Starting phenix.real_space_refine
on Wed Mar 12 00:53:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ysn_34077/03_2025/7ysn_34077.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ysn_34077/03_2025/7ysn_34077.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ysn_34077/03_2025/7ysn_34077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ysn_34077/03_2025/7ysn_34077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ysn_34077/03_2025/7ysn_34077.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ysn_34077/03_2025/7ysn_34077.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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       6      5.49       5
     S      48      5.16       5
     C    4296      2.51       5
     N    1167      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6844
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3404
          Classifications: {'peptide': 434}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3376
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'G2P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.24, per 1000 atoms: 0.62
  Number of scatterers: 6844
  At special positions: 0
  Unit cell: (112.136, 70.192, 69.336, 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      48     16.00
     P       6     15.00
     O    1327      8.00
     N    1167      7.00
     C    4296      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: 1.70
  Conformation dependent library (CDL) restraints added in 894.3 milliseconds
  

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      48.6% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 71 through 81
      removed outlier: 4.566A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 4.312A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.330A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 194
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.961A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 287 through 294
    Processing helix  chain 'A' and resid 324 through 337
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 4.035A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.955A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 3.970A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 48 through 51
    Processing helix  chain 'B' and resid 57 through 59
      No H-bonds generated for 'chain 'B' and resid 57 through 59'
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.647A  pdb=" N   ASP B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 102 through 108
    Processing helix  chain 'B' and resid 110 through 127
      removed outlier: 3.519A  pdb=" N   LEU B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASP B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
    Processing helix  chain 'B' and resid 182 through 197
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 244
      removed outlier: 3.626A  pdb=" N   LEU B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   CYS B 241 " --> pdb=" O   GLY B 237 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   LEU B 242 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 293
    Processing helix  chain 'B' and resid 324 through 339
    Processing helix  chain 'B' and resid 384 through 398
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 415 through 438
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93
      removed outlier: 8.871A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 8.185A  pdb=" N   ASN A 356 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR A 319 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68
      removed outlier: 6.857A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   PHE B 135 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ILE B 204 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   SER B 170 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68
      removed outlier: 6.857A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   PHE B 135 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   MET B 166 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR B 202 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   THR B 168 " --> pdb=" O   TYR B 202 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   THR B 201 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   PHE B 267 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   SER B 381 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   LYS B 352 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL B 315 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   CYS B 356 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   PHE B 319 " --> pdb=" O   CYS B 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 55

