Starting phenix.real_space_refine
on Sat May 10 18:12:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erl_28554/05_2025/8erl_28554.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erl_28554/05_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_28554/05_2025/8erl_28554.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erl_28554/05_2025/8erl_28554.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erl_28554/05_2025/8erl_28554.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erl_28554/05_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-5687/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: 4.87, per 1000 atoms: 0.74
  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: 1.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.75
  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: 1.67

  Time building geometry restraints manager: 1.78 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:             3.330
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.070
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.690
-------------------------------------------------------------------------------
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   6784  Z= 0.258
  Angle     :  1.277  18.484   9192  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16812 (  172)
  hydrogen bonds       : angle       9.12999 (  468)
  SS BOND              : bond        0.00115 (    8)
  SS BOND              : angle       0.86224 (   16)
  covalent geometry    : bond        0.00540 ( 6776)
  covalent geometry    : angle       1.27713 ( 9176)

*********************** 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  : 0.706 
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: 0.1618
  time to fit residues: 20.7477
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  : 0.742 
-------------------------------------------------------------------------------
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 = 0.074433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.056695 restraints weight = 30070.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.058917 restraints weight = 19743.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.060560 restraints weight = 14678.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
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   6784  Z= 0.121
  Angle     :  0.684  11.807   9192  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  172)
  hydrogen bonds       : angle       6.80145 (  468)
  SS BOND              : bond        0.00108 (    8)
  SS BOND              : angle       0.53692 (   16)
  covalent geometry    : bond        0.00256 ( 6776)
  covalent geometry    : angle       0.68429 ( 9176)

*********************** 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  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8431 (mp0)
REVERT: A  407 MET cc_start: 0.8812 (ppp) cc_final: 0.8391 (ppp)
REVERT: A  453 MET cc_start: 0.8187 (pmm) cc_final: 0.6636 (mmm)
REVERT: B  181 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8280 (mmt-90)
REVERT: B  407 MET cc_start: 0.8798 (ppp) cc_final: 0.8484 (ppp)
REVERT: B  409 LYS cc_start: 0.8513 (tptm) cc_final: 0.8131 (tptt)
REVERT: B  453 MET cc_start: 0.8239 (pmm) cc_final: 0.6762 (mmm)
  outliers start: 19
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1791
  time to fit residues: 21.5865
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  : 0.686 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3801 r_free = 0.3801 target = 0.067410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.049913 restraints weight = 31953.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.051882 restraints weight = 21219.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.053375 restraints weight = 16038.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6784  Z= 0.211
  Angle     :  0.698   9.349   9192  Z= 0.360
  Chirality :  0.045   0.174    980
  Planarity :  0.004   0.040   1174
  Dihedral  :  5.442  44.967    901
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 18.41 %
    Favored  : 76.10 %
  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: -2.91 (0.26), residues: 822
  helix: -0.85 (0.37), residues: 152
  sheet: -1.35 (0.40), residues: 160
  loop : -2.61 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 412 
 HIS   0.004   0.001   HIS B  83 
 PHE   0.013   0.002   PHE A 278 
 TYR   0.020   0.002   TYR B 124 
 ARG   0.009   0.001   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (  172)
  hydrogen bonds       : angle       6.50604 (  468)
  SS BOND              : bond        0.00223 (    8)
  SS BOND              : angle       0.68473 (   16)
  covalent geometry    : bond        0.00431 ( 6776)
  covalent geometry    : angle       0.69809 ( 9176)

*********************** 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
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 73
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8638 (mp0)
REVERT: A  331 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7471 (mtp)
REVERT: A  333 LEU cc_start: 0.9059 (mt) cc_final: 0.8816 (mt)
REVERT: A  407 MET cc_start: 0.9012 (ppp) cc_final: 0.8380 (ppp)
REVERT: A  453 MET cc_start: 0.8224 (pmm) cc_final: 0.6840 (mmm)
REVERT: B  333 LEU cc_start: 0.9057 (mt) cc_final: 0.8813 (mt)
REVERT: B  407 MET cc_start: 0.8935 (ppp) cc_final: 0.8533 (ppp)
REVERT: B  409 LYS cc_start: 0.8699 (tptm) cc_final: 0.8369 (tptt)
  outliers start: 40
  outliers final: 30
  residues processed: 102
  average time/residue: 0.1599
  time to fit residues: 22.9839
Evaluate side-chains
  99 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 67
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  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  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 A residue  466 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  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  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:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 70 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 191 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 = 0.3843 r_free = 0.3843 target = 0.069201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.051186 restraints weight = 31195.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.053347 restraints weight = 20158.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.054923 restraints weight = 14897.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6784  Z= 0.114
  Angle     :  0.656  14.014   9192  Z= 0.316
  Chirality :  0.044   0.127    980
  Planarity :  0.003   0.027   1174
  Dihedral  :  4.969  36.552    901
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 19.23 %
    Favored  : 76.10 %
  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: -2.76 (0.27), residues: 822
  helix: -0.41 (0.38), residues: 152
  sheet: -1.68 (0.38), residues: 184
  loop : -2.47 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 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 B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02914 (  172)
  hydrogen bonds       : angle       6.12617 (  468)
  SS BOND              : bond        0.00105 (    8)
  SS BOND              : angle       0.60083 (   16)
  covalent geometry    : bond        0.00245 ( 6776)
  covalent geometry    : angle       0.65578 ( 9176)

