Starting phenix.real_space_refine
on Thu Jul  2 05:30:30 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ysn_34077/07_2026/7ysn_34077.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

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

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6844
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3404
          Classifications: {'peptide': 434}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3376
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'G2P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.03, per 1000 atoms: 0.15
  Number of scatterers: 6844
  At special positions: 0
  Unit cell: (112.136, 70.192, 69.336, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       6     15.00
     O    1327      8.00
     N    1167      7.00
     C    4296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 286.2 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: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 71 through 81
      removed outlier: 4.566A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 4.312A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.330A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 194
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.961A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 287 through 294
    Processing helix  chain 'A' and resid 324 through 337
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 4.035A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.955A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 3.970A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 48 through 51
    Processing helix  chain 'B' and resid 57 through 59
      No H-bonds generated for 'chain 'B' and resid 57 through 59'
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.647A  pdb=" N   ASP B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 102 through 108
    Processing helix  chain 'B' and resid 110 through 127
      removed outlier: 3.519A  pdb=" N   LEU B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASP B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
    Processing helix  chain 'B' and resid 182 through 197
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 244
      removed outlier: 3.626A  pdb=" N   LEU B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   CYS B 241 " --> pdb=" O   GLY B 237 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   LEU B 242 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 293
    Processing helix  chain 'B' and resid 324 through 339
    Processing helix  chain 'B' and resid 384 through 398
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 415 through 438
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93
      removed outlier: 8.871A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 8.185A  pdb=" N   ASN A 356 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR A 319 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68
      removed outlier: 6.857A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   PHE B 135 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ILE B 204 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   SER B 170 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68
      removed outlier: 6.857A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   PHE B 135 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   MET B 166 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR B 202 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   THR B 168 " --> pdb=" O   TYR B 202 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   THR B 201 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   PHE B 267 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   SER B 381 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   LYS B 352 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL B 315 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   CYS B 356 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   PHE B 319 " --> pdb=" O   CYS B 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 55

    314 hydrogen bonds defined for protein.
    918 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.64

  Time building geometry restraints manager: 0.52 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: 4000
       28.12 -    56.23: 138
       56.23 -    84.35: 16
       84.35 -   112.46: 1
      112.46 -   140.58: 2
  Dihedral angle restraints: 4157
    sinusoidal: 1660
      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 4154 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.530