    314 hydrogen bonds defined for protein.
    918 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: 1.98

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2285
        1.35 -     1.48: 1715
        1.48 -     1.61: 2913
        1.61 -     1.73: 9
        1.73 -     1.86: 78
  Bond restraints: 7000
  Sorted by residual:
  bond pdb=" C2' G2P B 501 "
       pdb=" C3' G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.528  1.298  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C6  G2P B 501 "
       pdb=" O6  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.223  1.400 -0.177 2.00e-02 2.50e+03 7.84e+01
  bond pdb=" C1' G2P B 501 "
       pdb=" O4' G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.389  1.548 -0.159 2.00e-02 2.50e+03 6.36e+01
  bond pdb=" C4' G2P B 501 "
       pdb=" O4' G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.426  1.300  0.126 2.00e-02 2.50e+03 3.99e+01
  bond pdb=" C1' G2P B 501 "
       pdb=" N9  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.448  1.333  0.115 2.00e-02 2.50e+03 3.31e+01
  ... (remaining 6995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 9323
        2.12 -     4.25: 149
        4.25 -     6.37: 25
        6.37 -     8.49: 8
        8.49 -    10.62: 4
  Bond angle restraints: 9509
  Sorted by residual:
  angle pdb=" N   VAL A 182 "
        pdb=" CA  VAL A 182 "
        pdb=" C   VAL A 182 "
      ideal   model   delta    sigma   weight residual
     112.29  107.82    4.47 9.40e-01 1.13e+00 2.26e+01
  angle pdb=" N   GLU A 420 "
        pdb=" CA  GLU A 420 "
        pdb=" CB  GLU A 420 "
      ideal   model   delta    sigma   weight residual
     110.28  116.26   -5.98 1.55e+00 4.16e-01 1.49e+01
  angle pdb=" C   LYS B 124 "
        pdb=" N   GLU B 125 "
        pdb=" CA  GLU B 125 "
      ideal   model   delta    sigma   weight residual
     121.14  114.89    6.25 1.75e+00 3.27e-01 1.27e+01
  angle pdb=" C3A G2P B 501 "
        pdb=" PA  G2P B 501 "
        pdb=" O5' G2P B 501 "
      ideal   model   delta    sigma   weight residual
      99.14  109.76  -10.62 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" C3A G2P B 501 "
        pdb=" PB  G2P B 501 "
        pdb=" O3B G2P B 501 "
      ideal   model   delta    sigma   weight residual
      99.71  109.83  -10.12 3.00e+00 1.11e-01 1.14e+01
  ... (remaining 9504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.12: 4022
       28.12 -    56.23: 143
       56.23 -    84.35: 17
       84.35 -   112.46: 1
      112.46 -   140.58: 2
  Dihedral angle restraints: 4185
    sinusoidal: 1688
      harmonic: 2497
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -35.98  140.58     1      2.00e+01 2.50e-03 4.25e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -176.82 -113.91     1      2.00e+01 2.50e-03 3.37e+01
  dihedral pdb=" CA  ALA B 304 "
           pdb=" C   ALA B 304 "
           pdb=" N   CYS B 305 "
           pdb=" CA  CYS B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.51  -17.49     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 4182 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 785
       0.049 -    0.098: 208
       0.098 -    0.147: 43
       0.147 -    0.196: 2
       0.196 -    0.245: 1
  Chirality restraints: 1039
  Sorted by residual:
  chirality pdb=" C3' G2P B 501 "
            pdb=" C2' G2P B 501 "
            pdb=" C4' G2P B 501 "
            pdb=" O3' G2P B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.46   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  GLU A 420 "
            pdb=" N   GLU A 420 "
            pdb=" C   GLU A 420 "
            pdb=" CB  GLU A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CA  GLU A 183 "
            pdb=" N   GLU A 183 "
            pdb=" C   GLU A 183 "
            pdb=" CB  GLU A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.67e-01
  ... (remaining 1036 not shown)

  Planarity restraints: 1238
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 407 "    0.011 2.00e-02 2.50e+03   9.53e-03 2.27e+00
