Starting phenix.real_space_refine
on Fri Aug 22 18:45:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ysn_34077/08_2025/7ysn_34077.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ysn_34077/08_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_34077/08_2025/7ysn_34077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ysn_34077/08_2025/7ysn_34077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ysn_34077/08_2025/7ysn_34077.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ysn_34077/08_2025/7ysn_34077.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.64, per 1000 atoms: 0.24
  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: 0.56
  Conformation dependent library (CDL) restraints added in 360.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.14
  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: 0.81

  Time building geometry restraints manager: 0.68 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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.700
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.270
-------------------------------------------------------------------------------
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= 0.286
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 229 
 TYR   0.014   0.001   TYR A 432 
 PHE   0.009   0.001   PHE B 388 
 TRP   0.026   0.002   TRP B 407 
 HIS   0.003   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 7000)
  covalent geometry    : angle       0.69256 ( 9509)
  hydrogen bonds       : bond        0.15625 (  311)
  hydrogen bonds       : angle       6.48918 (  918)

*********************** 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  : 0.264 
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: 0.0621
  time to fit residues: 13.7093
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  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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**
B 136 GLN
B 186 ASN
** B 309 HIS ** 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 = 0.4248 r_free = 0.4248 target = 0.123593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.097039 restraints weight = 16603.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.101005 restraints weight = 10069.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.103752 restraints weight = 7071.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.105697 restraints weight = 5466.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.106946 restraints weight = 4510.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7000  Z= 0.166
  Angle     :  0.638   7.255   9509  Z= 0.329
  Chirality :  0.046   0.247   1039
  Planarity :  0.004   0.050   1238
  Dihedral  :  8.634 135.496    984
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.63 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.29), residues: 858
  helix:  0.91 (0.26), residues: 385
  sheet: -0.31 (0.48), residues: 123
  loop : -0.50 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 373 
 TYR   0.010   0.001   TYR A 210 
 PHE   0.010   0.001   PHE B 388 
 TRP   0.027   0.003   TRP B 407 
 HIS   0.005   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7000)
  covalent geometry    : angle       0.63847 ( 9509)
  hydrogen bonds       : bond        0.04482 (  311)
  hydrogen bonds       : angle       5.20560 (  918)

*********************** 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
  159 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9273 (t0) cc_final: 0.8687 (t0)
REVERT: A  153 LEU cc_start: 0.9640 (tp) cc_final: 0.9405 (tp)
REVERT: A  157 LEU cc_start: 0.9532 (mt) cc_final: 0.9253 (mt)
REVERT: A  377 MET cc_start: 0.8676 (tmm) cc_final: 0.8273 (tmm)
REVERT: A  386 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8411 (mp0)
REVERT: A  398 MET cc_start: 0.7814 (tpt) cc_final: 0.7379 (tpt)
REVERT: A  420 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7927 (mp0)
REVERT: B   70 LEU cc_start: 0.8602 (mm) cc_final: 0.8337 (mm)
REVERT: B  103 TRP cc_start: 0.6778 (t60) cc_final: 0.5867 (t60)
REVERT: B  105 LYS cc_start: 0.9285 (tptp) cc_final: 0.8863 (tppt)
REVERT: B  137 LEU cc_start: 0.9408 (tp) cc_final: 0.9206 (tp)
REVERT: B  156 LYS cc_start: 0.9658 (mmpt) cc_final: 0.9435 (mmmt)
REVERT: B  196 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8394 (mm-30)
REVERT: B  259 MET cc_start: 0.8747 (mmm) cc_final: 0.8446 (mmm)
REVERT: B  325 MET cc_start: 0.8432 (ttm) cc_final: 0.8191 (ttm)
REVERT: B  417 GLU cc_start: 0.8683 (mp0) cc_final: 0.8473 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 154
  average time/residue: 0.0558
  time to fit residues: 12.1614
Evaluate side-chains
  141 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0070
   chunk 61 optimal weight:    0.9990
   chunk 35 optimal weight:   40.0000
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.6006

