Starting phenix.real_space_refine
on Tue Mar 11 21:15:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erl_28554/03_2025/8erl_28554.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erl_28554/03_2025/8erl_28554.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8erl_28554/03_2025/8erl_28554.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erl_28554/03_2025/8erl_28554.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erl_28554/03_2025/8erl_28554.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erl_28554/03_2025/8erl_28554.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4208      2.51       5
     N    1130      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6600
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3300
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3300
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Chain breaks: 1
  Time building chain proxies: 4.56, per 1000 atoms: 0.69
  Number of scatterers: 6600
  At special positions: 0
  Unit cell: (76.56, 157.52, 58.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1226      8.00
     N    1130      7.00
     C    4208      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 294 " - pdb=" SG  CYS A 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 448 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 294 " - pdb=" SG  CYS B 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 308 " - pdb=" SG  CYS B 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 448 " - pdb=" SG  CYS B 468 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 942.8 milliseconds
  

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 6 sheets defined
      23.7% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 106
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.826A  pdb=" N   ALA A 120 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 149
      removed outlier: 4.393A  pdb=" N   LYS A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   MET A 145 " --> pdb=" O   PHE A 141 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ASP A 147 " --> pdb=" O   ASN A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 202 through 206
      removed outlier: 3.762A  pdb=" N   ALA A 206 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 241
      No H-bonds generated for 'chain 'A' and resid 239 through 241'
    Processing helix  chain 'A' and resid 270 through 284
    Processing helix  chain 'A' and resid 296 through 303
    Processing helix  chain 'A' and resid 451 through 455
      removed outlier: 3.964A  pdb=" N   SER A 454 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TYR A 455 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 451 through 455'
    Processing helix  chain 'B' and resid 94 through 106
    Processing helix  chain 'B' and resid 116 through 120
      removed outlier: 3.826A  pdb=" N   ALA B 120 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 149
      removed outlier: 4.393A  pdb=" N   LYS B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   MET B 145 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ASP B 147 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 175
    Processing helix  chain 'B' and resid 196 through 200
    Processing helix  chain 'B' and resid 202 through 206
      removed outlier: 3.761A  pdb=" N   ALA B 206 " --> pdb=" O   PRO B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 241
      No H-bonds generated for 'chain 'B' and resid 239 through 241'
    Processing helix  chain 'B' and resid 271 through 284
      removed outlier: 3.696A  pdb=" N   PHE B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 303
    Processing helix  chain 'B' and resid 451 through 455
      removed outlier: 3.964A  pdb=" N   SER B 454 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR B 455 " --> pdb=" O   LYS B 452 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 451 through 455'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47
      removed outlier: 4.704A  pdb=" N   VAL A 111 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS A  77 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ILE A 112 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   PHE A  79 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
      removed outlier: 9.158A  pdb=" N   VAL A 114 " --> pdb=" O   PHE A  79 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   VAL A  81 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   TYR A 161 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   THR A 183 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU A 158 " --> pdb=" O   THR A 183 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU A 185 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   GLY A 160 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   SER A 162 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 212 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASP A 186 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   VAL A 209 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   ILE A 235 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   VAL A 211 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   ASP A 234 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   LEU A 333 " --> pdb=" O   ASP A 234 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   TYR A 236 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS A 330 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398
      removed outlier: 4.239A  pdb=" N   VAL A 436 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   VAL A 445 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 381
      removed outlier: 5.731A  pdb=" N   GLU A 375 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLY A 371 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   GLU A 377 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   LEU A 369 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE A 367 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE A 365 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   TYR A 370 " --> pdb=" O   MET A 407 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   MET A 407 " --> pdb=" O   TYR A 370 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 47
      removed outlier: 4.705A  pdb=" N   VAL B 111 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS B  77 " --> pdb=" O   ASN B 110 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   ILE B 112 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   PHE B  79 " --> pdb=" O   ILE B 112 " (cutoff:3.500A)
      removed outlier: 9.156A  pdb=" N   VAL B 114 " --> pdb=" O   PHE B  79 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   VAL B  81 " --> pdb=" O   VAL B 114 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   TYR B 161 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   THR B 183 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU B 158 " --> pdb=" O   THR B 183 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU B 185 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLY B 160 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   SER B 162 " --> pdb=" O   PRO B 187 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 212 " --> pdb=" O   GLY B 184 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP B 186 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B 209 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   ILE B 235 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   VAL B 211 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      removed outlier: 5.611A  pdb=" N   ASP B 234 " --> pdb=" O   MET B 331 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   LEU B 333 " --> pdb=" O   ASP B 234 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   TYR B 236 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LYS B 330 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 398
      removed outlier: 4.238A  pdb=" N   VAL B 436 " --> pdb=" O   VAL B 445 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   VAL B 445 " --> pdb=" O   VAL B 436 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 375 through 381
      removed outlier: 5.730A  pdb=" N   GLU B 375 " --> pdb=" O   GLY B 371 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   GLY B 371 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   GLU B 377 " --> pdb=" O   LEU B 369 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   LEU B 369 " --> pdb=" O   GLU B 377 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE B 367 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE B 365 " --> pdb=" O   PHE B 381 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   TYR B 370 " --> pdb=" O   MET B 407 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   MET B 407 " --> pdb=" O   TYR B 370 " (cutoff:3.500A)

    172 hydrogen bonds defined for protein.