        pdb=" CG  TRP B 407 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 407 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 407 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 407 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 407 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 407 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 407 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 407 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 407 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  31 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B  32 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 324 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 325 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1235 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 201
        2.69 -     3.24: 7262
        3.24 -     3.79: 11969
        3.79 -     4.35: 15296
        4.35 -     4.90: 24874
  Nonbonded interactions: 59602
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 416 "
            pdb=" OG  SER A 419 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OH  TYR B 185 "
            pdb=" O   MET B 398 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   LEU B 194 "
            pdb=" OG1 THR B 198 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OG  SER B  25 "
            pdb=" OH  TYR B  53 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR A 292 "
            pdb=" OH  TYR A 319 "
     model   vdw
     2.257 3.040
  ... (remaining 59597 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:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.060
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
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      :  0.006   0.230   7000  Z= 0.343
  Angle     :  0.693  10.618   9509  Z= 0.330
  Chirality :  0.045   0.245   1039
  Planarity :  0.003   0.036   1238
  Dihedral  : 14.723 140.575   2583
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.29), residues: 858
  helix:  0.98 (0.26), residues: 382
  sheet: -0.16 (0.50), residues: 125
  loop : -0.37 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 407 
 HIS   0.003   0.001   HIS B 406 
 PHE   0.009   0.001   PHE B 388 
 TYR   0.014   0.001   TYR A 432 
 ARG   0.003   0.000   ARG A 229 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9158 (t0) cc_final: 0.8905 (t0)
REVERT: A  153 LEU cc_start: 0.9594 (tp) cc_final: 0.9393 (tp)
REVERT: A  157 LEU cc_start: 0.9565 (mt) cc_final: 0.9299 (mt)
REVERT: A  377 MET cc_start: 0.8810 (tmm) cc_final: 0.8608 (tmm)
REVERT: A  386 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: A  398 MET cc_start: 0.7572 (tpt) cc_final: 0.7369 (tpt)
REVERT: A  420 GLU cc_start: 0.8501 (pm20) cc_final: 0.8066 (pm20)
REVERT: B   70 LEU cc_start: 0.8505 (mm) cc_final: 0.8268 (mm)
REVERT: B   75 MET cc_start: 0.9112 (ttt) cc_final: 0.8605 (ttm)
REVERT: B   79 ARG cc_start: 0.8805 (mpp80) cc_final: 0.8288 (mpt-90)
REVERT: B   86 ILE cc_start: 0.8807 (pt) cc_final: 0.8538 (pt)
REVERT: B  105 LYS cc_start: 0.8988 (tptp) cc_final: 0.8674 (tppt)
REVERT: B  108 TYR cc_start: 0.8359 (m-10) cc_final: 0.8033 (m-10)
REVERT: B  137 LEU cc_start: 0.9413 (tp) cc_final: 0.9171 (tp)
REVERT: B  156 LYS cc_start: 0.9673 (mmpt) cc_final: 0.9453 (mmmt)
REVERT: B  196 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8459 (mm-30)
REVERT: B  398 MET cc_start: 0.8391 (mmp) cc_final: 0.7955 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1668
  time to fit residues: 35.8708
Evaluate side-chains
  128 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
B 186 ASN
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.125759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.099710 restraints weight = 16221.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.103661 restraints weight = 9712.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.106455 restraints weight = 6784.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7000  Z= 0.190
  Angle     :  0.628   7.163   9509  Z= 0.321
  Chirality :  0.046   0.252   1039
  Planarity :  0.004   0.046   1238
  Dihedral  :  8.554 133.495    984
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.55 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.29), residues: 858
  helix:  0.96 (0.26), residues: 384
  sheet: -0.28 (0.48), residues: 123
  loop : -0.57 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 407 
 HIS   0.005   0.001   HIS B 192 
 PHE   0.011   0.001   PHE B 388 
 TYR   0.009   0.001   TYR A 210 
 ARG   0.003   0.000   ARG A 373 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9202 (t0) cc_final: 0.8593 (t0)
REVERT: A  153 LEU cc_start: 0.9638 (tp) cc_final: 0.9411 (tp)
REVERT: A  157 LEU cc_start: 0.9542 (mt) cc_final: 0.9265 (mt)