-------------------------------------------------------------------------------
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 ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.124291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.097752 restraints weight = 16455.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.101793 restraints weight = 9757.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.104541 restraints weight = 6772.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.106591 restraints weight = 5201.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.107980 restraints weight = 4282.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1863

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= 0.138
  Angle     :  0.645   9.636   9509  Z= 0.328
  Chirality :  0.046   0.171   1039
  Planarity :  0.004   0.041   1238
  Dihedral  :  8.611 135.725    984
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.52 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.28), residues: 858
  helix:  0.73 (0.26), residues: 386
  sheet: -0.65 (0.45), residues: 125
  loop : -0.52 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 373 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.011   0.001   PHE B 319 
 TRP   0.033   0.002   TRP B 407 
 HIS   0.003   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7000)
  covalent geometry    : angle       0.64455 ( 9509)
  hydrogen bonds       : bond        0.04193 (  311)
  hydrogen bonds       : angle       5.01226 (  918)

*********************** 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
  148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9266 (t0) cc_final: 0.8668 (t0)
REVERT: A  153 LEU cc_start: 0.9649 (tp) cc_final: 0.9408 (tp)
REVERT: A  157 LEU cc_start: 0.9524 (mt) cc_final: 0.9247 (mt)
REVERT: A  171 ILE cc_start: 0.8605 (mm) cc_final: 0.8340 (mt)
REVERT: A  302 MET cc_start: 0.6565 (mmp) cc_final: 0.6342 (mtm)
REVERT: A  377 MET cc_start: 0.8678 (tmm) cc_final: 0.8239 (tmm)
REVERT: A  386 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8410 (mp0)
REVERT: A  398 MET cc_start: 0.7913 (tpt) cc_final: 0.7499 (tpt)
REVERT: A  420 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8033 (mp0)
REVERT: B   21 TRP cc_start: 0.9056 (m100) cc_final: 0.8723 (m100)
REVERT: B  105 LYS cc_start: 0.9244 (tptp) cc_final: 0.8936 (tppt)
REVERT: B  156 LYS cc_start: 0.9666 (mmpt) cc_final: 0.9437 (mmmt)
REVERT: B  325 MET cc_start: 0.8306 (ttm) cc_final: 0.8006 (ttm)
REVERT: B  380 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7217 (m-40)
REVERT: B  417 GLU cc_start: 0.8740 (mp0) cc_final: 0.8242 (mp0)
  outliers start: 10
  outliers final: 5
  residues processed: 143
  average time/residue: 0.0560
  time to fit residues: 11.7219
Evaluate side-chains
  134 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 73 optimal weight:    8.9990
   chunk 83 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.121281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.094725 restraints weight = 16888.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.098626 restraints weight = 9992.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.101346 restraints weight = 6974.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.103293 restraints weight = 5389.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.104654 restraints weight = 4461.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7000  Z= 0.196
  Angle     :  0.672   9.426   9509  Z= 0.345
  Chirality :  0.047   0.169   1039
  Planarity :  0.005   0.047   1238
  Dihedral  :  8.745 138.705    984
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 16.55 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.28), residues: 858
  helix:  0.53 (0.26), residues: 392
  sheet: -0.75 (0.44), residues: 126
  loop : -0.53 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  88 
 TYR   0.016   0.001   TYR A 408 
 PHE   0.009   0.002   PHE B 388 
 TRP   0.028   0.003   TRP B 407 
 HIS   0.005   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7000)
  covalent geometry    : angle       0.67161 ( 9509)
  hydrogen bonds       : bond        0.04228 (  311)
  hydrogen bonds       : angle       5.04629 (  918)

