 HIS   0.005   0.001   HIS A  29 
 PHE   0.024   0.003   PHE B 382 
 TYR   0.025   0.002   TYR A 179 
 ARG   0.007   0.001   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05999 (  322)
  hydrogen bonds       : angle       5.33385 (  924)
  covalent geometry    : bond        0.00522 ( 6700)
  covalent geometry    : angle       0.75140 ( 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
  173 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 GLU cc_start: 0.8012 (pp20) cc_final: 0.7654 (pm20)
REVERT: A  180 ASN cc_start: 0.7362 (m-40) cc_final: 0.7151 (m-40)
REVERT: A  201 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7127 (mt-10)
REVERT: A  220 ASP cc_start: 0.6822 (m-30) cc_final: 0.6029 (t0)
REVERT: A  331 GLU cc_start: 0.7699 (pt0) cc_final: 0.7481 (pt0)
REVERT: B  121 LYS cc_start: 0.8235 (mttt) cc_final: 0.7879 (mttt)
REVERT: B  266 MET cc_start: 0.6259 (mtp) cc_final: 0.5973 (mtm)
REVERT: B  329 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6997 (mt)
REVERT: B  379 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6112 (mt)
  outliers start: 30
  outliers final: 22
  residues processed: 166
  average time/residue: 0.1656
  time to fit residues: 37.6394
Evaluate side-chains
  150 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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  235 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  344 THR
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:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 69 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.208665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.177166 restraints weight = 7779.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.183013 restraints weight = 4323.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.187135 restraints weight = 2879.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6302
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6700  Z= 0.167
  Angle     :  0.667   9.824   9076  Z= 0.345
  Chirality :  0.045   0.163   1017
  Planarity :  0.004   0.042   1169
  Dihedral  : 10.714 161.071    919
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 13.68 %
    Favored  : 82.76 %
  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: -0.47 (0.28), residues: 841
  helix:  0.35 (0.26), residues: 365
  sheet:  0.77 (0.47), residues: 120
  loop : -1.37 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  22 
 HIS   0.004   0.001   HIS A 104 
 PHE   0.021   0.002   PHE A 379 
 TYR   0.023   0.002   TYR A 179 
 ARG   0.004   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05282 (  322)
  hydrogen bonds       : angle       5.10385 (  924)
  covalent geometry    : bond        0.00377 ( 6700)
  covalent geometry    : angle       0.66694 ( 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: 25
    poor density    : 136
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 GLU cc_start: 0.8025 (pp20) cc_final: 0.7660 (pm20)
REVERT: A  180 ASN cc_start: 0.7329 (m-40) cc_final: 0.7043 (m110)
REVERT: A  183 MET cc_start: 0.8262 (mmm) cc_final: 0.7940 (tpt)
REVERT: A  201 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7176 (mt-10)
REVERT: A  220 ASP cc_start: 0.6729 (m-30) cc_final: 0.6033 (t0)
REVERT: A  391 TRP cc_start: 0.6680 (m100) cc_final: 0.6305 (m-10)
REVERT: A  418 LYS cc_start: 0.8227 (tppt) cc_final: 0.7944 (tppt)
REVERT: B  121 LYS cc_start: 0.8213 (mttt) cc_final: 0.7899 (mttp)
REVERT: B  130 GLN cc_start: 0.6395 (tt0) cc_final: 0.6117 (tt0)
REVERT: B  249 MET cc_start: 0.5057 (mtm) cc_final: 0.4274 (mtm)
REVERT: B  266 MET cc_start: 0.6397 (mtp) cc_final: 0.6127 (mtm)
  outliers start: 25
  outliers final: 19
  residues processed: 153
  average time/residue: 0.1625
  time to fit residues: 34.2343
Evaluate side-chains
  145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ILE
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  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 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  285 THR
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:    6.9990
   chunk 5 optimal weight:    0.0470
   chunk 37 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0570
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 263 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.213428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.182962 restraints weight = 7866.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.188591 restraints weight = 4525.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.192600 restraints weight = 3060.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6245
