Starting phenix.real_space_refine
on Wed Feb 12 01:17:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ysn_34077/02_2025/7ysn_34077.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ysn_34077/02_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_34077/02_2025/7ysn_34077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ysn_34077/02_2025/7ysn_34077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ysn_34077/02_2025/7ysn_34077.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ysn_34077/02_2025/7ysn_34077.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      48      5.16       5
     C    4296      2.51       5
     N    1167      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6844
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3404
          Classifications: {'peptide': 434}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3376
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'G2P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.35, per 1000 atoms: 0.64
  Number of scatterers: 6844
  At special positions: 0
  Unit cell: (112.136, 70.192, 69.336, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       6     15.00
     O    1327      8.00
     N    1167      7.00
     C    4296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 965.4 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      48.6% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  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: 2.26

  Time building geometry restraints manager: 2.06 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:             0.430
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.480
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.230   7000  Z= 0.343
  Angle     :  0.693  10.618   9509  Z= 0.330
  Chirality :  0.045   0.245   1039
  Planarity :  0.003   0.036   1238
  Dihedral  : 14.723 140.575   2583
  Min Nonbonded Distance : 2.131

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

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

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

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.754 
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: 0.1684
  time to fit residues: 36.1199
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  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.1784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.125759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.099710 restraints weight = 16221.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.103642 restraints weight = 9712.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.106508 restraints weight = 6786.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1392

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

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

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

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

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9200 (t0) cc_final: 0.8590 (t0)
REVERT: A  153 LEU cc_start: 0.9638 (tp) cc_final: 0.9411 (tp)
REVERT: A  157 LEU cc_start: 0.9542 (mt) cc_final: 0.9264 (mt)
REVERT: A  171 ILE cc_start: 0.8624 (mm) cc_final: 0.8307 (mt)
REVERT: A  377 MET cc_start: 0.8704 (tmm) cc_final: 0.8286 (tmm)
REVERT: A  386 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8394 (mp0)
REVERT: A  398 MET cc_start: 0.7759 (tpt) cc_final: 0.7368 (tpt)
REVERT: A  420 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7990 (mp0)
REVERT: B   70 LEU cc_start: 0.8605 (mm) cc_final: 0.8338 (mm)
REVERT: B  102 ASN cc_start: 0.8964 (t0) cc_final: 0.8759 (t0)
REVERT: B  103 TRP cc_start: 0.6707 (t60) cc_final: 0.5823 (t60)
REVERT: B  105 LYS cc_start: 0.9265 (tptp) cc_final: 0.8836 (tppt)
REVERT: B  137 LEU cc_start: 0.9408 (tp) cc_final: 0.9197 (tp)
REVERT: B  156 LYS cc_start: 0.9673 (mmpt) cc_final: 0.9452 (mmmt)
REVERT: B  196 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8452 (mm-30)
REVERT: B  325 MET cc_start: 0.8438 (ttm) cc_final: 0.8182 (ttm)
  outliers start: 8
  outliers final: 5
  residues processed: 158
  average time/residue: 0.1735
  time to fit residues: 37.2820
Evaluate side-chains
  139 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 75 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.118090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.091860 restraints weight = 17129.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.095561 restraints weight = 10149.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.098303 restraints weight = 7121.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7000  Z= 0.406
  Angle     :  0.745  13.296   9509  Z= 0.389
  Chirality :  0.049   0.185   1039
  Planarity :  0.005   0.063   1238
  Dihedral  :  9.096 142.492    984
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 20.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.65 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.28), residues: 858
  helix:  0.41 (0.26), residues: 384
  sheet: -0.68 (0.43), residues: 133
  loop : -0.61 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 407 
 HIS   0.007   0.002   HIS B 266 
 PHE   0.012   0.002   PHE A 255 
 TYR   0.018   0.002   TYR A 408 
 ARG   0.005   0.001   ARG B  88 