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.230   7000  Z= 0.286
  Angle     :  0.693  10.618   9509  Z= 0.330
  Chirality :  0.045   0.245   1039
  Planarity :  0.003   0.036   1238
  Dihedral  : 14.581 140.575   2555
  Min Nonbonded Distance : 2.131

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.29), residues: 858
  helix:  0.98 (0.26), residues: 382
  sheet: -0.16 (0.50), residues: 125
  loop : -0.37 (0.33), residues: 351

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00577 /  0.29 ( 7000)
  covalent geometry    : angle       0.69256 /  0.33 ( 9509)
  hydrogen bonds       : bond        0.15625 / 10.46 (  311)
  hydrogen bonds       : angle       6.48918 /  4.73 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.153 
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: 0.8390 (mmp) cc_final: 0.7955 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0553
  time to fit residues: 12.1087
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  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 107 HIS
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
B 186 ASN
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.123605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.097143 restraints weight = 16598.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.101075 restraints weight = 10027.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.103727 restraints weight = 7039.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.105667 restraints weight = 5478.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.107053 restraints weight = 4536.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7000  Z= 0.166
  Angle     :  0.640   7.278   9509  Z= 0.330
  Chirality :  0.046   0.258   1039
  Planarity :  0.004   0.052   1238
  Dihedral  :  7.914 135.525    956
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.96 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.29), residues: 858
  helix:  0.93 (0.26), residues: 384
  sheet: -0.32 (0.48), residues: 123
  loop : -0.53 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 373 
 TYR   0.010   0.001   TYR A 210 
 PHE   0.011   0.001   PHE B 388 
 TRP   0.027   0.003   TRP B 407 
 HIS   0.005   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 ( 7000)
  covalent geometry    : angle       0.63978 /  0.33 ( 9509)
  hydrogen bonds       : bond        0.04474 /  2.96 (  311)
  hydrogen bonds       : angle       5.22175 /  3.75 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9273 (t0) cc_final: 0.8656 (t0)
REVERT: A  153 LEU cc_start: 0.9643 (tp) cc_final: 0.9408 (tp)
REVERT: A  157 LEU cc_start: 0.9541 (mt) cc_final: 0.9261 (mt)
REVERT: A  171 ILE cc_start: 0.8643 (mm) cc_final: 0.8413 (mt)
REVERT: A  377 MET cc_start: 0.8688 (tmm) cc_final: 0.8282 (tmm)
REVERT: A  386 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8420 (mp0)
REVERT: A  398 MET cc_start: 0.7829 (tpt) cc_final: 0.7389 (tpt)
REVERT: A  420 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7943 (mp0)
REVERT: B   70 LEU cc_start: 0.8604 (mm) cc_final: 0.8337 (mm)
REVERT: B  103 TRP cc_start: 0.6770 (t60) cc_final: 0.5848 (t60)
REVERT: B  105 LYS cc_start: 0.9279 (tptp) cc_final: 0.8857 (tppt)
REVERT: B  137 LEU cc_start: 0.9420 (tp) cc_final: 0.9217 (tp)
REVERT: B  156 LYS cc_start: 0.9661 (mmpt) cc_final: 0.9441 (mmmt)
REVERT: B  196 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8408 (mm-30)
REVERT: B  259 MET cc_start: 0.8767 (mmm) cc_final: 0.8447 (mmm)
REVERT: B  325 MET cc_start: 0.8419 (ttm) cc_final: 0.8167 (ttm)
REVERT: B  417 GLU cc_start: 0.8683 (mp0) cc_final: 0.8464 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 153
  average time/residue: 0.0585
  time to fit residues: 12.8162
Evaluate side-chains
  139 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:   40.0000
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 45 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   overall best weight:    3.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.121498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.095093 restraints weight = 16724.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.098963 restraints weight = 9944.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.101688 restraints weight = 6948.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.103617 restraints weight = 5376.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.105030 restraints weight = 4446.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7000  Z= 0.192
  Angle     :  0.662   8.568   9509  Z= 0.342
  Chirality :  0.047   0.176   1039
  Planarity :  0.005   0.051   1238
  Dihedral  :  8.113 138.404    956