    468 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2071
        1.34 -     1.46: 1655
        1.46 -     1.59: 2998
        1.59 -     1.71: 0
        1.71 -     1.83: 52
  Bond restraints: 6776
  Sorted by residual:
  bond pdb=" C   VAL A  95 "
       pdb=" N   PRO A  96 "
    ideal  model  delta    sigma   weight residual
    1.336  1.361 -0.025 1.20e-02 6.94e+03 4.38e+00
  bond pdb=" C   VAL B  95 "
       pdb=" N   PRO B  96 "
    ideal  model  delta    sigma   weight residual
    1.336  1.361 -0.025 1.20e-02 6.94e+03 4.22e+00
  bond pdb=" CB  TRP A 412 "
       pdb=" CG  TRP A 412 "
    ideal  model  delta    sigma   weight residual
    1.498  1.551 -0.053 3.10e-02 1.04e+03 2.89e+00
  bond pdb=" CB  TRP B 412 "
       pdb=" CG  TRP B 412 "
    ideal  model  delta    sigma   weight residual
    1.498  1.550 -0.052 3.10e-02 1.04e+03 2.79e+00
  bond pdb=" CB  PHE B  79 "
       pdb=" CG  PHE B  79 "
    ideal  model  delta    sigma   weight residual
    1.502  1.539 -0.037 2.30e-02 1.89e+03 2.59e+00
  ... (remaining 6771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.70: 8977
        3.70 -     7.39: 159
        7.39 -    11.09: 30
       11.09 -    14.79: 4
       14.79 -    18.48: 6
  Bond angle restraints: 9176
  Sorted by residual:
  angle pdb=" CA  LEU B 102 "
        pdb=" CB  LEU B 102 "
        pdb=" CG  LEU B 102 "
      ideal   model   delta    sigma   weight residual
     116.30  134.78  -18.48 3.50e+00 8.16e-02 2.79e+01
  angle pdb=" CA  LEU A 102 "
        pdb=" CB  LEU A 102 "
        pdb=" CG  LEU A 102 "
      ideal   model   delta    sigma   weight residual
     116.30  134.76  -18.46 3.50e+00 8.16e-02 2.78e+01
  angle pdb=" CG1 ILE A 320 "
        pdb=" CB  ILE A 320 "
        pdb=" CG2 ILE A 320 "
      ideal   model   delta    sigma   weight residual
     110.70   95.02   15.68 3.00e+00 1.11e-01 2.73e+01
  angle pdb=" CG1 ILE B 320 "
        pdb=" CB  ILE B 320 "
        pdb=" CG2 ILE B 320 "
      ideal   model   delta    sigma   weight residual
     110.70   95.04   15.66 3.00e+00 1.11e-01 2.72e+01
  angle pdb=" CA  LEU B 277 "
        pdb=" CB  LEU B 277 "
        pdb=" CG  LEU B 277 "
      ideal   model   delta    sigma   weight residual
     116.30  133.94  -17.64 3.50e+00 8.16e-02 2.54e+01
  ... (remaining 9171 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3541
       17.79 -    35.57: 392
       35.57 -    53.35: 84
       53.35 -    71.14: 12
       71.14 -    88.92: 9
  Dihedral angle restraints: 4038
    sinusoidal: 1626
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" CB  CYS B 448 "
           pdb=" SG  CYS B 448 "
           pdb=" SG  CYS B 468 "
           pdb=" CB  CYS B 468 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.57   86.57     1      1.00e+01 1.00e-02 9.03e+01
  dihedral pdb=" CB  CYS A 448 "
           pdb=" SG  CYS A 448 "
           pdb=" SG  CYS A 468 "
           pdb=" CB  CYS A 468 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.53   86.53     1      1.00e+01 1.00e-02 9.02e+01
  dihedral pdb=" CB  CYS B 294 "
           pdb=" SG  CYS B 294 "
           pdb=" SG  CYS B 305 "
           pdb=" CB  CYS B 305 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.28   51.72     1      1.00e+01 1.00e-02 3.65e+01
  ... (remaining 4035 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 715
       0.062 -    0.124: 196
       0.124 -    0.186: 57
       0.186 -    0.248: 8
       0.248 -    0.311: 4
  Chirality restraints: 980
  Sorted by residual:
  chirality pdb=" CG  LEU B 333 "
            pdb=" CB  LEU B 333 "
            pdb=" CD1 LEU B 333 "
            pdb=" CD2 LEU B 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.90    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.90    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CB  ILE B 320 "
            pdb=" CA  ILE B 320 "
            pdb=" CG1 ILE B 320 "
            pdb=" CG2 ILE B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 977 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 273 "    0.014 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   ARG B 273 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG B 273 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 274 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  79 "    0.016 2.00e-02 2.50e+03   2.02e-02 7.17e+00
        pdb=" CG  PHE B  79 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  79 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  79 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  79 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  79 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  79 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  79 "   -0.016 2.00e-02 2.50e+03   2.02e-02 7.12e+00