*********************** 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
  143 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8138 (m-10) cc_final: 0.7445 (m-80)
REVERT: A  102 ASN cc_start: 0.9311 (t0) cc_final: 0.8720 (t0)
REVERT: A  153 LEU cc_start: 0.9653 (tp) cc_final: 0.9396 (tp)
REVERT: A  157 LEU cc_start: 0.9528 (mt) cc_final: 0.9261 (mt)
REVERT: A  377 MET cc_start: 0.8657 (tmm) cc_final: 0.8215 (tmm)
REVERT: A  386 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8446 (mp0)
REVERT: A  398 MET cc_start: 0.8116 (tpt) cc_final: 0.7680 (tpt)
REVERT: A  420 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8093 (mp0)
REVERT: A  430 LYS cc_start: 0.9555 (pttm) cc_final: 0.9252 (pttm)
REVERT: B  105 LYS cc_start: 0.9405 (tptp) cc_final: 0.9089 (tppt)
REVERT: B  108 TYR cc_start: 0.8056 (m-80) cc_final: 0.7694 (m-80)
REVERT: B  196 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8429 (mm-30)
REVERT: B  325 MET cc_start: 0.8296 (ttm) cc_final: 0.7970 (ttm)
REVERT: B  417 GLU cc_start: 0.8767 (mp0) cc_final: 0.8554 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 140
  average time/residue: 0.0564
  time to fit residues: 11.5939
Evaluate side-chains
  130 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    0.2980
   chunk 41 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.6588

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.121362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.094938 restraints weight = 16880.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.098894 restraints weight = 9901.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.101675 restraints weight = 6844.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.103461 restraints weight = 5262.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.104945 restraints weight = 4380.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7000  Z= 0.170
  Angle     :  0.657   9.903   9509  Z= 0.334
  Chirality :  0.046   0.159   1039
  Planarity :  0.004   0.048   1238
  Dihedral  :  8.783 139.081    984
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.91 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.28), residues: 858
  helix:  0.46 (0.26), residues: 392
  sheet: -0.71 (0.43), residues: 127
  loop : -0.48 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.013   0.001   TYR B 185 
 PHE   0.016   0.001   PHE B 319 
 TRP   0.025   0.002   TRP B 407 
 HIS   0.004   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7000)
  covalent geometry    : angle       0.65708 ( 9509)
  hydrogen bonds       : bond        0.04070 (  311)
  hydrogen bonds       : angle       4.93253 (  918)

*********************** 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
  144 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8135 (m-10) cc_final: 0.7444 (m-80)
REVERT: A  102 ASN cc_start: 0.9306 (t0) cc_final: 0.8689 (t0)
REVERT: A  153 LEU cc_start: 0.9651 (tp) cc_final: 0.9409 (tp)
REVERT: A  157 LEU cc_start: 0.9541 (mt) cc_final: 0.9279 (mt)
REVERT: A  302 MET cc_start: 0.6457 (mmp) cc_final: 0.6102 (mtm)
REVERT: A  377 MET cc_start: 0.8664 (tmm) cc_final: 0.8249 (tmm)
REVERT: A  386 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8456 (mp0)
REVERT: A  398 MET cc_start: 0.8302 (tpt) cc_final: 0.7882 (tpt)
REVERT: A  420 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8121 (mp0)
REVERT: B   19 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8677 (tttp)
REVERT: B  105 LYS cc_start: 0.9421 (tptp) cc_final: 0.9050 (tppt)
REVERT: B  108 TYR cc_start: 0.8094 (m-80) cc_final: 0.7696 (m-80)
REVERT: B  196 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8390 (mm-30)
REVERT: B  259 MET cc_start: 0.8831 (mmm) cc_final: 0.8323 (mmm)
REVERT: B  325 MET cc_start: 0.8213 (ttm) cc_final: 0.7870 (ttm)
REVERT: B  417 GLU cc_start: 0.8886 (mp0) cc_final: 0.8326 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 139
  average time/residue: 0.0586
  time to fit residues: 11.4767
Evaluate side-chains
  133 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  420 GLU
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  214 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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**
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 = 0.4206 r_free = 0.4206 target = 0.120776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.094427 restraints weight = 16808.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.098406 restraints weight = 9858.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.101200 restraints weight = 6802.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.103000 restraints weight = 5211.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.104483 restraints weight = 4327.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7000  Z= 0.177
  Angle     :  0.682  10.722   9509  Z= 0.344
  Chirality :  0.046   0.157   1039
  Planarity :  0.005   0.050   1238
  Dihedral  :  8.810 139.679    984
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.67 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.28), residues: 858
  helix:  0.40 (0.26), residues: 392
  sheet: -0.68 (0.43), residues: 124
  loop : -0.54 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.015   0.001   TYR B 185 
 PHE   0.013   0.001   PHE B 319 
 TRP   0.020   0.002   TRP B 407 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7000)
  covalent geometry    : angle       0.68183 ( 9509)
  hydrogen bonds       : bond        0.04093 (  311)
  hydrogen bonds       : angle       4.95232 (  918)