*********************** 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
  151 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8297 (m-10) cc_final: 0.7542 (m-80)
REVERT: A   88 HIS cc_start: 0.8618 (m-70) cc_final: 0.8368 (t-90)
REVERT: A  102 ASN cc_start: 0.9331 (t0) cc_final: 0.8824 (t0)
REVERT: A  153 LEU cc_start: 0.9672 (tp) cc_final: 0.9412 (tp)
REVERT: A  157 LEU cc_start: 0.9561 (mt) cc_final: 0.9282 (mt)
REVERT: A  377 MET cc_start: 0.8677 (tmm) cc_final: 0.8244 (tmm)
REVERT: A  386 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8490 (mp0)
REVERT: A  392 ASP cc_start: 0.7666 (p0) cc_final: 0.7308 (p0)
REVERT: A  398 MET cc_start: 0.8191 (tpt) cc_final: 0.7682 (tpt)
REVERT: A  420 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8185 (pm20)
REVERT: B   70 LEU cc_start: 0.8550 (mm) cc_final: 0.8257 (mm)
REVERT: B  102 ASN cc_start: 0.9049 (t0) cc_final: 0.8763 (t0)
REVERT: B  105 LYS cc_start: 0.9309 (tptp) cc_final: 0.8860 (tppt)
REVERT: B  325 MET cc_start: 0.8232 (ttm) cc_final: 0.8011 (ttm)
REVERT: B  417 GLU cc_start: 0.8830 (mp0) cc_final: 0.8570 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 145
  average time/residue: 0.1704
  time to fit residues: 34.6515
Evaluate side-chains
  135 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    2.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.120464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.094021 restraints weight = 16810.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.097934 restraints weight = 9950.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.100678 restraints weight = 6918.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7000  Z= 0.256
  Angle     :  0.665  10.211   9509  Z= 0.340
  Chirality :  0.046   0.163   1039
  Planarity :  0.005   0.049   1238
  Dihedral  :  8.962 140.177    984
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.55 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 858
  helix:  0.39 (0.26), residues: 391
  sheet: -0.71 (0.44), residues: 132
  loop : -0.60 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B 407 
 HIS   0.010   0.001   HIS B 406 
 PHE   0.008   0.002   PHE B 388 
 TYR   0.012   0.001   TYR B 108 
 ARG   0.003   0.000   ARG A 105 

*********************** 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
  153 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8201 (m-10) cc_final: 0.7494 (m-80)
REVERT: A   88 HIS cc_start: 0.8596 (m-70) cc_final: 0.8355 (t-90)
REVERT: A  102 ASN cc_start: 0.9264 (t0) cc_final: 0.8989 (t0)
REVERT: A  153 LEU cc_start: 0.9653 (tp) cc_final: 0.9403 (tp)
REVERT: A  157 LEU cc_start: 0.9575 (mt) cc_final: 0.9317 (mt)
REVERT: A  313 MET cc_start: 0.6855 (mpp) cc_final: 0.6653 (mpp)
REVERT: A  377 MET cc_start: 0.8684 (tmm) cc_final: 0.8305 (tmm)
REVERT: A  386 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8454 (mp0)
REVERT: A  392 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7244 (p0)
REVERT: A  398 MET cc_start: 0.8353 (tpt) cc_final: 0.7893 (tpt)
REVERT: A  430 LYS cc_start: 0.9538 (pttm) cc_final: 0.9261 (pttm)
REVERT: B   70 LEU cc_start: 0.8549 (mm) cc_final: 0.8293 (mm)
REVERT: B  102 ASN cc_start: 0.8989 (t0) cc_final: 0.8707 (t0)
REVERT: B  105 LYS cc_start: 0.9281 (tptp) cc_final: 0.8826 (tppt)
REVERT: B  108 TYR cc_start: 0.8016 (m-80) cc_final: 0.7605 (m-80)
REVERT: B  196 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8449 (mm-30)
REVERT: B  325 MET cc_start: 0.8320 (ttm) cc_final: 0.7988 (ttm)
REVERT: B  380 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7637 (m-40)
REVERT: B  417 GLU cc_start: 0.8991 (mp0) cc_final: 0.8701 (mp0)
  outliers start: 17
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1597
  time to fit residues: 32.2901
Evaluate side-chains
  140 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.1986

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.122842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.096533 restraints weight = 16495.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.100486 restraints weight = 9696.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103265 restraints weight = 6722.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7000  Z= 0.184
  Angle     :  0.638   9.152   9509  Z= 0.323
  Chirality :  0.045   0.167   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  8.837 139.015    984
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.86 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 858
  helix:  0.49 (0.26), residues: 391
  sheet: -0.63 (0.45), residues: 131
  loop : -0.59 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 407 
 HIS   0.010   0.001   HIS B 406 
 PHE   0.011   0.001   PHE B  83 
 TYR   0.010   0.001   TYR A 408 
 ARG   0.004   0.000   ARG B  64 