        pdb=" CG  PHE A  79 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  79 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  79 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  79 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  79 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  79 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1885
        2.82 -     3.34: 5895
        3.34 -     3.86: 11272
        3.86 -     4.38: 12283
        4.38 -     4.90: 20881
  Nonbonded interactions: 52216
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 457 "
            pdb=" O   GLY B 459 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NE2 GLN A 457 "
            pdb=" O   GLY A 459 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   ALA B 128 "
            pdb=" OG1 THR B 131 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ALA A 128 "
            pdb=" OG1 THR A 131 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASN B  73 "
            pdb=" OG  SER B  76 "
     model   vdw
     2.337 3.040
  ... (remaining 52211 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.190
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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      :  0.005   0.053   6776  Z= 0.358
  Angle     :  1.277  18.484   9176  Z= 0.623
  Chirality :  0.065   0.311    980
  Planarity :  0.006   0.042   1174
  Dihedral  : 15.420  88.923   2466
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 23.08 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.24), residues: 822
  helix: -2.63 (0.29), residues: 156
  sheet: -1.66 (0.35), residues: 206
  loop : -3.01 (0.23), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.005   TRP A 420 
 HIS   0.028   0.003   HIS A  83 
 PHE   0.047   0.002   PHE B  79 
 TYR   0.026   0.002   TYR A 124 
 ARG   0.013   0.001   ARG A 336 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.9184 (tpm170) cc_final: 0.8844 (tpt90)
REVERT: A  272 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8345 (mp0)
REVERT: A  365 PHE cc_start: 0.8462 (m-80) cc_final: 0.7838 (m-10)
REVERT: A  453 MET cc_start: 0.8235 (pmm) cc_final: 0.6581 (mmm)
REVERT: B  409 LYS cc_start: 0.8138 (tptm) cc_final: 0.7652 (tptp)
REVERT: B  453 MET cc_start: 0.8261 (pmm) cc_final: 0.6675 (mmm)
REVERT: B  464 ILE cc_start: 0.9099 (pt) cc_final: 0.8870 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 92
  average time/residue: 0.1653
  time to fit residues: 21.0416
Evaluate side-chains
  87 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  272 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 271 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.074432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.056694 restraints weight = 30070.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.058925 restraints weight = 19723.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.060580 restraints weight = 14659.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6776  Z= 0.168
  Angle     :  0.684  11.807   9176  Z= 0.335
  Chirality :  0.045   0.199    980
  Planarity :  0.004   0.062   1174
  Dihedral  :  5.793  57.316    905
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.09 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.26), residues: 822
  helix: -1.73 (0.33), residues: 168
  sheet: -1.57 (0.35), residues: 208
  loop : -2.58 (0.25), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 423 
 HIS   0.005   0.001   HIS B  83 
 PHE   0.011   0.001   PHE A  79 
 TYR   0.021   0.001   TYR B 124 
 ARG   0.005   0.000   ARG B 336 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8434 (mp0)
REVERT: A  407 MET cc_start: 0.8815 (ppp) cc_final: 0.8394 (ppp)
REVERT: A  453 MET cc_start: 0.8190 (pmm) cc_final: 0.6644 (mmm)
REVERT: B  181 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8281 (mmt-90)
REVERT: B  407 MET cc_start: 0.8803 (ppp) cc_final: 0.8486 (ppp)
REVERT: B  409 LYS cc_start: 0.8511 (tptm) cc_final: 0.8130 (tptt)
REVERT: B  453 MET cc_start: 0.8237 (pmm) cc_final: 0.6764 (mmm)
  outliers start: 19
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1758
  time to fit residues: 21.0780
Evaluate side-chains
  83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 44 optimal weight:    0.4980
   chunk 49 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.066038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.048755 restraints weight = 31090.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.050673 restraints weight = 20570.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.052120 restraints weight = 15420.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6776  Z= 0.315
  Angle     :  0.729   8.465   9176  Z= 0.379