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.38 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.28), residues: 858
  helix:  0.65 (0.26), residues: 386
  sheet: -0.75 (0.44), residues: 126
  loop : -0.49 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 390 
 TYR   0.011   0.001   TYR A 210 
 PHE   0.012   0.001   PHE B 319 
 TRP   0.033   0.003   TRP B 407 
 HIS   0.005   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.19 ( 7000)
  covalent geometry    : angle       0.66181 /  0.34 ( 9509)
  hydrogen bonds       : bond        0.04418 /  2.95 (  311)
  hydrogen bonds       : angle       5.08599 /  3.57 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8145 (m-10) cc_final: 0.7462 (m-80)
REVERT: A  102 ASN cc_start: 0.9327 (t0) cc_final: 0.8762 (t0)
REVERT: A  153 LEU cc_start: 0.9656 (tp) cc_final: 0.9399 (tp)
REVERT: A  157 LEU cc_start: 0.9531 (mt) cc_final: 0.9247 (mt)
REVERT: A  377 MET cc_start: 0.8673 (tmm) cc_final: 0.8245 (tmm)
REVERT: A  386 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8445 (mp0)
REVERT: A  392 ASP cc_start: 0.7524 (p0) cc_final: 0.7178 (p0)
REVERT: A  398 MET cc_start: 0.8010 (tpt) cc_final: 0.7590 (tpt)
REVERT: A  420 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8011 (mp0)
REVERT: B   21 TRP cc_start: 0.9139 (m100) cc_final: 0.8888 (m100)
REVERT: B  105 LYS cc_start: 0.9254 (tptp) cc_final: 0.8971 (tppt)
REVERT: B  325 MET cc_start: 0.8337 (ttm) cc_final: 0.8039 (ttm)
REVERT: B  380 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7345 (m-40)
REVERT: B  417 GLU cc_start: 0.8753 (mp0) cc_final: 0.8217 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 143
  average time/residue: 0.0620
  time to fit residues: 12.8659
Evaluate side-chains
  136 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  380 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 62 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.1980
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0770
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.0142

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** 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 = 0.4229 r_free = 0.4229 target = 0.122308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.095670 restraints weight = 16762.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.099597 restraints weight = 9890.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.102407 restraints weight = 6880.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.104353 restraints weight = 5290.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.105665 restraints weight = 4388.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7000  Z= 0.149
  Angle     :  0.656   9.882   9509  Z= 0.335
  Chirality :  0.046   0.163   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  8.079 137.606    956
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.55 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.28), residues: 858
  helix:  0.54 (0.26), residues: 391
  sheet: -0.74 (0.44), residues: 125
  loop : -0.55 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.014   0.001   TYR B 108 
 PHE   0.010   0.001   PHE B 267 
 TRP   0.032   0.002   TRP B 407 
 HIS   0.009   0.001   HIS B 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.15 ( 7000)
  covalent geometry    : angle       0.65640 /  0.33 ( 9509)
  hydrogen bonds       : bond        0.04119 /  2.75 (  311)
  hydrogen bonds       : angle       4.96300 /  3.47 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9290 (t0) cc_final: 0.8985 (t0)
REVERT: A  153 LEU cc_start: 0.9646 (tp) cc_final: 0.9394 (tp)
REVERT: A  157 LEU cc_start: 0.9533 (mt) cc_final: 0.9261 (mt)
REVERT: A  377 MET cc_start: 0.8686 (tmm) cc_final: 0.8288 (tmm)
REVERT: A  386 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8418 (mp0)
REVERT: A  392 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7104 (p0)
REVERT: A  398 MET cc_start: 0.8111 (tpt) cc_final: 0.7655 (tpt)
REVERT: A  420 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8109 (mp0)
REVERT: A  430 LYS cc_start: 0.9543 (pttm) cc_final: 0.9207 (pttm)
REVERT: B  105 LYS cc_start: 0.9402 (tptp) cc_final: 0.8966 (tptp)
REVERT: B  108 TYR cc_start: 0.8028 (m-80) cc_final: 0.7674 (m-80)
REVERT: B  196 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8403 (mm-30)
REVERT: B  259 MET cc_start: 0.8823 (mmm) cc_final: 0.8326 (mmm)
REVERT: B  325 MET cc_start: 0.8308 (ttm) cc_final: 0.7977 (ttm)
REVERT: B  417 GLU cc_start: 0.8770 (mp0) cc_final: 0.8539 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 138
  average time/residue: 0.0570
  time to fit residues: 11.4885
Evaluate side-chains