moved from start:          0.5879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6700  Z= 0.132
  Angle     :  0.627   8.607   9076  Z= 0.321
  Chirality :  0.044   0.156   1017
  Planarity :  0.004   0.040   1169
  Dihedral  : 10.503 162.277    919
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 14.39 %
    Favored  : 81.91 %
  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: -0.32 (0.28), residues: 841
  helix:  0.60 (0.26), residues: 365
  sheet:  0.75 (0.48), residues: 120
  loop : -1.41 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.023   0.002   PHE A 379 
 TYR   0.018   0.002   TYR A 179 
 ARG   0.003   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  322)
  hydrogen bonds       : angle       4.92222 (  924)
  covalent geometry    : bond        0.00284 ( 6700)
  covalent geometry    : angle       0.62730 ( 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
  167 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7878 (m) cc_final: 0.7229 (p)
REVERT: A  177 GLU cc_start: 0.8066 (pp20) cc_final: 0.7640 (pm20)
REVERT: A  180 ASN cc_start: 0.7307 (m-40) cc_final: 0.6921 (m110)
REVERT: A  183 MET cc_start: 0.8263 (mmm) cc_final: 0.7831 (tpt)
REVERT: A  220 ASP cc_start: 0.6531 (m-30) cc_final: 0.5912 (t0)
REVERT: A  391 TRP cc_start: 0.6572 (m100) cc_final: 0.6305 (m-10)
REVERT: A  397 PHE cc_start: 0.5068 (m-80) cc_final: 0.4684 (m-10)
REVERT: A  418 LYS cc_start: 0.8307 (tppt) cc_final: 0.8078 (tppt)
REVERT: B  121 LYS cc_start: 0.8089 (mttt) cc_final: 0.7777 (mttp)
REVERT: B  249 MET cc_start: 0.4917 (mtm) cc_final: 0.4518 (mtm)
REVERT: B  266 MET cc_start: 0.6477 (mtp) cc_final: 0.6196 (mtm)
REVERT: B  268 SER cc_start: 0.6511 (OUTLIER) cc_final: 0.5925 (p)
  outliers start: 26
  outliers final: 20
  residues processed: 159
  average time/residue: 0.1586
  time to fit residues: 34.5242
Evaluate side-chains
  154 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 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  151 ILE
Chi-restraints excluded: chain A residue  165 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  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 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  268 SER
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  287 ASN
Chi-restraints excluded: chain B residue  368 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 76 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0370
   chunk 11 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.213527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.181971 restraints weight = 7835.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.187946 restraints weight = 4435.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.192080 restraints weight = 2972.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.4448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6238
moved from start:          0.6103

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= 0.130
  Angle     :  0.628   8.024   9076  Z= 0.322
  Chirality :  0.044   0.154   1017
  Planarity :  0.004   0.040   1169
  Dihedral  : 10.363 162.255    919
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.67 %
    Favored  : 79.91 %
  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: -0.33 (0.28), residues: 841
  helix:  0.61 (0.26), residues: 368
  sheet:  0.71 (0.48), residues: 120
  loop : -1.44 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.025   0.002   PHE A 379 
 TYR   0.026   0.002   TYR A 155 
 ARG   0.003   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04620 (  322)
  hydrogen bonds       : angle       4.85032 (  924)
  covalent geometry    : bond        0.00277 ( 6700)
  covalent geometry    : angle       0.62769 ( 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
  161 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7843 (m) cc_final: 0.7179 (p)
REVERT: A  177 GLU cc_start: 0.8032 (pp20) cc_final: 0.7503 (pt0)
REVERT: A  180 ASN cc_start: 0.7353 (m-40) cc_final: 0.6943 (m110)
REVERT: A  183 MET cc_start: 0.8261 (mmm) cc_final: 0.7905 (tpt)
REVERT: A  201 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6996 (mt-10)
REVERT: A  220 ASP cc_start: 0.6545 (m-30) cc_final: 0.5954 (t0)
REVERT: A  386 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7150 (pttm)