  Chirality :  0.046   0.165    980
  Planarity :  0.005   0.036   1174
  Dihedral  :  5.676  48.481    901
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 17.86 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.26), residues: 822
  helix: -0.95 (0.36), residues: 152
  sheet: -1.39 (0.41), residues: 160
  loop : -2.62 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 412 
 HIS   0.004   0.001   HIS B 271 
 PHE   0.018   0.002   PHE A 278 
 TYR   0.019   0.002   TYR B 124 
 ARG   0.004   0.001   ARG B  38 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 71
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8502 (m)
REVERT: A  272 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8647 (mp0)
REVERT: A  333 LEU cc_start: 0.9063 (mt) cc_final: 0.8830 (mt)
REVERT: A  407 MET cc_start: 0.9018 (ppp) cc_final: 0.8424 (ppp)
REVERT: B  333 LEU cc_start: 0.9059 (mt) cc_final: 0.8823 (mt)
REVERT: B  407 MET cc_start: 0.8941 (ppp) cc_final: 0.8531 (ppp)
REVERT: B  409 LYS cc_start: 0.8635 (tptm) cc_final: 0.8320 (tptt)
  outliers start: 45
  outliers final: 34
  residues processed: 104
  average time/residue: 0.1536
  time to fit residues: 22.5438
Evaluate side-chains
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 67
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0470
   chunk 33 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.067899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.050452 restraints weight = 30682.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.052547 restraints weight = 19631.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.054102 restraints weight = 14455.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6776  Z= 0.177
  Angle     :  0.666  12.825   9176  Z= 0.324
  Chirality :  0.044   0.126    980
  Planarity :  0.003   0.028   1174
  Dihedral  :  5.140  39.784    901
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 19.51 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.27), residues: 822
  helix: -0.52 (0.38), residues: 152
  sheet: -1.65 (0.38), residues: 182
  loop : -2.45 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.017   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 181 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 74
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8585 (mp0)
REVERT: A  407 MET cc_start: 0.9045 (ppp) cc_final: 0.7995 (ppp)
REVERT: B  407 MET cc_start: 0.8956 (ppp) cc_final: 0.8253 (ppp)
REVERT: B  409 LYS cc_start: 0.8608 (tptm) cc_final: 0.8333 (tptt)
  outliers start: 34
  outliers final: 26
  residues processed: 98
  average time/residue: 0.2265
  time to fit residues: 29.3797
Evaluate side-chains
  96 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0670
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    0.3980
   chunk 1 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    1.1720

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 HIS
B 469 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.067660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.050206 restraints weight = 30459.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.052297 restraints weight = 19536.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.053818 restraints weight = 14368.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6776  Z= 0.178
  Angle     :  0.658  13.314   9176  Z= 0.320
  Chirality :  0.044   0.137    980
  Planarity :  0.003   0.025   1174
  Dihedral  :  4.978  33.370    901
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 20.19 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.27), residues: 822
  helix: -0.31 (0.39), residues: 152
  sheet: -1.69 (0.38), residues: 174
  loop : -2.33 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.009   0.001   PHE A 278 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A  47 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9056 (ppp) cc_final: 0.8156 (ppp)
REVERT: A  453 MET cc_start: 0.7882 (pmm) cc_final: 0.6444 (mmm)
REVERT: B  407 MET cc_start: 0.9011 (ppp) cc_final: 0.8152 (ppp)
REVERT: B  409 LYS cc_start: 0.8600 (tptm) cc_final: 0.8366 (tptt)
  outliers start: 36
  outliers final: 26
  residues processed: 97
  average time/residue: 0.1700
  time to fit residues: 22.7486
Evaluate side-chains
  98 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 363 GLN
B 363 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.066988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.049645 restraints weight = 32057.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.051672 restraints weight = 20957.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.053120 restraints weight = 15682.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6776  Z= 0.209