  134 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
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  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  380 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 64 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** 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 = 0.4231 r_free = 0.4231 target = 0.122170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.095645 restraints weight = 16806.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.099611 restraints weight = 9866.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.102420 restraints weight = 6853.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.104384 restraints weight = 5258.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.105791 restraints weight = 4338.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2320

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= 0.146
  Angle     :  0.645   9.981   9509  Z= 0.327
  Chirality :  0.046   0.162   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  8.070 138.392    956
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.55 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.28), residues: 858
  helix:  0.49 (0.26), residues: 395
  sheet: -0.77 (0.44), residues: 126
  loop : -0.50 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.011   0.001   TYR B 108 
 PHE   0.012   0.001   PHE B 319 
 TRP   0.025   0.002   TRP B 407 
 HIS   0.009   0.001   HIS B 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 7000)
  covalent geometry    : angle       0.64451 /  0.33 ( 9509)
  hydrogen bonds       : bond        0.03998 /  2.66 (  311)
  hydrogen bonds       : angle       4.89304 /  3.41 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9277 (t0) cc_final: 0.8960 (t0)
REVERT: A  153 LEU cc_start: 0.9648 (tp) cc_final: 0.9410 (tp)
REVERT: A  157 LEU cc_start: 0.9538 (mt) cc_final: 0.9272 (mt)
REVERT: A  377 MET cc_start: 0.8690 (tmm) cc_final: 0.8260 (tmm)
REVERT: A  386 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8413 (mp0)
REVERT: A  392 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7121 (p0)
REVERT: A  398 MET cc_start: 0.8270 (tpt) cc_final: 0.7833 (tpt)
REVERT: A  420 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8111 (mp0)
REVERT: B  105 LYS cc_start: 0.9415 (tptp) cc_final: 0.9119 (tppt)
REVERT: B  108 TYR cc_start: 0.8060 (m-80) cc_final: 0.7685 (m-80)
REVERT: B  196 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8404 (mm-30)
REVERT: B  259 MET cc_start: 0.8796 (mmm) cc_final: 0.7889 (mmm)
REVERT: B  325 MET cc_start: 0.8215 (ttm) cc_final: 0.7889 (ttm)
REVERT: B  416 MET cc_start: 0.8671 (ppp) cc_final: 0.8162 (ppp)
REVERT: B  417 GLU cc_start: 0.8886 (mp0) cc_final: 0.8632 (mp0)
  outliers start: 16
  outliers final: 10
  residues processed: 140
  average time/residue: 0.0491
  time to fit residues: 9.9639
Evaluate side-chains
  134 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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  214 PHE
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 18 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 67 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  31 GLN
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.122131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.095765 restraints weight = 16741.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.099726 restraints weight = 9828.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.102586 restraints weight = 6779.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.104392 restraints weight = 5170.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.105850 restraints weight = 4296.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7000  Z= 0.144
  Angle     :  0.661  10.718   9509  Z= 0.334
  Chirality :  0.046   0.160   1039
  Planarity :  0.004   0.044   1238
  Dihedral  :  8.036 138.373    956
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.00 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.28), residues: 858
  helix:  0.43 (0.26), residues: 394
  sheet: -0.76 (0.43), residues: 127
  loop : -0.44 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.013   0.001   TYR B 185 
 PHE   0.016   0.001   PHE B 319 
 TRP   0.022   0.002   TRP B 407 
 HIS   0.008   0.001   HIS B 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 7000)
  covalent geometry    : angle       0.66086 /  0.33 ( 9509)
  hydrogen bonds       : bond        0.04006 /  2.65 (  311)
  hydrogen bonds       : angle       4.90629 /  3.42 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9272 (t0) cc_final: 0.8949 (t0)