*********************** 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
  148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8172 (m-10) cc_final: 0.7448 (m-80)
REVERT: A  102 ASN cc_start: 0.9337 (t0) cc_final: 0.9014 (t0)
REVERT: A  153 LEU cc_start: 0.9655 (tp) cc_final: 0.9439 (tp)
REVERT: A  157 LEU cc_start: 0.9570 (mt) cc_final: 0.9329 (mt)
REVERT: A  377 MET cc_start: 0.8717 (tmm) cc_final: 0.8274 (tmm)
REVERT: A  386 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8480 (mp0)
REVERT: A  392 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7352 (p0)
REVERT: A  398 MET cc_start: 0.8397 (tpt) cc_final: 0.7994 (tpt)
REVERT: A  420 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8179 (mp0)
REVERT: A  430 LYS cc_start: 0.9541 (pttm) cc_final: 0.9285 (pttm)
REVERT: A  435 VAL cc_start: 0.8712 (t) cc_final: 0.8488 (m)
REVERT: B   19 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8623 (tttp)
REVERT: B  105 LYS cc_start: 0.9439 (tptp) cc_final: 0.9133 (tppt)
REVERT: B  108 TYR cc_start: 0.8164 (m-80) cc_final: 0.7766 (m-80)
REVERT: B  196 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: B  259 MET cc_start: 0.8830 (mmm) cc_final: 0.7846 (mmm)
REVERT: B  325 MET cc_start: 0.8171 (ttm) cc_final: 0.7821 (ttm)
REVERT: B  380 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7216 (m-40)
REVERT: B  417 GLU cc_start: 0.8866 (mp0) cc_final: 0.8513 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 142
  average time/residue: 0.0635
  time to fit residues: 12.9389
Evaluate side-chains
  139 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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   19 LYS
Chi-restraints excluded: chain B residue   42 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 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 = 0.4235 r_free = 0.4235 target = 0.122537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.096643 restraints weight = 16551.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.100555 restraints weight = 9662.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.103383 restraints weight = 6663.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.105181 restraints weight = 5082.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.106694 restraints weight = 4205.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7000  Z= 0.135
  Angle     :  0.669  10.842   9509  Z= 0.336
  Chirality :  0.046   0.169   1039
  Planarity :  0.004   0.048   1238
  Dihedral  :  8.702 138.337    984
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.49 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.28), residues: 858
  helix:  0.43 (0.26), residues: 394
  sheet: -0.71 (0.43), residues: 127
  loop : -0.50 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.012   0.001   TYR B 185 
 PHE   0.018   0.001   PHE B 319 
 TRP   0.023   0.002   TRP B 407 
 HIS   0.009   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7000)
  covalent geometry    : angle       0.66891 ( 9509)
  hydrogen bonds       : bond        0.03999 (  311)
  hydrogen bonds       : angle       4.87646 (  918)