REVERT: A  171 ILE cc_start: 0.8625 (mm) cc_final: 0.8311 (mt)
REVERT: A  377 MET cc_start: 0.8710 (tmm) cc_final: 0.8287 (tmm)
REVERT: A  386 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8394 (mp0)
REVERT: A  398 MET cc_start: 0.7757 (tpt) cc_final: 0.7368 (tpt)
REVERT: A  420 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: B   70 LEU cc_start: 0.8606 (mm) cc_final: 0.8338 (mm)
REVERT: B   88 ARG cc_start: 0.8892 (mmm160) cc_final: 0.8692 (mmm160)
REVERT: B  102 ASN cc_start: 0.8965 (t0) cc_final: 0.8759 (t0)
REVERT: B  103 TRP cc_start: 0.6709 (t60) cc_final: 0.5826 (t60)
REVERT: B  105 LYS cc_start: 0.9264 (tptp) cc_final: 0.8836 (tppt)
REVERT: B  137 LEU cc_start: 0.9409 (tp) cc_final: 0.9198 (tp)
REVERT: B  156 LYS cc_start: 0.9673 (mmpt) cc_final: 0.9452 (mmmt)
REVERT: B  196 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8451 (mm-30)
REVERT: B  325 MET cc_start: 0.8439 (ttm) cc_final: 0.8183 (ttm)
  outliers start: 8
  outliers final: 5
  residues processed: 158
  average time/residue: 0.1647
  time to fit residues: 35.7406
Evaluate side-chains
  141 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.119559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.093488 restraints weight = 16965.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.097276 restraints weight = 9951.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.099959 restraints weight = 6955.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7000  Z= 0.345
  Angle     :  0.710  12.831   9509  Z= 0.367
  Chirality :  0.048   0.188   1039
  Planarity :  0.005   0.059   1238
  Dihedral  :  8.932 140.846    984
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.93 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.28), residues: 858
  helix:  0.54 (0.26), residues: 383
  sheet: -0.63 (0.44), residues: 132
  loop : -0.52 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP B 407 
 HIS   0.006   0.002   HIS B 266 
 PHE   0.013   0.002   PHE B 319 
 TYR   0.017   0.002   TYR A 408 
 ARG   0.003   0.000   ARG A 390 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8235 (m-10) cc_final: 0.7522 (m-80)
REVERT: A  102 ASN cc_start: 0.9308 (t0) cc_final: 0.8771 (t0)
REVERT: A  153 LEU cc_start: 0.9668 (tp) cc_final: 0.9404 (tp)
REVERT: A  157 LEU cc_start: 0.9565 (mt) cc_final: 0.9284 (mt)
REVERT: A  377 MET cc_start: 0.8668 (tmm) cc_final: 0.8231 (tmm)
REVERT: A  386 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8481 (mp0)
REVERT: A  392 ASP cc_start: 0.7692 (p0) cc_final: 0.7323 (p0)
REVERT: A  398 MET cc_start: 0.8180 (tpt) cc_final: 0.7718 (tpt)
REVERT: A  420 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8151 (pm20)
REVERT: B   70 LEU cc_start: 0.8541 (mm) cc_final: 0.8250 (mm)
REVERT: B  102 ASN cc_start: 0.9030 (t0) cc_final: 0.8748 (t0)
REVERT: B  105 LYS cc_start: 0.9300 (tptp) cc_final: 0.8840 (tppt)
REVERT: B  325 MET cc_start: 0.8210 (ttm) cc_final: 0.7893 (ttm)
REVERT: B  417 GLU cc_start: 0.8844 (mp0) cc_final: 0.8577 (mp0)
  outliers start: 11
  outliers final: 8
  residues processed: 144
  average time/residue: 0.1585
  time to fit residues: 32.0010
Evaluate side-chains
  136 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  214 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 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 = 0.4197 r_free = 0.4197 target = 0.119884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.093552 restraints weight = 16886.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.097340 restraints weight = 9954.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.100073 restraints weight = 6948.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7000  Z= 0.293
  Angle     :  0.673  10.339   9509  Z= 0.345
  Chirality :  0.047   0.166   1039
  Planarity :  0.005   0.049   1238
  Dihedral  :  8.945 140.381    984
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.10 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.28), residues: 858
  helix:  0.48 (0.26), residues: 385
  sheet: -0.64 (0.44), residues: 129
  loop : -0.60 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP B 407 
 HIS   0.009   0.001   HIS B 406 
 PHE   0.008   0.002   PHE B  83 
 TYR   0.012   0.001   TYR B 108 
 ARG   0.004   0.000   ARG B  64 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8218 (m-10) cc_final: 0.7502 (m-80)
REVERT: A   88 HIS cc_start: 0.8592 (m-70) cc_final: 0.8355 (t-90)
REVERT: A  102 ASN cc_start: 0.9276 (t0) cc_final: 0.8747 (t0)
REVERT: A  153 LEU cc_start: 0.9663 (tp) cc_final: 0.9417 (tp)