REVERT: A  153 LEU cc_start: 0.9644 (tp) cc_final: 0.9410 (tp)
REVERT: A  157 LEU cc_start: 0.9535 (mt) cc_final: 0.9279 (mt)
REVERT: A  377 MET cc_start: 0.8708 (tmm) cc_final: 0.8264 (tmm)
REVERT: A  386 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8406 (mp0)
REVERT: A  392 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7131 (p0)
REVERT: A  398 MET cc_start: 0.8294 (tpt) cc_final: 0.7929 (tpt)
REVERT: A  420 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8224 (mp0)
REVERT: B  105 LYS cc_start: 0.9427 (tptp) cc_final: 0.9071 (tppt)
REVERT: B  108 TYR cc_start: 0.8102 (m-80) cc_final: 0.7684 (m-80)
REVERT: B  196 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8435 (mm-30)
REVERT: B  259 MET cc_start: 0.8780 (mmm) cc_final: 0.7917 (mmm)
REVERT: B  325 MET cc_start: 0.8209 (ttm) cc_final: 0.7861 (ttm)
REVERT: B  416 MET cc_start: 0.8700 (ppp) cc_final: 0.8266 (ppp)
REVERT: B  417 GLU cc_start: 0.8927 (mp0) cc_final: 0.8612 (mp0)
  outliers start: 14
  outliers final: 11
  residues processed: 140
  average time/residue: 0.0454
  time to fit residues: 9.4774
Evaluate side-chains
  140 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 58 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
B 380 ASN
** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.123828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.097879 restraints weight = 16449.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.101846 restraints weight = 9575.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.104714 restraints weight = 6599.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.106513 restraints weight = 5026.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.108042 restraints weight = 4155.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7000  Z= 0.125
  Angle     :  0.658  10.861   9509  Z= 0.331
  Chirality :  0.046   0.178   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  7.927 136.781    956
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.67 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.28), residues: 858
  helix:  0.46 (0.26), residues: 392
  sheet: -0.70 (0.43), residues: 127
  loop : -0.50 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.016   0.001   TYR B 185 
 PHE   0.016   0.001   PHE B 319 
 TRP   0.023   0.002   TRP B 407 
 HIS   0.010   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 ( 7000)
  covalent geometry    : angle       0.65813 /  0.33 ( 9509)
  hydrogen bonds       : bond        0.03876 /  2.55 (  311)
  hydrogen bonds       : angle       4.87677 /  3.41 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9284 (t0) cc_final: 0.8698 (t0)
REVERT: A  153 LEU cc_start: 0.9621 (tp) cc_final: 0.9418 (tp)
REVERT: A  157 LEU cc_start: 0.9535 (mt) cc_final: 0.9296 (mt)
REVERT: A  377 MET cc_start: 0.8701 (tmm) cc_final: 0.8233 (tmm)
REVERT: A  386 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8389 (mp0)
REVERT: A  392 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7056 (p0)
REVERT: A  398 MET cc_start: 0.8298 (tpt) cc_final: 0.7945 (tpt)
REVERT: A  420 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8178 (mp0)
REVERT: A  430 LYS cc_start: 0.9528 (pttm) cc_final: 0.9203 (pttm)
REVERT: B    1 MET cc_start: 0.6801 (mpp) cc_final: 0.6461 (pmm)
REVERT: B  105 LYS cc_start: 0.9428 (tptp) cc_final: 0.9105 (tppt)
REVERT: B  108 TYR cc_start: 0.8082 (m-80) cc_final: 0.7679 (m-80)
REVERT: B  149 MET cc_start: 0.9007 (mmm) cc_final: 0.8766 (mmm)
REVERT: B  196 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8491 (mm-30)
REVERT: B  259 MET cc_start: 0.8754 (mmm) cc_final: 0.7986 (mmm)
REVERT: B  269 MET cc_start: 0.8257 (mtp) cc_final: 0.7997 (mtp)
REVERT: B  272 PHE cc_start: 0.8646 (t80) cc_final: 0.8439 (t80)
REVERT: B  325 MET cc_start: 0.8136 (ttm) cc_final: 0.7762 (ttm)
REVERT: B  413 MET cc_start: 0.5471 (ppp) cc_final: 0.5176 (ppp)
REVERT: B  416 MET cc_start: 0.8713 (ppp) cc_final: 0.8314 (ppp)
REVERT: B  417 GLU cc_start: 0.8952 (mp0) cc_final: 0.8565 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 153
  average time/residue: 0.0558
  time to fit residues: 12.3715
Evaluate side-chains
  144 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** 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 = 0.4241 r_free = 0.4241 target = 0.122857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.096494 restraints weight = 16633.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.100451 restraints weight = 9752.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.103242 restraints weight = 6765.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.105213 restraints weight = 5191.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.106655 restraints weight = 4294.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7000  Z= 0.150