*********************** 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
  110 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 76
  time to evaluate  : 0.769 
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  267 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8547 (m)
REVERT: A  272 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8549 (mp0)
REVERT: A  407 MET cc_start: 0.9028 (ppp) cc_final: 0.7951 (ppp)
REVERT: A  453 MET cc_start: 0.8055 (pmm) cc_final: 0.6762 (mmm)
REVERT: A  464 ILE cc_start: 0.9117 (pt) cc_final: 0.8894 (mm)
REVERT: B  407 MET cc_start: 0.8949 (ppp) cc_final: 0.8214 (ppp)
REVERT: B  409 LYS cc_start: 0.8613 (tptm) cc_final: 0.8353 (tptt)
  outliers start: 34
  outliers final: 24
  residues processed: 101
  average time/residue: 0.1924
  time to fit residues: 25.8339
Evaluate side-chains
  97 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  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:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 1 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 469 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.065955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.048636 restraints weight = 32253.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.050615 restraints weight = 21212.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.052022 restraints weight = 15930.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
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      :  0.004   0.032   6784  Z= 0.193
  Angle     :  0.679  10.717   9192  Z= 0.344
  Chirality :  0.044   0.135    980
  Planarity :  0.004   0.029   1174
  Dihedral  :  5.212  33.703    901
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 19.37 %
    Favored  : 75.00 %
  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: -2.73 (0.26), residues: 822
  helix: -0.33 (0.40), residues: 152
  sheet: -1.85 (0.39), residues: 144
  loop : -2.39 (0.24), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B 271 
 PHE   0.014   0.002   PHE A 278 
 TYR   0.016   0.002   TYR A 124 
 ARG   0.003   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03090 (  172)
  hydrogen bonds       : angle       6.32017 (  468)
  SS BOND              : bond        0.00180 (    8)
  SS BOND              : angle       0.71529 (   16)
  covalent geometry    : bond        0.00400 ( 6776)
  covalent geometry    : angle       0.67875 ( 9176)

*********************** 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
  110 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 69
  time to evaluate  : 0.755 
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: 0.9121 (ppp) cc_final: 0.8279 (ppp)
REVERT: A  453 MET cc_start: 0.8061 (pmm) cc_final: 0.6631 (mmm)
REVERT: B  407 MET cc_start: 0.8975 (ppp) cc_final: 0.8237 (ppp)
REVERT: B  409 LYS cc_start: 0.8643 (tptm) cc_final: 0.8371 (tptp)
  outliers start: 41
  outliers final: 31
  residues processed: 100
  average time/residue: 0.1703
  time to fit residues: 23.2872
Evaluate side-chains
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
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  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   80 VAL
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  373 VAL
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0170
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
B 469 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.068623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.051059 restraints weight = 30022.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.053221 restraints weight = 19219.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.054816 restraints weight = 14100.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6784  Z= 0.108
  Angle     :  0.686  15.413   9192  Z= 0.321
  Chirality :  0.045   0.147    980
  Planarity :  0.003   0.026   1174
  Dihedral  :  4.705  19.843    898
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 21.15 %
    Favored  : 74.73 %
  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: -2.58 (0.27), residues: 822
  helix: -0.25 (0.41), residues: 152
  sheet: -1.81 (0.38), residues: 176
  loop : -2.24 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02869 (  172)
  hydrogen bonds       : angle       6.03053 (  468)
  SS BOND              : bond        0.00086 (    8)
  SS BOND              : angle       0.62429 (   16)
  covalent geometry    : bond        0.00238 ( 6776)
  covalent geometry    : angle       0.68602 ( 9176)