REVERT: A  157 LEU cc_start: 0.9570 (mt) cc_final: 0.9300 (mt)
REVERT: A  377 MET cc_start: 0.8692 (tmm) cc_final: 0.8285 (tmm)
REVERT: A  386 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8465 (mp0)
REVERT: A  392 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7255 (p0)
REVERT: A  398 MET cc_start: 0.8230 (tpt) cc_final: 0.7799 (tpt)
REVERT: A  430 LYS cc_start: 0.9554 (pttm) cc_final: 0.9284 (mmtm)
REVERT: B   70 LEU cc_start: 0.8562 (mm) cc_final: 0.8302 (mm)
REVERT: B   88 ARG cc_start: 0.8970 (mmm160) cc_final: 0.8736 (mmm160)
REVERT: B  102 ASN cc_start: 0.9001 (t0) cc_final: 0.8723 (t0)
REVERT: B  105 LYS cc_start: 0.9287 (tptp) cc_final: 0.8840 (tppt)
REVERT: B  108 TYR cc_start: 0.8083 (m-80) cc_final: 0.7630 (m-80)
REVERT: B  196 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8422 (mm-30)
REVERT: B  325 MET cc_start: 0.8302 (ttm) cc_final: 0.7977 (ttm)
REVERT: B  380 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7639 (m-40)
REVERT: B  417 GLU cc_start: 0.8992 (mp0) cc_final: 0.8693 (mp0)
  outliers start: 17
  outliers final: 9
  residues processed: 144
  average time/residue: 0.1627
  time to fit residues: 32.5681
Evaluate side-chains
  136 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:   40.0000
   chunk 52 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0870
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.119764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.093570 restraints weight = 16760.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.097289 restraints weight = 9884.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.100020 restraints weight = 6921.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7000  Z= 0.279
  Angle     :  0.672   9.305   9509  Z= 0.344
  Chirality :  0.047   0.160   1039
  Planarity :  0.005   0.049   1238
  Dihedral  :  8.966 140.583    984
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.27 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.28), residues: 858
  helix:  0.45 (0.26), residues: 384
  sheet: -0.68 (0.44), residues: 132
  loop : -0.57 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 407 
 HIS   0.009   0.001   HIS B 406 
 PHE   0.014   0.002   PHE B 319 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.004   0.000   ARG B  64 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8174 (m-10) cc_final: 0.7459 (m-80)
REVERT: A   88 HIS cc_start: 0.8571 (m-70) cc_final: 0.8344 (t-90)
REVERT: A  102 ASN cc_start: 0.9256 (t0) cc_final: 0.8713 (t0)
REVERT: A  153 LEU cc_start: 0.9658 (tp) cc_final: 0.9423 (tp)
REVERT: A  157 LEU cc_start: 0.9563 (mt) cc_final: 0.9302 (mt)
REVERT: A  377 MET cc_start: 0.8636 (tmm) cc_final: 0.8238 (tmm)
REVERT: A  386 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8461 (mp0)
REVERT: A  392 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7191 (p0)
REVERT: A  398 MET cc_start: 0.8319 (tpt) cc_final: 0.7983 (tpt)
REVERT: B   70 LEU cc_start: 0.8548 (mm) cc_final: 0.8287 (mm)
REVERT: B  102 ASN cc_start: 0.9004 (t0) cc_final: 0.8735 (t0)
REVERT: B  105 LYS cc_start: 0.9283 (tptp) cc_final: 0.8849 (tppt)
REVERT: B  108 TYR cc_start: 0.8091 (m-80) cc_final: 0.7623 (m-80)
REVERT: B  196 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8416 (mm-30)
REVERT: B  259 MET cc_start: 0.8884 (mmm) cc_final: 0.8462 (mmm)
REVERT: B  325 MET cc_start: 0.8269 (ttm) cc_final: 0.7938 (ttm)
REVERT: B  417 GLU cc_start: 0.9062 (mp0) cc_final: 0.8813 (mp0)
  outliers start: 18
  outliers final: 14
  residues processed: 142
  average time/residue: 0.1615
  time to fit residues: 32.4840
Evaluate side-chains
  138 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 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 = 0.4243 r_free = 0.4243 target = 0.123214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.096423 restraints weight = 16617.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.100466 restraints weight = 9756.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103324 restraints weight = 6767.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7000  Z= 0.186
  Angle     :  0.674  11.312   9509  Z= 0.337
  Chirality :  0.046   0.170   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  8.814 138.189    984
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.62 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.29), residues: 858
  helix:  0.46 (0.26), residues: 392
  sheet: -0.64 (0.44), residues: 133
  loop : -0.57 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 407 