*********************** 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
  150 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9300 (t0) cc_final: 0.8987 (t0)
REVERT: A  157 LEU cc_start: 0.9557 (mt) cc_final: 0.9327 (mt)
REVERT: A  377 MET cc_start: 0.8681 (tmm) cc_final: 0.8256 (tmm)
REVERT: A  386 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8419 (mp0)
REVERT: A  398 MET cc_start: 0.8283 (tpt) cc_final: 0.7955 (tpt)
REVERT: A  420 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8134 (mp0)
REVERT: A  430 LYS cc_start: 0.9525 (pttm) cc_final: 0.9202 (pttm)
REVERT: B    1 MET cc_start: 0.6215 (ptp) cc_final: 0.5718 (ptp)
REVERT: B   19 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8679 (tttp)
REVERT: B  105 LYS cc_start: 0.9422 (tptp) cc_final: 0.9112 (tppt)
REVERT: B  108 TYR cc_start: 0.8113 (m-80) cc_final: 0.7779 (m-80)
REVERT: B  196 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8482 (mm-30)
REVERT: B  259 MET cc_start: 0.8794 (mmm) cc_final: 0.8100 (mmm)
REVERT: B  272 PHE cc_start: 0.8683 (t80) cc_final: 0.8460 (t80)
REVERT: B  325 MET cc_start: 0.8153 (ttm) cc_final: 0.7812 (ttm)
REVERT: B  380 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7192 (m-40)
REVERT: B  413 MET cc_start: 0.5511 (ppp) cc_final: 0.5129 (ppp)
REVERT: B  416 MET cc_start: 0.8637 (ppp) cc_final: 0.7957 (ppp)
REVERT: B  417 GLU cc_start: 0.8927 (mp0) cc_final: 0.8569 (mp0)
  outliers start: 16
  outliers final: 10
  residues processed: 143
  average time/residue: 0.0610
  time to fit residues: 12.2306
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  : 0.258 
-------------------------------------------------------------------------------
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  420 GLU
Chi-restraints excluded: chain B residue   19 LYS
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  214 PHE
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 49 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0770
   overall best weight:    1.8146

-------------------------------------------------------------------------------
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 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 = 0.4234 r_free = 0.4234 target = 0.122556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.096321 restraints weight = 16618.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.100334 restraints weight = 9766.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103125 restraints weight = 6735.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.104946 restraints weight = 5151.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.106455 restraints weight = 4272.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7000  Z= 0.146
  Angle     :  0.672   9.543   9509  Z= 0.338
  Chirality :  0.046   0.168   1039
  Planarity :  0.004   0.046   1238
  Dihedral  :  8.685 138.208    984
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.76 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.28), residues: 858
  helix:  0.41 (0.26), residues: 396
  sheet: -0.74 (0.43), residues: 127
  loop : -0.41 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  88 
 TYR   0.019   0.001   TYR A 408 
 PHE   0.014   0.001   PHE B 319 
 TRP   0.030   0.003   TRP B 407 
 HIS   0.012   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7000)
  covalent geometry    : angle       0.67238 ( 9509)
  hydrogen bonds       : bond        0.03967 (  311)
  hydrogen bonds       : angle       4.89162 (  918)

*********************** 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
  147 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9307 (t0) cc_final: 0.8694 (t0)
REVERT: A  157 LEU cc_start: 0.9527 (mt) cc_final: 0.9311 (mt)
REVERT: A  377 MET cc_start: 0.8665 (tmm) cc_final: 0.8223 (tmm)
REVERT: A  386 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8446 (mp0)
REVERT: A  398 MET cc_start: 0.8300 (tpt) cc_final: 0.7979 (tpt)
REVERT: B    1 MET cc_start: 0.6263 (ptp) cc_final: 0.5670 (ptp)
REVERT: B   21 TRP cc_start: 0.9254 (m100) cc_final: 0.8843 (m100)
REVERT: B  108 TYR cc_start: 0.8115 (m-80) cc_final: 0.7780 (m-80)
REVERT: B  196 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8480 (mm-30)
REVERT: B  259 MET cc_start: 0.8815 (mmm) cc_final: 0.8112 (mmm)
REVERT: B  272 PHE cc_start: 0.8658 (t80) cc_final: 0.8325 (t80)
REVERT: B  325 MET cc_start: 0.8121 (ttm) cc_final: 0.7855 (ttm)
REVERT: B  380 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7546 (m-40)
REVERT: B  417 GLU cc_start: 0.8948 (mp0) cc_final: 0.8368 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 140
  average time/residue: 0.0624
  time to fit residues: 12.3903
Evaluate side-chains
  145 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  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  214 PHE
Chi-restraints excluded: chain B residue  376 THR
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 12 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0870
   chunk 73 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    3.0166