REVERT: A  391 TRP cc_start: 0.6571 (m100) cc_final: 0.6334 (m-10)
REVERT: B   43 LYS cc_start: 0.6384 (tptt) cc_final: 0.6119 (tptt)
REVERT: B   67 LEU cc_start: 0.6544 (mt) cc_final: 0.6227 (mp)
REVERT: B  104 TYR cc_start: 0.6991 (t80) cc_final: 0.6665 (t80)
REVERT: B  121 LYS cc_start: 0.8104 (mttt) cc_final: 0.7768 (mtmt)
REVERT: B  252 PHE cc_start: 0.6945 (m-80) cc_final: 0.6705 (m-80)
REVERT: B  268 SER cc_start: 0.6408 (t) cc_final: 0.5897 (p)
REVERT: B  272 MET cc_start: 0.4507 (ptt) cc_final: 0.4141 (mtm)
REVERT: B  350 MET cc_start: 0.6985 (ptp) cc_final: 0.6312 (mpp)
REVERT: B  420 LYS cc_start: 0.8055 (tppt) cc_final: 0.7739 (tppt)
  outliers start: 24
  outliers final: 21
  residues processed: 154
  average time/residue: 0.1676
  time to fit residues: 35.3330
Evaluate side-chains
  149 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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  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  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
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 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  285 THR
Chi-restraints excluded: chain B residue  368 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
** A 227 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 = 0.4521 r_free = 0.4521 target = 0.208293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.176988 restraints weight = 7677.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.182680 restraints weight = 4398.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.186628 restraints weight = 2994.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.6371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6700  Z= 0.168
  Angle     :  0.672   7.721   9076  Z= 0.347
  Chirality :  0.046   0.158   1017
  Planarity :  0.004   0.074   1169
  Dihedral  : 10.344 162.182    919
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 17.24 %
    Favored  : 78.49 %
  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: -0.48 (0.28), residues: 841
  helix:  0.53 (0.26), residues: 366
  sheet:  0.54 (0.47), residues: 121
  loop : -1.52 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.027   0.003   PHE A 379 
 TYR   0.020   0.002   TYR A 155 
 ARG   0.003   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04947 (  322)
  hydrogen bonds       : angle       4.98209 (  924)
  covalent geometry    : bond        0.00377 ( 6700)
  covalent geometry    : angle       0.67173 ( 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
  162 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7842 (m) cc_final: 0.7409 (p)
REVERT: A  177 GLU cc_start: 0.8090 (pp20) cc_final: 0.7552 (pt0)
REVERT: A  180 ASN cc_start: 0.7334 (m-40) cc_final: 0.7103 (m-40)
REVERT: A  183 MET cc_start: 0.8192 (mmm) cc_final: 0.7938 (tpt)
REVERT: A  220 ASP cc_start: 0.6575 (m-30) cc_final: 0.6037 (t0)
REVERT: B   43 LYS cc_start: 0.6591 (tptt) cc_final: 0.6208 (tptt)
REVERT: B  121 LYS cc_start: 0.8163 (mttt) cc_final: 0.7862 (mttp)
REVERT: B  252 PHE cc_start: 0.7005 (m-80) cc_final: 0.6657 (m-80)
REVERT: B  266 MET cc_start: 0.6503 (mtp) cc_final: 0.6294 (mtm)
REVERT: B  268 SER cc_start: 0.6567 (OUTLIER) cc_final: 0.6136 (p)
REVERT: B  272 MET cc_start: 0.4175 (ptt) cc_final: 0.3944 (mtm)
REVERT: B  350 MET cc_start: 0.6768 (ptp) cc_final: 0.6420 (mpp)
  outliers start: 30
  outliers final: 27
  residues processed: 154
  average time/residue: 0.1582
  time to fit residues: 33.6845
Evaluate side-chains
  152 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  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  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
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  198 THR
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  268 SER
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:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0970
   chunk 40 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.3980
   chunk 13 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.211609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.180604 restraints weight = 7660.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.186099 restraints weight = 4264.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.190362 restraints weight = 2853.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6276
moved from start:          0.6627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6700  Z= 0.138
  Angle     :  0.662   9.694   9076  Z= 0.340