 HIS   0.009   0.001   HIS B 406 
 PHE   0.011   0.001   PHE B  83 
 TYR   0.010   0.001   TYR A 210 
 ARG   0.004   0.000   ARG B  64 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 HIS cc_start: 0.8578 (m-70) cc_final: 0.8339 (t-90)
REVERT: A  102 ASN cc_start: 0.9222 (t0) cc_final: 0.8614 (t0)
REVERT: A  153 LEU cc_start: 0.9655 (tp) cc_final: 0.9419 (tp)
REVERT: A  157 LEU cc_start: 0.9580 (mt) cc_final: 0.9338 (mt)
REVERT: A  377 MET cc_start: 0.8659 (tmm) cc_final: 0.8237 (tmm)
REVERT: A  386 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8416 (mp0)
REVERT: A  392 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7226 (p0)
REVERT: A  398 MET cc_start: 0.8364 (tpt) cc_final: 0.8053 (tpt)
REVERT: A  430 LYS cc_start: 0.9544 (pttm) cc_final: 0.9173 (pttm)
REVERT: A  434 GLU cc_start: 0.8460 (pp20) cc_final: 0.8243 (pp20)
REVERT: A  435 VAL cc_start: 0.8706 (t) cc_final: 0.8383 (m)
REVERT: B   21 TRP cc_start: 0.9226 (m100) cc_final: 0.8712 (m100)
REVERT: B  102 ASN cc_start: 0.8951 (t0) cc_final: 0.8684 (t0)
REVERT: B  105 LYS cc_start: 0.9279 (tptp) cc_final: 0.9072 (tppt)
REVERT: B  108 TYR cc_start: 0.8104 (m-80) cc_final: 0.7606 (m-80)
REVERT: B  196 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8494 (mm-30)
REVERT: B  259 MET cc_start: 0.8780 (mmm) cc_final: 0.8120 (mmm)
REVERT: B  325 MET cc_start: 0.8167 (ttm) cc_final: 0.7843 (ttm)
REVERT: B  413 MET cc_start: 0.5475 (ppp) cc_final: 0.4641 (ppp)
REVERT: B  417 GLU cc_start: 0.9056 (mp0) cc_final: 0.8799 (mp0)
  outliers start: 14
  outliers final: 12
  residues processed: 146
  average time/residue: 0.1708
  time to fit residues: 35.2338
Evaluate side-chains
  141 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 57 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 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 = 0.4257 r_free = 0.4257 target = 0.123790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.097706 restraints weight = 16392.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.101839 restraints weight = 9609.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.104760 restraints weight = 6591.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7000  Z= 0.177
  Angle     :  0.670  10.153   9509  Z= 0.334
  Chirality :  0.046   0.178   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  8.693 137.010    984
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 22.25 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.29), residues: 858
  helix:  0.51 (0.26), residues: 392
  sheet: -0.60 (0.44), residues: 133
  loop : -0.60 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 407 
 HIS   0.010   0.001   HIS B 406 
 PHE   0.011   0.001   PHE B 319 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.003   0.000   ARG B  64 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.8903 (mm) cc_final: 0.8653 (mm)
REVERT: A  102 ASN cc_start: 0.9233 (t0) cc_final: 0.8682 (t0)
REVERT: A  157 LEU cc_start: 0.9571 (mt) cc_final: 0.9343 (mt)
REVERT: A  377 MET cc_start: 0.8694 (tmm) cc_final: 0.8235 (tmm)
REVERT: A  386 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8396 (mp0)
REVERT: A  392 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7192 (p0)
REVERT: A  398 MET cc_start: 0.8310 (tpt) cc_final: 0.8008 (tpt)
REVERT: A  430 LYS cc_start: 0.9497 (pttm) cc_final: 0.9215 (pttm)
REVERT: A  434 GLU cc_start: 0.8406 (pp20) cc_final: 0.8197 (pp20)
REVERT: B    1 MET cc_start: 0.7000 (mpp) cc_final: 0.6769 (pmm)
REVERT: B   21 TRP cc_start: 0.9216 (m100) cc_final: 0.8700 (m100)
REVERT: B   88 ARG cc_start: 0.9159 (mmp80) cc_final: 0.8906 (mmp80)
REVERT: B  102 ASN cc_start: 0.8939 (t0) cc_final: 0.8655 (t0)
REVERT: B  105 LYS cc_start: 0.9418 (tptp) cc_final: 0.9020 (tptp)
REVERT: B  108 TYR cc_start: 0.8104 (m-80) cc_final: 0.7613 (m-80)
REVERT: B  196 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8514 (mm-30)
REVERT: B  313 LEU cc_start: 0.8937 (mm) cc_final: 0.8680 (mm)
REVERT: B  325 MET cc_start: 0.8157 (ttm) cc_final: 0.7918 (ttm)
REVERT: B  413 MET cc_start: 0.5367 (ppp) cc_final: 0.4788 (ppp)
REVERT: B  417 GLU cc_start: 0.9088 (mp0) cc_final: 0.8807 (mp0)
  outliers start: 14
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1615
  time to fit residues: 32.6580
Evaluate side-chains
  142 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.0000
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 61 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.1790