-------------------------------------------------------------------------------
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 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 = 0.4208 r_free = 0.4208 target = 0.120803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.094457 restraints weight = 16862.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.098444 restraints weight = 9902.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.101222 restraints weight = 6832.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.103140 restraints weight = 5229.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.104528 restraints weight = 4318.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7000  Z= 0.192
  Angle     :  0.722  10.490   9509  Z= 0.366
  Chirality :  0.047   0.169   1039
  Planarity :  0.005   0.049   1238
  Dihedral  :  8.761 138.544    984
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.30 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.28), residues: 858
  helix:  0.31 (0.26), residues: 395
  sheet: -0.71 (0.44), residues: 126
  loop : -0.44 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  88 
 TYR   0.025   0.002   TYR A 408 
 PHE   0.020   0.002   PHE B 319 
 TRP   0.027   0.003   TRP B 407 
 HIS   0.013   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 7000)
  covalent geometry    : angle       0.72185 ( 9509)
  hydrogen bonds       : bond        0.04193 (  311)
  hydrogen bonds       : angle       5.02796 (  918)

*********************** 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  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8185 (m-10) cc_final: 0.7442 (m-80)
REVERT: A   75 ILE cc_start: 0.8944 (mm) cc_final: 0.8724 (mm)
REVERT: A  102 ASN cc_start: 0.9311 (t0) cc_final: 0.8662 (t0)
REVERT: A  157 LEU cc_start: 0.9545 (mt) cc_final: 0.9344 (mt)
REVERT: A  377 MET cc_start: 0.8671 (tmm) cc_final: 0.8219 (tmm)
REVERT: A  386 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8476 (mp0)
REVERT: A  398 MET cc_start: 0.8361 (tpt) cc_final: 0.8048 (tpt)
REVERT: A  430 LYS cc_start: 0.9544 (pttm) cc_final: 0.9285 (mmtm)
REVERT: A  435 VAL cc_start: 0.8859 (t) cc_final: 0.8569 (m)
REVERT: B   21 TRP cc_start: 0.9275 (m100) cc_final: 0.8851 (m100)
REVERT: B  108 TYR cc_start: 0.8148 (m-80) cc_final: 0.7778 (m-80)
REVERT: B  259 MET cc_start: 0.8848 (mmm) cc_final: 0.7912 (mmm)
REVERT: B  272 PHE cc_start: 0.8678 (t80) cc_final: 0.8260 (t80)
REVERT: B  301 MET cc_start: 0.8937 (mmm) cc_final: 0.8627 (mmm)
REVERT: B  325 MET cc_start: 0.8122 (ttm) cc_final: 0.7855 (ttm)
REVERT: B  373 MET cc_start: 0.7444 (mmm) cc_final: 0.6944 (tpp)
REVERT: B  380 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7525 (m-40)
REVERT: B  413 MET cc_start: 0.5192 (ppp) cc_final: 0.4595 (ppp)
REVERT: B  417 GLU cc_start: 0.8899 (mp0) cc_final: 0.8448 (mp0)
  outliers start: 16
  outliers final: 14
  residues processed: 141
  average time/residue: 0.0602
  time to fit residues: 12.2420
Evaluate side-chains
  141 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  167 LEU
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  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  214 PHE
Chi-restraints excluded: chain B residue  376 THR
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 34 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 55 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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  96 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.121386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.095151 restraints weight = 16631.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.099075 restraints weight = 9767.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.101885 restraints weight = 6764.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103704 restraints weight = 5193.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.105222 restraints weight = 4309.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7000  Z= 0.170
  Angle     :  0.735  11.370   9509  Z= 0.369
  Chirality :  0.047   0.160   1039
  Planarity :  0.004   0.051   1238
  Dihedral  :  8.767 138.461    984
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.30 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.28), residues: 858
  helix:  0.31 (0.26), residues: 393
  sheet: -0.81 (0.44), residues: 129
  loop : -0.42 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  88 
 TYR   0.023   0.001   TYR A 408 
 PHE   0.018   0.001   PHE B 319 
 TRP   0.024   0.003   TRP B 407 
 HIS   0.014   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7000)
  covalent geometry    : angle       0.73519 ( 9509)
  hydrogen bonds       : bond        0.04170 (  311)
  hydrogen bonds       : angle       4.99615 (  918)