  Angle     :  0.686  13.281   9176  Z= 0.330
  Chirality :  0.044   0.138    980
  Planarity :  0.003   0.028   1174
  Dihedral  :  4.891  19.735    898
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 18.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.05 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.27), residues: 822
  helix: -0.15 (0.41), residues: 152
  sheet: -1.73 (0.38), residues: 174
  loop : -2.23 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 412 
 HIS   0.003   0.001   HIS B 271 
 PHE   0.012   0.001   PHE A 278 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A  47 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 71
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9644 (pmm) cc_final: 0.9422 (pmm)
REVERT: A  407 MET cc_start: 0.9094 (ppp) cc_final: 0.8180 (ppp)
REVERT: A  409 LYS cc_start: 0.8635 (tptm) cc_final: 0.8390 (tptp)
REVERT: A  453 MET cc_start: 0.7765 (pmm) cc_final: 0.6444 (mmm)
REVERT: B  407 MET cc_start: 0.9021 (ppp) cc_final: 0.8108 (ppp)
REVERT: B  409 LYS cc_start: 0.8641 (tptm) cc_final: 0.8381 (tptp)
  outliers start: 42
  outliers final: 36
  residues processed: 101
  average time/residue: 0.1909
  time to fit residues: 25.8560
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    0.0170
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    0.1980
   chunk 2 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 61 optimal weight:    0.1980
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.0420

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

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN
B 362 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.067705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.050214 restraints weight = 31180.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.052325 restraints weight = 20317.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.053827 restraints weight = 15088.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6776  Z= 0.167
  Angle     :  0.676  14.720   9176  Z= 0.321
  Chirality :  0.044   0.129    980
  Planarity :  0.003   0.027   1174
  Dihedral  :  4.756  19.085    898
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.29 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.28), residues: 822
  helix: -0.06 (0.41), residues: 152
  sheet: -1.78 (0.38), residues: 174
  loop : -2.12 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A  47 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7896 (t-100) cc_final: 0.7480 (t-100)
REVERT: A  136 GLN cc_start: 0.9766 (mt0) cc_final: 0.9490 (mt0)
REVERT: A  407 MET cc_start: 0.9091 (ppp) cc_final: 0.8174 (ppp)
REVERT: A  453 MET cc_start: 0.7588 (pmm) cc_final: 0.6491 (mmm)
REVERT: B  407 MET cc_start: 0.9048 (ppp) cc_final: 0.8042 (ppp)
REVERT: B  409 LYS cc_start: 0.8582 (tptm) cc_final: 0.8337 (tptp)
REVERT: B  453 MET cc_start: 0.7470 (pmm) cc_final: 0.6460 (mmm)
  outliers start: 31
  outliers final: 31
  residues processed: 100
  average time/residue: 0.1729
  time to fit residues: 23.5348
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0370
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 70 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7864

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

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.067632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.050446 restraints weight = 30163.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.052542 restraints weight = 19472.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.054075 restraints weight = 14313.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6776  Z= 0.157
  Angle     :  0.691  15.590   9176  Z= 0.325
  Chirality :  0.044   0.129    980
  Planarity :  0.003   0.026   1174
  Dihedral  :  4.663  18.685    898
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 21.98 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.28), residues: 822
  helix: -0.06 (0.41), residues: 152
  sheet: -1.84 (0.37), residues: 176
  loop : -2.08 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.009   0.001   PHE B  44 
 TYR   0.017   0.001   TYR B 124 
 ARG   0.002   0.000   ARG A  47 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7845 (t-100) cc_final: 0.7447 (t-100)
REVERT: A  136 GLN cc_start: 0.9763 (mt0) cc_final: 0.9487 (mt0)
REVERT: A  407 MET cc_start: 0.9079 (ppp) cc_final: 0.8182 (ppp)
REVERT: A  453 MET cc_start: 0.7477 (pmm) cc_final: 0.6414 (mmm)
REVERT: B  116 TRP cc_start: 0.7845 (t-100) cc_final: 0.7442 (t-100)
REVERT: B  407 MET cc_start: 0.9015 (ppp) cc_final: 0.8052 (ppp)
REVERT: B  409 LYS cc_start: 0.8618 (tptm) cc_final: 0.8415 (tptt)
REVERT: B  453 MET cc_start: 0.7456 (pmm) cc_final: 0.6500 (mmm)