  Chirality :  0.045   0.162   1017
  Planarity :  0.004   0.039   1169
  Dihedral  : 10.286 162.905    919
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.66 %
    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: -0.52 (0.28), residues: 841
  helix:  0.55 (0.26), residues: 368
  sheet:  0.41 (0.48), residues: 120
  loop : -1.57 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 338 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.040   0.002   PHE B 100 
 TYR   0.027   0.002   TYR B 280 
 ARG   0.002   0.000   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04618 (  322)
  hydrogen bonds       : angle       4.90687 (  924)
  covalent geometry    : bond        0.00305 ( 6700)
  covalent geometry    : angle       0.66200 ( 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
  157 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7794 (m) cc_final: 0.7302 (p)
REVERT: A  177 GLU cc_start: 0.8106 (pp20) cc_final: 0.7570 (pt0)
REVERT: A  180 ASN cc_start: 0.7307 (m-40) cc_final: 0.7076 (m-40)
REVERT: A  201 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6772 (mt-10)
REVERT: A  220 ASP cc_start: 0.6504 (m-30) cc_final: 0.6043 (t0)
REVERT: A  361 MET cc_start: 0.7360 (tmm) cc_final: 0.7122 (tmm)
REVERT: B   43 LYS cc_start: 0.6451 (tptt) cc_final: 0.6115 (tptt)
REVERT: B   67 LEU cc_start: 0.6868 (mt) cc_final: 0.6596 (mp)
REVERT: B  121 LYS cc_start: 0.8132 (mttt) cc_final: 0.7758 (mtmt)
REVERT: B  268 SER cc_start: 0.6438 (t) cc_final: 0.5961 (p)
REVERT: B  272 MET cc_start: 0.4150 (ptt) cc_final: 0.3840 (mtm)
REVERT: B  350 MET cc_start: 0.6705 (ptp) cc_final: 0.6496 (mpp)
  outliers start: 25
  outliers final: 23
  residues processed: 150
  average time/residue: 0.1586
  time to fit residues: 32.9146
Evaluate side-chains
  151 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  113 MET
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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0060
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 69 optimal weight:   20.0000
   overall best weight:    1.1398

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.208638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.178277 restraints weight = 7797.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.183706 restraints weight = 4521.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.187554 restraints weight = 3089.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.6788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6700  Z= 0.157
  Angle     :  0.682  10.350   9076  Z= 0.350
  Chirality :  0.045   0.156   1017
  Planarity :  0.006   0.156   1169
  Dihedral  : 10.259 162.261    919
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.80 %
    Favored  : 77.49 %
  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: -0.55 (0.28), residues: 841
  helix:  0.53 (0.26), residues: 364
  sheet:  0.36 (0.47), residues: 121
  loop : -1.57 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 338 
 HIS   0.004   0.001   HIS B 368 
 PHE   0.035   0.003   PHE B 100 
 TYR   0.023   0.002   TYR A 155 
 ARG   0.016   0.001   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04814 (  322)
  hydrogen bonds       : angle       4.94289 (  924)
  covalent geometry    : bond        0.00354 ( 6700)
  covalent geometry    : angle       0.68190 ( 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
  152 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7874 (m) cc_final: 0.7427 (p)
REVERT: A  177 GLU cc_start: 0.8042 (pp20) cc_final: 0.7562 (pt0)
REVERT: A  180 ASN cc_start: 0.7292 (m-40) cc_final: 0.7083 (m-40)
REVERT: A  183 MET cc_start: 0.7952 (tpt) cc_final: 0.7739 (tpt)
REVERT: A  201 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6840 (mt-10)
REVERT: A  220 ASP cc_start: 0.6494 (m-30) cc_final: 0.6111 (t0)
REVERT: A  386 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7190 (pttm)
REVERT: B   43 LYS cc_start: 0.6565 (tptt) cc_final: 0.6162 (tptt)
REVERT: B  121 LYS cc_start: 0.8126 (mttt) cc_final: 0.7815 (mttp)
REVERT: B  268 SER cc_start: 0.6507 (t) cc_final: 0.6035 (p)
REVERT: B  272 MET cc_start: 0.4292 (ptt) cc_final: 0.3911 (mtm)
  outliers start: 26
  outliers final: 25
  residues processed: 142
  average time/residue: 0.1790
  time to fit residues: 35.2474
Evaluate side-chains
  148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
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  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  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