*********************** 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
  110 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.756 
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  116 TRP cc_start: 0.7870 (t-100) cc_final: 0.7263 (t-100)
REVERT: A  407 MET cc_start: 0.9110 (ppp) cc_final: 0.8146 (ppp)
REVERT: A  453 MET cc_start: 0.7955 (pmm) cc_final: 0.6586 (mmm)
REVERT: B  116 TRP cc_start: 0.7811 (t-100) cc_final: 0.7231 (t-100)
REVERT: B  407 MET cc_start: 0.8988 (ppp) cc_final: 0.8092 (ppp)
REVERT: B  409 LYS cc_start: 0.8621 (tptm) cc_final: 0.8382 (tptt)
REVERT: B  453 MET cc_start: 0.7561 (pmm) cc_final: 0.6503 (mmm)
  outliers start: 30
  outliers final: 22
  residues processed: 100
  average time/residue: 0.1825
  time to fit residues: 24.5420
Evaluate side-chains
  101 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
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  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 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  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:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0470
   chunk 2 optimal weight:    0.0770
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.9840

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.067751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.050330 restraints weight = 30316.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.052466 restraints weight = 19375.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.054012 restraints weight = 14191.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6784  Z= 0.118
  Angle     :  0.674  12.801   9192  Z= 0.321
  Chirality :  0.044   0.131    980
  Planarity :  0.003   0.026   1174
  Dihedral  :  4.668  19.398    898
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 21.43 %
    Favored  : 74.04 %
  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: -2.57 (0.27), residues: 822
  helix: -0.23 (0.40), residues: 152
  sheet: -2.03 (0.38), residues: 156
  loop : -2.15 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.009   0.001   PHE A 278 
 TYR   0.016   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02658 (  172)
  hydrogen bonds       : angle       5.99821 (  468)
  SS BOND              : bond        0.00108 (    8)
  SS BOND              : angle       0.59840 (   16)
  covalent geometry    : bond        0.00256 ( 6776)
  covalent geometry    : angle       0.67392 ( 9176)

*********************** 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
  112 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.809 
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: 0.9086 (OUTLIER) cc_final: 0.8540 (mp0)
REVERT: A  407 MET cc_start: 0.9143 (ppp) cc_final: 0.8235 (ppp)
REVERT: A  453 MET cc_start: 0.7988 (pmm) cc_final: 0.6673 (mmm)
REVERT: B  407 MET cc_start: 0.9027 (ppp) cc_final: 0.8082 (ppp)
REVERT: B  409 LYS cc_start: 0.8608 (tptm) cc_final: 0.8357 (tptp)
REVERT: B  453 MET cc_start: 0.7469 (pmm) cc_final: 0.6480 (mmm)
  outliers start: 33
  outliers final: 26
  residues processed: 102
  average time/residue: 0.1760
  time to fit residues: 24.0534
Evaluate side-chains
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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  272 GLU
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 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  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:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 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 = 0.3766 r_free = 0.3766 target = 0.066040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.048804 restraints weight = 30779.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.050877 restraints weight = 19701.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.052367 restraints weight = 14485.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6784  Z= 0.146
  Angle     :  0.680  13.162   9192  Z= 0.330
  Chirality :  0.044   0.131    980
  Planarity :  0.003   0.028   1174
  Dihedral  :  4.793  17.917    898
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 22.12 %
    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: -2.50 (0.28), residues: 822
  helix: -0.18 (0.41), residues: 152
  sheet: -1.95 (0.38), residues: 144
  loop : -2.13 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B 276 
 PHE   0.013   0.001   PHE A 278 
 TYR   0.017   0.001   TYR B 124 
 ARG   0.003   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02755 (  172)
  hydrogen bonds       : angle       6.07435 (  468)
  SS BOND              : bond        0.00139 (    8)
  SS BOND              : angle       0.61920 (   16)
  covalent geometry    : bond        0.00311 ( 6776)
  covalent geometry    : angle       0.67976 ( 9176)

*********************** 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
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7905 (t-100) cc_final: 0.7493 (t-100)
REVERT: A  136 GLN cc_start: 0.9765 (mt0) cc_final: 0.9541 (mp10)
REVERT: A  407 MET cc_start: 0.9132 (ppp) cc_final: 0.8228 (ppp)
REVERT: A  453 MET cc_start: 0.7965 (pmm) cc_final: 0.6793 (mmm)
REVERT: B  116 TRP cc_start: 0.7910 (t-100) cc_final: 0.7497 (t-100)
REVERT: B  407 MET cc_start: 0.9024 (ppp) cc_final: 0.8053 (ppp)
REVERT: B  417 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7787 (m-80)
  outliers start: 32
  outliers final: 26
  residues processed: 97
  average time/residue: 0.1756
  time to fit residues: 22.9852
Evaluate side-chains
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
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  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  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 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  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  417 TYR
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:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   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:    0.6980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 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 = 0.3767 r_free = 0.3767 target = 0.066311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.049181 restraints weight = 30992.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.051261 restraints weight = 20094.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.052750 restraints weight = 14822.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6784  Z= 0.140
  Angle     :  0.694  13.200   9192  Z= 0.334
  Chirality :  0.044   0.129    980
  Planarity :  0.004   0.083   1174
  Dihedral  :  4.779  18.864    898
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.25 %
    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: -2.42 (0.28), residues: 822
  helix: -0.14 (0.42), residues: 152
  sheet: -1.77 (0.38), residues: 162
  loop : -2.10 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.016   0.001   TYR B 124 
 ARG   0.015   0.001   ARG B 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02746 (  172)
  hydrogen bonds       : angle       6.09179 (  468)
  SS BOND              : bond        0.00150 (    8)
  SS BOND              : angle       0.59361 (   16)
  covalent geometry    : bond        0.00301 ( 6776)
  covalent geometry    : angle       0.69432 ( 9176)