********************** 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
  150 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8158 (m-10) cc_final: 0.7429 (m-80)
REVERT: A   75 ILE cc_start: 0.8934 (mm) cc_final: 0.8691 (mm)
REVERT: A  102 ASN cc_start: 0.9300 (t0) cc_final: 0.8639 (t0)
REVERT: A  157 LEU cc_start: 0.9550 (mt) cc_final: 0.9342 (mt)
REVERT: A  377 MET cc_start: 0.8675 (tmm) cc_final: 0.8223 (tmm)
REVERT: A  386 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8467 (mp0)
REVERT: A  398 MET cc_start: 0.8408 (tpt) cc_final: 0.8118 (tpt)
REVERT: A  435 VAL cc_start: 0.8834 (t) cc_final: 0.8613 (m)
REVERT: B   21 TRP cc_start: 0.9261 (m100) cc_final: 0.8828 (m100)
REVERT: B  105 LYS cc_start: 0.9393 (tptp) cc_final: 0.9141 (tppt)
REVERT: B  108 TYR cc_start: 0.8137 (m-80) cc_final: 0.7823 (m-80)
REVERT: B  196 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8496 (mm-30)
REVERT: B  259 MET cc_start: 0.8818 (mmm) cc_final: 0.8122 (mmm)
REVERT: B  325 MET cc_start: 0.8152 (ttm) cc_final: 0.7886 (ttm)
REVERT: B  373 MET cc_start: 0.7433 (mmm) cc_final: 0.6939 (tpp)
REVERT: B  402 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8572 (tppt)
REVERT: B  413 MET cc_start: 0.5247 (ppp) cc_final: 0.4723 (ppp)
REVERT: B  417 GLU cc_start: 0.8897 (mp0) cc_final: 0.8447 (mp0)
  outliers start: 16
  outliers final: 15
  residues processed: 142
  average time/residue: 0.0577
  time to fit residues: 11.6042
Evaluate side-chains
  143 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  152 LEU
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  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
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
Chi-restraints excluded: chain B residue  406 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 66 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 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 = 0.4253 r_free = 0.4253 target = 0.124163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.097461 restraints weight = 16534.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.101429 restraints weight = 9812.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.104318 restraints weight = 6822.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.106167 restraints weight = 5223.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.107691 restraints weight = 4336.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7000  Z= 0.135
  Angle     :  0.732  11.153   9509  Z= 0.365
  Chirality :  0.046   0.176   1039
  Planarity :  0.004   0.040   1238
  Dihedral  :  8.649 135.660    984
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 21.85 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.28), residues: 858
  helix:  0.36 (0.26), residues: 396
  sheet: -0.59 (0.45), residues: 127
  loop : -0.60 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.016   0.001   TYR A 408 
 PHE   0.017   0.001   PHE B 319 
 TRP   0.025   0.003   TRP B 103 
 HIS   0.013   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7000)
  covalent geometry    : angle       0.73226 ( 9509)
  hydrogen bonds       : bond        0.04043 (  311)
  hydrogen bonds       : angle       4.93090 (  918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1232.46 seconds
wall clock time: 22 minutes 6.97 seconds (1326.97 seconds total)