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.8906 (mm) cc_final: 0.8653 (mm)
REVERT: A   88 HIS cc_start: 0.8533 (m-70) cc_final: 0.8301 (t-90)
REVERT: A  102 ASN cc_start: 0.9244 (t0) cc_final: 0.8935 (t0)
REVERT: A  153 LEU cc_start: 0.9642 (tp) cc_final: 0.9404 (tp)
REVERT: A  157 LEU cc_start: 0.9577 (mt) cc_final: 0.9334 (mt)
REVERT: A  302 MET cc_start: 0.6360 (mmp) cc_final: 0.6097 (mtm)
REVERT: A  377 MET cc_start: 0.8690 (tmm) cc_final: 0.8282 (tmm)
REVERT: A  386 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8425 (mp0)
REVERT: A  392 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7188 (p0)
REVERT: A  398 MET cc_start: 0.8310 (tpt) cc_final: 0.7950 (tpt)
REVERT: A  430 LYS cc_start: 0.9502 (pttm) cc_final: 0.9174 (pttm)
REVERT: A  434 GLU cc_start: 0.8468 (pp20) cc_final: 0.8261 (pp20)
REVERT: B  102 ASN cc_start: 0.8952 (t0) cc_final: 0.8685 (t0)
REVERT: B  105 LYS cc_start: 0.9268 (tptp) cc_final: 0.9065 (tppt)
REVERT: B  108 TYR cc_start: 0.8007 (m-80) cc_final: 0.7534 (m-80)
REVERT: B  196 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8454 (mm-30)
REVERT: B  259 MET cc_start: 0.8818 (mmm) cc_final: 0.8438 (mmm)
REVERT: B  325 MET cc_start: 0.8212 (ttm) cc_final: 0.7896 (ttm)
REVERT: B  413 MET cc_start: 0.5477 (ppp) cc_final: 0.4908 (ppp)
REVERT: B  417 GLU cc_start: 0.9056 (mp0) cc_final: 0.8822 (mp0)
  outliers start: 14
  outliers final: 11
  residues processed: 151
  average time/residue: 0.1893
  time to fit residues: 38.9301
Evaluate side-chains
  143 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    6.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.115722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.089030 restraints weight = 17322.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.092692 restraints weight = 10314.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.095273 restraints weight = 7298.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   7000  Z= 0.469
  Angle     :  0.768   8.963   9509  Z= 0.403
  Chirality :  0.050   0.171   1039
  Planarity :  0.005   0.067   1238
  Dihedral  :  9.315 143.305    984
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 21.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.76 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.28), residues: 858
  helix:  0.19 (0.25), residues: 389
  sheet: -0.86 (0.44), residues: 132
  loop : -0.79 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B 407 
 HIS   0.009   0.002   HIS B 406 
 PHE   0.020   0.002   PHE B 319 
 TYR   0.016   0.002   TYR B 432 
 ARG   0.005   0.001   ARG B  64 