  Angle     :  0.661   9.428   9509  Z= 0.335
  Chirality :  0.046   0.168   1039
  Planarity :  0.004   0.044   1238
  Dihedral  :  7.931 136.163    956
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.17 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.28), residues: 858
  helix:  0.45 (0.26), residues: 395
  sheet: -0.68 (0.44), residues: 127
  loop : -0.46 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.023   0.001   TYR A 408 
 PHE   0.022   0.001   PHE B 319 
 TRP   0.023   0.002   TRP B 103 
 HIS   0.012   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 7000)
  covalent geometry    : angle       0.66071 /  0.34 ( 9509)
  hydrogen bonds       : bond        0.03937 /  2.60 (  311)
  hydrogen bonds       : angle       4.88169 /  3.42 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9281 (t0) cc_final: 0.8676 (t0)
REVERT: A  157 LEU cc_start: 0.9543 (mt) cc_final: 0.9317 (mt)
REVERT: A  377 MET cc_start: 0.8708 (tmm) cc_final: 0.8247 (tmm)
REVERT: A  386 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8400 (mp0)
REVERT: A  398 MET cc_start: 0.8261 (tpt) cc_final: 0.7920 (tpt)
REVERT: A  420 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8220 (mp0)
REVERT: B    1 MET cc_start: 0.6810 (mpp) cc_final: 0.6050 (pmm)
REVERT: B  108 TYR cc_start: 0.8098 (m-80) cc_final: 0.7696 (m-80)
REVERT: B  272 PHE cc_start: 0.8642 (t80) cc_final: 0.8281 (t80)
REVERT: B  325 MET cc_start: 0.8100 (ttm) cc_final: 0.7742 (ttm)
REVERT: B  380 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7537 (m-40)
REVERT: B  416 MET cc_start: 0.8877 (ppp) cc_final: 0.8464 (ppp)
REVERT: B  417 GLU cc_start: 0.9054 (mp0) cc_final: 0.8629 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 141
  average time/residue: 0.0504
  time to fit residues: 10.7341
Evaluate side-chains
  143 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  167 LEU
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   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.124698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.097601 restraints weight = 16496.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.101706 restraints weight = 9755.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.104568 restraints weight = 6753.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.106614 restraints weight = 5185.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.108067 restraints weight = 4263.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7000  Z= 0.132
  Angle     :  0.701  10.820   9509  Z= 0.354
  Chirality :  0.046   0.184   1039
  Planarity :  0.004   0.043   1238
  Dihedral  :  7.875 134.685    956
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.57 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.28), residues: 858
  helix:  0.39 (0.26), residues: 395
  sheet: -0.49 (0.45), residues: 127
  loop : -0.47 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.021   0.001   TYR A 408 
 PHE   0.019   0.001   PHE B 319 
 TRP   0.024   0.002   TRP B 103 
 HIS   0.013   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 7000)
  covalent geometry    : angle       0.70077 /  0.35 ( 9509)
  hydrogen bonds       : bond        0.03990 /  2.61 (  311)
  hydrogen bonds       : angle       4.91006 /  3.45 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9251 (t0) cc_final: 0.8638 (t0)
REVERT: A  157 LEU cc_start: 0.9527 (mt) cc_final: 0.9308 (mt)
REVERT: A  377 MET cc_start: 0.8685 (tmm) cc_final: 0.8187 (tmm)
REVERT: A  386 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8383 (mp0)
REVERT: A  398 MET cc_start: 0.8345 (tpt) cc_final: 0.8008 (tpt)
REVERT: A  430 LYS cc_start: 0.9507 (pttm) cc_final: 0.9232 (mmtm)
REVERT: B    1 MET cc_start: 0.6774 (mpp) cc_final: 0.6517 (pmm)
REVERT: B  105 LYS cc_start: 0.9392 (tptp) cc_final: 0.9104 (tppt)
REVERT: B  108 TYR cc_start: 0.8067 (m-80) cc_final: 0.7637 (m-80)
REVERT: B  168 THR cc_start: 0.9297 (p) cc_final: 0.9068 (t)
REVERT: B  196 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: B  259 MET cc_start: 0.8850 (mmm) cc_final: 0.8427 (mmm)
REVERT: B  325 MET cc_start: 0.8054 (ttm) cc_final: 0.7828 (ttm)
REVERT: B  402 LYS cc_start: 0.8784 (tppt) cc_final: 0.8547 (tppt)
REVERT: B  413 MET cc_start: 0.5097 (ppp) cc_final: 0.4291 (ppp)
  outliers start: 16
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0607
  time to fit residues: 12.3850
Evaluate side-chains
  142 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  167 LEU
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   75 MET