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 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 = 0.4258 r_free = 0.4258 target = 0.123779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.097385 restraints weight = 16616.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.101397 restraints weight = 9727.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.104310 restraints weight = 6728.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7000  Z= 0.188
  Angle     :  0.680   9.670   9509  Z= 0.338
  Chirality :  0.046   0.183   1039
  Planarity :  0.004   0.039   1238
  Dihedral  :  8.602 135.011    984
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.52 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.28), residues: 858
  helix:  0.49 (0.26), residues: 393
  sheet: -0.53 (0.44), residues: 133
  loop : -0.57 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 407 
 HIS   0.011   0.001   HIS A 107 
 PHE   0.016   0.001   PHE B 319 
 TYR   0.017   0.001   TYR A 408 
 ARG   0.003   0.000   ARG B 401 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.8905 (mm) cc_final: 0.8661 (mm)
REVERT: A  102 ASN cc_start: 0.9252 (t0) cc_final: 0.8653 (t0)
REVERT: A  157 LEU cc_start: 0.9565 (mt) cc_final: 0.9351 (mt)
REVERT: A  377 MET cc_start: 0.8744 (tmm) cc_final: 0.8251 (tmm)
REVERT: A  386 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8413 (mp0)
REVERT: A  392 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7203 (p0)
REVERT: A  398 MET cc_start: 0.8373 (tpt) cc_final: 0.8088 (tpt)
REVERT: A  430 LYS cc_start: 0.9483 (pttm) cc_final: 0.9210 (pttm)
REVERT: A  434 GLU cc_start: 0.8398 (pp20) cc_final: 0.8189 (pp20)
REVERT: B    1 MET cc_start: 0.7030 (mpp) cc_final: 0.6755 (pmm)
REVERT: B   21 TRP cc_start: 0.9252 (m100) cc_final: 0.8735 (m100)
REVERT: B   88 ARG cc_start: 0.9176 (mmp80) cc_final: 0.8959 (mmp80)
REVERT: B  102 ASN cc_start: 0.8959 (t0) cc_final: 0.8704 (t0)
REVERT: B  105 LYS cc_start: 0.9450 (tptp) cc_final: 0.9022 (tptp)
REVERT: B  108 TYR cc_start: 0.8165 (m-80) cc_final: 0.7737 (m-80)
REVERT: B  196 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8511 (mm-30)
REVERT: B  325 MET cc_start: 0.8090 (ttm) cc_final: 0.7837 (ttm)
REVERT: B  373 MET cc_start: 0.7236 (mmm) cc_final: 0.6790 (tpp)
REVERT: B  413 MET cc_start: 0.5325 (ppp) cc_final: 0.4819 (ppp)
REVERT: B  416 MET cc_start: 0.9033 (ppp) cc_final: 0.8754 (ppp)
REVERT: B  417 GLU cc_start: 0.9087 (mp0) cc_final: 0.8706 (mp0)
  outliers start: 15
  outliers final: 12
  residues processed: 141
  average time/residue: 0.1559
  time to fit residues: 31.2378
Evaluate side-chains
  141 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 78 optimal weight:    7.9990
   chunk 81 optimal weight:    0.0980
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 72 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:   20.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 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 = 0.4238 r_free = 0.4238 target = 0.122396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.095959 restraints weight = 16705.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.099849 restraints weight = 9835.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.102639 restraints weight = 6857.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7000  Z= 0.230
  Angle     :  0.682   9.464   9509  Z= 0.342
  Chirality :  0.047   0.175   1039
  Planarity :  0.004   0.041   1238
  Dihedral  :  8.635 136.391    984
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.52 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.28), residues: 858
  helix:  0.47 (0.26), residues: 394
  sheet: -0.49 (0.45), residues: 133
  loop : -0.49 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 407 
 HIS   0.012   0.001   HIS A 107 
 PHE   0.021   0.001   PHE B 319 
 TYR   0.023   0.001   TYR A 408 
 ARG   0.003   0.000   ARG B 401 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.8929 (mm) cc_final: 0.8685 (mm)
REVERT: A  102 ASN cc_start: 0.9259 (t0) cc_final: 0.8675 (t0)
REVERT: A  157 LEU cc_start: 0.9581 (mt) cc_final: 0.9375 (mt)
REVERT: A  377 MET cc_start: 0.8704 (tmm) cc_final: 0.8213 (tmm)
REVERT: A  386 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8447 (mp0)
REVERT: A  392 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7178 (p0)
REVERT: A  398 MET cc_start: 0.8360 (tpt) cc_final: 0.8090 (tpt)
REVERT: A  430 LYS cc_start: 0.9457 (pttm) cc_final: 0.9252 (pttm)
REVERT: B    1 MET cc_start: 0.7031 (mpp) cc_final: 0.6779 (pmm)