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8310 (m-10) cc_final: 0.7541 (m-80)
REVERT: A   88 HIS cc_start: 0.8567 (m-70) cc_final: 0.8367 (t-90)
REVERT: A  102 ASN cc_start: 0.9327 (t0) cc_final: 0.9092 (t0)
REVERT: A  157 LEU cc_start: 0.9585 (mt) cc_final: 0.9361 (mt)
REVERT: A  377 MET cc_start: 0.8647 (tmm) cc_final: 0.8254 (tmm)
REVERT: A  386 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8458 (mp0)
REVERT: A  392 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7275 (p0)
REVERT: A  398 MET cc_start: 0.8381 (tpt) cc_final: 0.8088 (tpt)
REVERT: B   21 TRP cc_start: 0.9345 (m100) cc_final: 0.8909 (m100)
REVERT: B  102 ASN cc_start: 0.9081 (t0) cc_final: 0.8801 (t0)
REVERT: B  105 LYS cc_start: 0.9410 (tptp) cc_final: 0.9032 (tptp)
REVERT: B  108 TYR cc_start: 0.8090 (m-80) cc_final: 0.7704 (m-80)
REVERT: B  196 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8395 (mm-30)
REVERT: B  325 MET cc_start: 0.8306 (ttm) cc_final: 0.8101 (ttm)
REVERT: B  380 ASN cc_start: 0.7906 (t0) cc_final: 0.7561 (m-40)
REVERT: B  413 MET cc_start: 0.5640 (ppp) cc_final: 0.5429 (ppp)
REVERT: B  417 GLU cc_start: 0.9076 (mp0) cc_final: 0.8810 (mp0)
  outliers start: 24
  outliers final: 20
  residues processed: 143
  average time/residue: 0.1520
  time to fit residues: 31.3725
Evaluate side-chains
  143 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
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  238 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 70 optimal weight:    0.1980
   chunk 71 optimal weight:    0.0470
   chunk 53 optimal weight:   20.0000
   chunk 40 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.8282

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.122540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.096640 restraints weight = 16506.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.100673 restraints weight = 9598.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103526 restraints weight = 6609.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7000  Z= 0.193
  Angle     :  0.699  12.213   9509  Z= 0.348
  Chirality :  0.046   0.173   1039
  Planarity :  0.004   0.045   1238
  Dihedral  :  8.974 138.370    984
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 22.25 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.28), residues: 858
  helix:  0.39 (0.26), residues: 391
  sheet: -0.62 (0.45), residues: 133
  loop : -0.70 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 407 
 HIS   0.012   0.001   HIS A 107 
 PHE   0.014   0.002   PHE B  83 
 TYR   0.015   0.001   TYR B 185 
 ARG   0.003   0.000   ARG B 401 

*********************** 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
  164 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8136 (m-10) cc_final: 0.7428 (m-80)
REVERT: A  102 ASN cc_start: 0.9221 (t0) cc_final: 0.8611 (t0)
REVERT: A  157 LEU cc_start: 0.9583 (mt) cc_final: 0.9373 (mt)
REVERT: A  183 GLU cc_start: 0.8576 (pt0) cc_final: 0.8359 (pt0)
REVERT: A  377 MET cc_start: 0.8687 (tmm) cc_final: 0.8230 (tmm)
REVERT: A  386 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8400 (mp0)
REVERT: A  392 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7154 (p0)
REVERT: A  398 MET cc_start: 0.8395 (tpt) cc_final: 0.8175 (tpt)
REVERT: A  434 GLU cc_start: 0.8361 (pp20) cc_final: 0.8140 (pp20)
REVERT: B    1 MET cc_start: 0.7008 (pmm) cc_final: 0.6744 (pmm)
REVERT: B   21 TRP cc_start: 0.9264 (m100) cc_final: 0.8793 (m100)
REVERT: B  102 ASN cc_start: 0.8965 (t0) cc_final: 0.8682 (t0)
REVERT: B  105 LYS cc_start: 0.9434 (tptp) cc_final: 0.8998 (tptp)
REVERT: B  108 TYR cc_start: 0.8104 (m-80) cc_final: 0.7618 (m-80)
REVERT: B  168 THR cc_start: 0.9345 (p) cc_final: 0.9114 (t)
REVERT: B  196 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8488 (mm-30)
REVERT: B  259 MET cc_start: 0.8736 (mmm) cc_final: 0.8248 (mmm)
REVERT: B  325 MET cc_start: 0.8253 (ttm) cc_final: 0.7939 (ttm)
REVERT: B  373 MET cc_start: 0.7637 (tpp) cc_final: 0.7055 (tpp)
REVERT: B  413 MET cc_start: 0.5363 (ppp) cc_final: 0.4777 (ppp)
REVERT: B  416 MET cc_start: 0.9066 (ppp) cc_final: 0.8859 (ppp)
REVERT: B  417 GLU cc_start: 0.9100 (mp0) cc_final: 0.8627 (mp0)
  outliers start: 18
  outliers final: 14
  residues processed: 155
  average time/residue: 0.1708
  time to fit residues: 38.0610
Evaluate side-chains
  148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   66 ILE
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 72 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 61 optimal weight:    9.9990
   chunk 28 optimal weight:    0.2980
   chunk 58 optimal weight:    0.0370
   chunk 82 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.8664