*********************** 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
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.691 
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: 0.7571 (t-100)
REVERT: A  136 GLN cc_start: 0.9769 (mt0) cc_final: 0.9547 (mp10)
REVERT: A  407 MET cc_start: 0.9122 (ppp) cc_final: 0.8214 (ppp)
REVERT: A  453 MET cc_start: 0.7992 (pmm) cc_final: 0.6834 (mmm)
REVERT: B  116 TRP cc_start: 0.7948 (t-100) cc_final: 0.7554 (t-100)
REVERT: B  333 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8806 (mt)
REVERT: B  407 MET cc_start: 0.8998 (ppp) cc_final: 0.8048 (ppp)
REVERT: B  409 LYS cc_start: 0.8646 (tptm) cc_final: 0.8394 (tptp)
REVERT: B  453 MET cc_start: 0.7403 (pmm) cc_final: 0.6456 (mmm)
  outliers start: 31
  outliers final: 30
  residues processed: 96
  average time/residue: 0.1650
  time to fit residues: 21.7130
Evaluate side-chains
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
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  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  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 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  333 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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**
B 176 ASN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.063285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.046326 restraints weight = 33241.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.048178 restraints weight = 22113.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.049555 restraints weight = 16736.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6784  Z= 0.244
  Angle     :  0.765  11.663   9192  Z= 0.386
  Chirality :  0.047   0.154    980
  Planarity :  0.004   0.042   1174
  Dihedral  :  5.453  18.230    898
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 23.08 %
    Favored  : 72.80 %
  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: -2.60 (0.28), residues: 822
  helix: -0.32 (0.43), residues: 152
  sheet: -1.76 (0.41), residues: 150
  loop : -2.27 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP B 412 
 HIS   0.006   0.001   HIS B 276 
 PHE   0.017   0.002   PHE B  44 
 TYR   0.016   0.002   TYR B 124 
 ARG   0.008   0.001   ARG B 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  172)
  hydrogen bonds       : angle       6.57944 (  468)
  SS BOND              : bond        0.00224 (    8)
  SS BOND              : angle       0.87556 (   16)
  covalent geometry    : bond        0.00506 ( 6776)
  covalent geometry    : angle       0.76451 ( 9176)

********************** 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
  104 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8001 (ppp) cc_final: 0.7089 (ppp)
REVERT: A  136 GLN cc_start: 0.9754 (mt0) cc_final: 0.9550 (mp10)
REVERT: A  407 MET cc_start: 0.9139 (ppp) cc_final: 0.8363 (ppp)
REVERT: B  333 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8714 (mt)
REVERT: B  407 MET cc_start: 0.8975 (ppp) cc_final: 0.8087 (ppp)
REVERT: B  409 LYS cc_start: 0.8684 (tptm) cc_final: 0.8467 (tptt)
REVERT: B  417 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7877 (m-80)
  outliers start: 30
  outliers final: 27
  residues processed: 95
  average time/residue: 0.1723
  time to fit residues: 22.4938
Evaluate side-chains
  101 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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  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  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 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  333 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.066270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.048952 restraints weight = 31499.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.051042 restraints weight = 20143.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.052566 restraints weight = 14849.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6784  Z= 0.122
  Angle     :  0.752  14.996   9192  Z= 0.355
  Chirality :  0.046   0.138    980
  Planarity :  0.003   0.033   1174
  Dihedral  :  4.961  19.502    898
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.35 %
    Favored  : 72.80 %
  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: -2.64 (0.28), residues: 822
  helix: -0.22 (0.42), residues: 152
  sheet: -2.26 (0.39), residues: 158
  loop : -2.15 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.012   0.001   PHE A  44 
 TYR   0.021   0.001   TYR A 318 
 ARG   0.011   0.001   ARG A 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02895 (  172)
  hydrogen bonds       : angle       6.17355 (  468)
  SS BOND              : bond        0.00150 (    8)
  SS BOND              : angle       0.51635 (   16)
  covalent geometry    : bond        0.00271 ( 6776)
  covalent geometry    : angle       0.75234 ( 9176)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2336.38 seconds
wall clock time: 41 minutes 55.81 seconds (2515.81 seconds total)