  outliers start: 33
  outliers final: 26
  residues processed: 103
  average time/residue: 0.1743
  time to fit residues: 24.5633
Evaluate side-chains
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0370
   chunk 4 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.0060

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.067298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.049909 restraints weight = 30723.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.052024 restraints weight = 19685.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.053590 restraints weight = 14425.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6776  Z= 0.168
  Angle     :  0.707  15.834   9176  Z= 0.332
  Chirality :  0.044   0.127    980
  Planarity :  0.003   0.028   1174
  Dihedral  :  4.636  18.677    898
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.63 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.28), residues: 822
  helix: -0.06 (0.41), residues: 152
  sheet: -2.25 (0.37), residues: 158
  loop : -2.09 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 412 
 HIS   0.002   0.001   HIS B  83 
 PHE   0.010   0.001   PHE B  44 
 TYR   0.017   0.001   TYR B 124 
 ARG   0.002   0.000   ARG A  47 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7848 (t-100) cc_final: 0.7436 (t-100)
REVERT: A  136 GLN cc_start: 0.9766 (mt0) cc_final: 0.9497 (mt0)
REVERT: A  407 MET cc_start: 0.9011 (ppp) cc_final: 0.8020 (ppp)
REVERT: A  417 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7835 (m-80)
REVERT: A  453 MET cc_start: 0.7465 (pmm) cc_final: 0.6519 (mmm)
REVERT: B  116 TRP cc_start: 0.7830 (t-100) cc_final: 0.7426 (t-100)
REVERT: B  407 MET cc_start: 0.8989 (ppp) cc_final: 0.7984 (ppp)
REVERT: B  409 LYS cc_start: 0.8592 (tptm) cc_final: 0.8348 (tptp)
REVERT: B  453 MET cc_start: 0.7401 (pmm) cc_final: 0.6435 (mmm)
  outliers start: 28
  outliers final: 27
  residues processed: 96
  average time/residue: 0.1802
  time to fit residues: 23.4864
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
B 176 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.064568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.047535 restraints weight = 31517.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.049482 restraints weight = 20705.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.050905 restraints weight = 15465.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6776  Z= 0.257
  Angle     :  0.743  14.567   9176  Z= 0.358
  Chirality :  0.045   0.137    980
  Planarity :  0.004   0.029   1174
  Dihedral  :  4.990  18.666    898
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 23.08 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.28), residues: 822
  helix: -0.13 (0.43), residues: 152
  sheet: -1.94 (0.37), residues: 162
  loop : -2.16 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 412 
 HIS   0.004   0.001   HIS B 276 
 PHE   0.015   0.002   PHE B  44 
 TYR   0.016   0.001   TYR B 124 
 ARG   0.004   0.001   ARG B 293 

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 73
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7959 (t-100) cc_final: 0.7533 (t-100)
REVERT: A  136 GLN cc_start: 0.9776 (mt0) cc_final: 0.9558 (mp10)
REVERT: A  407 MET cc_start: 0.9025 (ppp) cc_final: 0.8128 (ppp)
REVERT: A  417 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7839 (m-80)
REVERT: B  116 TRP cc_start: 0.7975 (t-100) cc_final: 0.7546 (t-100)
REVERT: B  407 MET cc_start: 0.8997 (ppp) cc_final: 0.8035 (ppp)
  outliers start: 33
  outliers final: 29
  residues processed: 96
  average time/residue: 0.1917
  time to fit residues: 24.7963
Evaluate side-chains
  102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0870
   chunk 73 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.067608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.050240 restraints weight = 31466.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.052353 restraints weight = 20422.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.053895 restraints weight = 15141.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6776  Z= 0.164
  Angle     :  0.735  16.170   9176  Z= 0.340
  Chirality :  0.045   0.127    980
  Planarity :  0.003   0.029   1174
  Dihedral  :  4.665  18.766    898
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 24.31 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.28), residues: 822
  helix: -0.04 (0.42), residues: 152
  sheet: -1.98 (0.38), residues: 170
  loop : -2.08 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.011   0.001   PHE B  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2290.75 seconds
wall clock time: 40 minutes 40.38 seconds (2440.38 seconds total)