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.121266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.095128 restraints weight = 16740.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.099090 restraints weight = 9824.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.101892 restraints weight = 6809.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7000  Z= 0.224
  Angle     :  0.686  10.555   9509  Z= 0.345
  Chirality :  0.047   0.172   1039
  Planarity :  0.004   0.044   1238
  Dihedral  :  8.925 138.549    984
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.66 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.28), residues: 858
  helix:  0.38 (0.26), residues: 391
  sheet: -0.59 (0.46), residues: 124
  loop : -0.75 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B 407 
 HIS   0.012   0.001   HIS A 107 
 PHE   0.018   0.001   PHE B 319 
 TYR   0.012   0.001   TYR B 185 
 ARG   0.003   0.000   ARG B 401 

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9280 (t0) cc_final: 0.8973 (t0)
REVERT: A  157 LEU cc_start: 0.9582 (mt) cc_final: 0.9377 (mt)
REVERT: A  377 MET cc_start: 0.8670 (tmm) cc_final: 0.8216 (tmm)
REVERT: A  386 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8407 (mp0)
REVERT: A  392 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7145 (p0)
REVERT: A  398 MET cc_start: 0.8411 (tpt) cc_final: 0.8182 (tpt)
REVERT: A  434 GLU cc_start: 0.8400 (pp20) cc_final: 0.8142 (pp20)
REVERT: B    1 MET cc_start: 0.7055 (pmm) cc_final: 0.6743 (pmm)
REVERT: B   21 TRP cc_start: 0.9285 (m100) cc_final: 0.8809 (m100)
REVERT: B  102 ASN cc_start: 0.8974 (t0) cc_final: 0.8709 (t0)
REVERT: B  105 LYS cc_start: 0.9437 (tptp) cc_final: 0.9008 (tptp)
REVERT: B  108 TYR cc_start: 0.8062 (m-80) cc_final: 0.7639 (m-80)
REVERT: B  196 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: B  325 MET cc_start: 0.8207 (ttm) cc_final: 0.7881 (ttm)
REVERT: B  373 MET cc_start: 0.7799 (tpp) cc_final: 0.7249 (tpp)
REVERT: B  413 MET cc_start: 0.5386 (ppp) cc_final: 0.4988 (ppp)
REVERT: B  417 GLU cc_start: 0.9108 (mp0) cc_final: 0.8639 (mp0)
  outliers start: 21
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1542
  time to fit residues: 31.7575
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  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  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  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 78 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.124694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.097935 restraints weight = 16492.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.101961 restraints weight = 9737.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.104869 restraints weight = 6752.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7000  Z= 0.188
  Angle     :  0.706  10.855   9509  Z= 0.355
  Chirality :  0.047   0.197   1039
  Planarity :  0.004   0.038   1238
  Dihedral  :  8.822 136.395    984
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.20 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.28), residues: 858
  helix:  0.39 (0.26), residues: 393
  sheet: -0.57 (0.47), residues: 124
  loop : -0.73 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 407 
 HIS   0.011   0.001   HIS A 107 
 PHE   0.015   0.001   PHE B 319 
 TYR   0.013   0.001   TYR A 408 
 ARG   0.003   0.000   ARG B 401 