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  128 SER
Chi-restraints excluded: chain B residue  134 MET
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  198 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 77 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0570
   chunk 7 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 215 ASN
** A 227 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 = 0.4560 r_free = 0.4560 target = 0.212267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.181288 restraints weight = 7750.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.187121 restraints weight = 4324.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.191145 restraints weight = 2878.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6239
moved from start:          0.6952

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= 0.138
  Angle     :  0.681  12.059   9076  Z= 0.351
  Chirality :  0.045   0.169   1017
  Planarity :  0.005   0.095   1169
  Dihedral  : 10.208 163.520    919
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.52 %
    Favored  : 77.64 %
  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:  0.67 (0.26), residues: 361
  sheet:  0.09 (0.47), residues: 124
  loop : -1.61 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 338 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.034   0.002   PHE B 100 
 TYR   0.022   0.002   TYR A 155 
 ARG   0.013   0.001   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04479 (  322)
  hydrogen bonds       : angle       4.87137 (  924)
  covalent geometry    : bond        0.00295 ( 6700)
  covalent geometry    : angle       0.68084 ( 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
  155 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.7802 (m) cc_final: 0.7279 (p)
REVERT: A  177 GLU cc_start: 0.8058 (pp20) cc_final: 0.7701 (pt0)
REVERT: A  183 MET cc_start: 0.7777 (tpt) cc_final: 0.7377 (tpt)
REVERT: A  201 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6643 (mt-10)
REVERT: A  386 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7062 (pttm)
REVERT: B   43 LYS cc_start: 0.6582 (tptt) cc_final: 0.6240 (tptt)
REVERT: B   67 LEU cc_start: 0.6731 (mt) cc_final: 0.6524 (mp)
REVERT: B  121 LYS cc_start: 0.8142 (mttt) cc_final: 0.7810 (mtmt)
REVERT: B  268 SER cc_start: 0.6273 (t) cc_final: 0.5894 (p)
REVERT: B  272 MET cc_start: 0.4077 (ptt) cc_final: 0.3748 (mtm)
  outliers start: 27
  outliers final: 20
  residues processed: 147
  average time/residue: 0.1556
  time to fit residues: 31.8680
Evaluate side-chains
  145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  143 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  371 VAL
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  198 THR
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  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:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0050
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.1196

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.208021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.178037 restraints weight = 7870.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.183330 restraints weight = 4519.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.186984 restraints weight = 3082.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6339
moved from start:          0.7056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6700  Z= 0.157
  Angle     :  0.693  12.470   9076  Z= 0.355
  Chirality :  0.046   0.161   1017
  Planarity :  0.005   0.084   1169
  Dihedral  : 10.212 162.964    919
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.95 %
    Favored  : 77.64 %
  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: -0.58 (0.28), residues: 841
  helix:  0.66 (0.26), residues: 355
  sheet: -0.08 (0.45), residues: 131
  loop : -1.58 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 338 
 HIS   0.003   0.001   HIS B 368 
 PHE   0.034   0.003   PHE A 397 
 TYR   0.022   0.002   TYR A 179 
 ARG   0.010   0.001   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04705 (  322)
  hydrogen bonds       : angle       4.91817 (  924)
  covalent geometry    : bond        0.00355 ( 6700)
  covalent geometry    : angle       0.69310 ( 9076)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2691.14 seconds
wall clock time: 47 minutes 44.99 seconds (2864.99 seconds total)