REVERT: B   21 TRP cc_start: 0.9280 (m100) cc_final: 0.8790 (m100)
REVERT: B  102 ASN cc_start: 0.8980 (t0) cc_final: 0.8737 (t0)
REVERT: B  105 LYS cc_start: 0.9464 (tptp) cc_final: 0.9039 (tptp)
REVERT: B  108 TYR cc_start: 0.8197 (m-80) cc_final: 0.7767 (m-80)
REVERT: B  259 MET cc_start: 0.8773 (mmm) cc_final: 0.7926 (mmm)
REVERT: B  325 MET cc_start: 0.8114 (ttm) cc_final: 0.7848 (ttm)
REVERT: B  373 MET cc_start: 0.7392 (mmm) cc_final: 0.6983 (tpp)
REVERT: B  413 MET cc_start: 0.5355 (ppp) cc_final: 0.4981 (ppp)
REVERT: B  417 GLU cc_start: 0.9105 (mp0) cc_final: 0.8828 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 141
  average time/residue: 0.1614
  time to fit residues: 32.3335
Evaluate side-chains
  144 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    0.0370
   chunk 9 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 53 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    3.2066

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 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 = 0.4206 r_free = 0.4206 target = 0.120337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.093966 restraints weight = 16992.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.097801 restraints weight = 10005.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.100583 restraints weight = 6966.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7000  Z= 0.288
  Angle     :  0.732  10.211   9509  Z= 0.368
  Chirality :  0.047   0.160   1039
  Planarity :  0.005   0.044   1238
  Dihedral  :  8.786 138.842    984
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.66 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.28), residues: 858
  helix:  0.42 (0.26), residues: 394
  sheet: -0.48 (0.44), residues: 130
  loop : -0.50 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 407 
 HIS   0.013   0.002   HIS A 107 
 PHE   0.017   0.002   PHE B 319 
 TYR   0.027   0.002   TYR A 408 
 ARG   0.008   0.000   ARG B  88 

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.8960 (mm) cc_final: 0.8724 (mm)
REVERT: A  102 ASN cc_start: 0.9279 (t0) cc_final: 0.8660 (t0)
REVERT: A  302 MET cc_start: 0.6372 (mmp) cc_final: 0.6098 (mtm)
REVERT: A  377 MET cc_start: 0.8681 (tmm) cc_final: 0.8206 (tmm)
REVERT: A  386 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8442 (mp0)
REVERT: A  392 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7195 (p0)
REVERT: A  398 MET cc_start: 0.8370 (tpt) cc_final: 0.8111 (tpt)
REVERT: A  430 LYS cc_start: 0.9458 (pttm) cc_final: 0.9241 (pttm)
REVERT: B    1 MET cc_start: 0.7163 (mpp) cc_final: 0.6851 (pmm)
REVERT: B  102 ASN cc_start: 0.9001 (t0) cc_final: 0.8739 (t0)
REVERT: B  105 LYS cc_start: 0.9460 (tptp) cc_final: 0.9058 (tptp)
REVERT: B  108 TYR cc_start: 0.8174 (m-80) cc_final: 0.7806 (m-80)
REVERT: B  196 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8482 (mm-30)
REVERT: B  259 MET cc_start: 0.8799 (mmm) cc_final: 0.7990 (mmm)
REVERT: B  325 MET cc_start: 0.8126 (ttm) cc_final: 0.7873 (ttm)
REVERT: B  373 MET cc_start: 0.7498 (mmm) cc_final: 0.7103 (tpp)
REVERT: B  413 MET cc_start: 0.5399 (ppp) cc_final: 0.5053 (ppp)
REVERT: B  417 GLU cc_start: 0.9115 (mp0) cc_final: 0.8847 (mp0)
  outliers start: 16
  outliers final: 14
  residues processed: 142
  average time/residue: 0.1455
  time to fit residues: 29.6928
Evaluate side-chains
  145 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
B 309 HIS
B 380 ASN
** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.123151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.096208 restraints weight = 16790.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.100275 restraints weight = 9904.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.103134 restraints weight = 6875.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7000  Z= 0.201
  Angle     :  0.708   9.986   9509  Z= 0.352
  Chirality :  0.046   0.181   1039
  Planarity :  0.004   0.037   1238
  Dihedral  :  8.662 136.564    984
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.66 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.28), residues: 858
  helix:  0.48 (0.26), residues: 394
  sheet: -0.44 (0.46), residues: 124
  loop : -0.48 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 103 
 HIS   0.019   0.001   HIS A 107 
 PHE   0.016   0.001   PHE B 319 
 TYR   0.021   0.001   TYR A 408 
 ARG   0.003   0.000   ARG B 401 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2436.79 seconds
wall clock time: 43 minutes 12.14 seconds (2592.14 seconds total)