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8135 (m-10) cc_final: 0.7389 (m-80)
REVERT: A  102 ASN cc_start: 0.9282 (t0) cc_final: 0.8725 (t0)
REVERT: A  377 MET cc_start: 0.8708 (tmm) cc_final: 0.8220 (tmm)
REVERT: A  386 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8390 (mp0)
REVERT: A  392 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7141 (p0)
REVERT: A  398 MET cc_start: 0.8374 (tpt) cc_final: 0.8157 (tpt)
REVERT: A  430 LYS cc_start: 0.9487 (pttm) cc_final: 0.9193 (pttm)
REVERT: B   21 TRP cc_start: 0.9261 (m100) cc_final: 0.8804 (m100)
REVERT: B  102 ASN cc_start: 0.8943 (t0) cc_final: 0.8685 (t0)
REVERT: B  105 LYS cc_start: 0.9429 (tptp) cc_final: 0.9027 (tptp)
REVERT: B  108 TYR cc_start: 0.8083 (m-80) cc_final: 0.7662 (m-80)
REVERT: B  196 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8552 (mm-30)
REVERT: B  259 MET cc_start: 0.8734 (mmm) cc_final: 0.8251 (mmm)
REVERT: B  325 MET cc_start: 0.8087 (ttm) cc_final: 0.7849 (ttm)
REVERT: B  373 MET cc_start: 0.7799 (tpp) cc_final: 0.7241 (tpp)
REVERT: B  400 ARG cc_start: 0.8892 (pmt-80) cc_final: 0.8297 (pmt-80)
REVERT: B  413 MET cc_start: 0.5319 (ppp) cc_final: 0.4960 (ppp)
REVERT: B  417 GLU cc_start: 0.9036 (mp0) cc_final: 0.8635 (mp0)
  outliers start: 17
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1552
  time to fit residues: 30.9873
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  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   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  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 72 optimal weight:    0.0020
   chunk 53 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    3.3996

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.120326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.093496 restraints weight = 17044.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.097425 restraints weight = 10162.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.100192 restraints weight = 7103.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2983

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= 0.296
  Angle     :  0.728  10.137   9509  Z= 0.372
  Chirality :  0.048   0.198   1039
  Planarity :  0.005   0.052   1238
  Dihedral  :  8.997 140.014    984
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.52 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.28), residues: 858
  helix:  0.35 (0.26), residues: 393
  sheet: -0.54 (0.47), residues: 122
  loop : -0.73 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 103 
 HIS   0.013   0.002   HIS A 107 
 PHE   0.021   0.002   PHE B 319 
 TYR   0.020   0.002   TYR A 408 
 ARG   0.003   0.000   ARG B 401 

********************** 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
  147 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9303 (t0) cc_final: 0.8998 (t0)
REVERT: A  377 MET cc_start: 0.8717 (tmm) cc_final: 0.8224 (tmm)
REVERT: A  386 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8413 (mp0)
REVERT: A  392 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7174 (p0)
REVERT: A  398 MET cc_start: 0.8409 (tpt) cc_final: 0.8187 (tpt)
REVERT: A  430 LYS cc_start: 0.9504 (pttm) cc_final: 0.9242 (pttm)
REVERT: A  435 VAL cc_start: 0.8884 (t) cc_final: 0.8652 (m)
REVERT: B    1 MET cc_start: 0.6927 (pmm) cc_final: 0.6620 (pmm)
REVERT: B  102 ASN cc_start: 0.9004 (t0) cc_final: 0.8742 (t0)
REVERT: B  105 LYS cc_start: 0.9434 (tptp) cc_final: 0.9047 (tptp)
REVERT: B  108 TYR cc_start: 0.8130 (m-80) cc_final: 0.7779 (m-80)
REVERT: B  325 MET cc_start: 0.8089 (ttm) cc_final: 0.7845 (ttm)
REVERT: B  373 MET cc_start: 0.7926 (tpp) cc_final: 0.7422 (tpp)
REVERT: B  413 MET cc_start: 0.5431 (ppp) cc_final: 0.5122 (ppp)
REVERT: B  416 MET cc_start: 0.9012 (ppp) cc_final: 0.8789 (ppp)
  outliers start: 20
  outliers final: 17
  residues processed: 138
  average time/residue: 0.1617
  time to fit residues: 31.7264
Evaluate side-chains
  144 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  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  392 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    1.7786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.122445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.095308 restraints weight = 16814.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.099292 restraints weight = 10041.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.102147 restraints weight = 7023.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7000  Z= 0.220
  Angle     :  0.712  10.264   9509  Z= 0.365
  Chirality :  0.048   0.210   1039
  Planarity :  0.004   0.047   1238
  Dihedral  :  8.905 138.360    984
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.20 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 858
  helix:  0.38 (0.26), residues: 393
  sheet: -0.40 (0.47), residues: 121
  loop : -0.75 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 103 
 HIS   0.018   0.002   HIS A 107 
 PHE   0.020   0.001   PHE B 319 
 TYR   0.018   0.001   TYR A 408 
 ARG   0.003   0.000   ARG B 401 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2360.65 seconds
wall clock time: 43 minutes 21.98 seconds (2601.98 seconds total)