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 18 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0040
   chunk 55 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   overall best weight:    1.3398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 ASN ** 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 = 0.4263 r_free = 0.4263 target = 0.124464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.098044 restraints weight = 16319.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.101997 restraints weight = 9599.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.104944 restraints weight = 6654.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.106786 restraints weight = 5069.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.108303 restraints weight = 4192.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7000  Z= 0.134
  Angle     :  0.694  10.516   9509  Z= 0.348
  Chirality :  0.046   0.187   1039
  Planarity :  0.004   0.044   1238
  Dihedral  :  7.874 135.691    956
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.85 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.28), residues: 858
  helix:  0.42 (0.26), residues: 395
  sheet: -0.50 (0.45), residues: 127
  loop : -0.46 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 422 
 TYR   0.020   0.001   TYR A 408 
 PHE   0.016   0.001   PHE B 319 
 TRP   0.025   0.002   TRP B 103 
 HIS   0.012   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 7000)
  covalent geometry    : angle       0.69435 /  0.35 ( 9509)
  hydrogen bonds       : bond        0.03889 /  2.55 (  311)
  hydrogen bonds       : angle       4.87363 /  3.42 (  918)

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

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.9263 (t0) cc_final: 0.8685 (t0)
REVERT: A  157 LEU cc_start: 0.9545 (mt) cc_final: 0.9341 (mt)
REVERT: A  377 MET cc_start: 0.8677 (tmm) cc_final: 0.8183 (tmm)
REVERT: A  386 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8398 (mp0)
REVERT: A  398 MET cc_start: 0.8297 (tpt) cc_final: 0.7962 (tpt)
REVERT: A  430 LYS cc_start: 0.9522 (pttm) cc_final: 0.9227 (mmtm)
REVERT: B    1 MET cc_start: 0.6735 (mpp) cc_final: 0.6476 (pmm)
REVERT: B  105 LYS cc_start: 0.9400 (tptp) cc_final: 0.9116 (tppt)
REVERT: B  108 TYR cc_start: 0.8017 (m-80) cc_final: 0.7635 (m-80)
REVERT: B  168 THR cc_start: 0.9298 (p) cc_final: 0.9064 (t)
REVERT: B  196 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8464 (mm-30)
REVERT: B  259 MET cc_start: 0.8908 (mmm) cc_final: 0.8381 (mmm)
REVERT: B  325 MET cc_start: 0.8033 (ttm) cc_final: 0.7827 (ttm)
REVERT: B  373 MET cc_start: 0.7355 (mmm) cc_final: 0.6915 (tpp)
REVERT: B  380 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7433 (m-40)
REVERT: B  402 LYS cc_start: 0.8750 (tppt) cc_final: 0.8511 (tppt)
REVERT: B  413 MET cc_start: 0.4917 (ppp) cc_final: 0.3897 (ppp)
REVERT: B  414 ASP cc_start: 0.7912 (p0) cc_final: 0.7480 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 140
  average time/residue: 0.0618
  time to fit residues: 12.5034
Evaluate side-chains
  143 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  380 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.124552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.097926 restraints weight = 16556.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.101912 restraints weight = 9875.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.104723 restraints weight = 6871.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.106509 restraints weight = 5275.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.107972 restraints weight = 4402.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7000  Z= 0.130
  Angle     :  0.709  12.229   9509  Z= 0.352
  Chirality :  0.046   0.187   1039
  Planarity :  0.004   0.031   1238
  Dihedral  :  7.848 135.241    956
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.98 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.28), residues: 858
  helix:  0.44 (0.26), residues: 395
  sheet: -0.50 (0.45), residues: 127
  loop : -0.48 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 400 
 TYR   0.019   0.001   TYR A 408 
 PHE   0.016   0.001   PHE B 272 
 TRP   0.025   0.002   TRP B 103 
 HIS   0.011   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 7000)
  covalent geometry    : angle       0.70881 /  0.35 ( 9509)
  hydrogen bonds       : bond        0.03865 /  2.53 (  311)
  hydrogen bonds       : angle       4.86075 /  3.42 (  918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1159.54 seconds
wall clock time: 20 minutes 48.79 seconds (1248.79 seconds total)