Starting phenix.real_space_refine
on Fri Aug 22 18:07:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erl_28554/08_2025/8erl_28554.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erl_28554/08_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_28554/08_2025/8erl_28554.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erl_28554/08_2025/8erl_28554.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erl_28554/08_2025/8erl_28554.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erl_28554/08_2025/8erl_28554.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.90, per 1000 atoms: 0.29
  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: 0.52
  Conformation dependent library (CDL) restraints added in 406.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.23
  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: 1.00

  Time building geometry restraints manager: 0.73 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.910
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.540
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.110
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.013   0.001   ARG A 336 
 TYR   0.026   0.002   TYR A 124 
 PHE   0.047   0.002   PHE B  79 
 TRP   0.038   0.005   TRP A 420 
 HIS   0.028   0.003   HIS A  83 

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

*********************** 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  : 0.290 
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: 0.0772
  time to fit residues: 9.9172
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  : 0.265 
-------------------------------------------------------------------------------
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 49 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0060
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6998

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.075256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.057319 restraints weight = 30284.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.059604 restraints weight = 19792.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.061309 restraints weight = 14649.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.062527 restraints weight = 11722.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.063520 restraints weight = 9910.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6784  Z= 0.115
  Angle     :  0.685  12.315   9192  Z= 0.334
  Chirality :  0.045   0.196    980
  Planarity :  0.004   0.063   1174
  Dihedral  :  5.809  57.713    905
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.82 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.18 (0.26), residues: 822
  helix: -1.75 (0.33), residues: 168
  sheet: -1.53 (0.35), residues: 208
  loop : -2.59 (0.25), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 336 
 TYR   0.021   0.001   TYR A 124 
 PHE   0.012   0.001   PHE B  79 
 TRP   0.016   0.002   TRP A 423 
 HIS   0.005   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6776)
  covalent geometry    : angle       0.68529 ( 9176)
  SS BOND              : bond        0.00091 (    8)
  SS BOND              : angle       0.53624 (   16)
  hydrogen bonds       : bond        0.03797 (  172)
  hydrogen bonds       : angle       6.83022 (  468)

*********************** 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
  93 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8376 (mp0)
REVERT: A  407 MET cc_start: 0.8723 (ppp) cc_final: 0.8235 (ppp)
REVERT: A  409 LYS cc_start: 0.8477 (tptm) cc_final: 0.8019 (tppt)
REVERT: A  453 MET cc_start: 0.8114 (pmm) cc_final: 0.6565 (mmm)
REVERT: A  464 ILE cc_start: 0.9089 (pt) cc_final: 0.8867 (mm)
REVERT: B  181 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8251 (mmt-90)
REVERT: B  407 MET cc_start: 0.8707 (ppp) cc_final: 0.8423 (ppp)
REVERT: B  409 LYS cc_start: 0.8503 (tptm) cc_final: 0.8129 (tptt)
REVERT: B  453 MET cc_start: 0.8211 (pmm) cc_final: 0.6692 (mmm)
  outliers start: 18
  outliers final: 8
  residues processed: 89
  average time/residue: 0.0889
  time to fit residues: 10.8061
Evaluate side-chains
  82 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 58 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 80 optimal weight:    0.3980
   chunk 18 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0040
   chunk 23 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5792

-------------------------------------------------------------------------------
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**
** 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 = 0.3953 r_free = 0.3953 target = 0.074223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.056311 restraints weight = 29566.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.058604 restraints weight = 19143.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.060277 restraints weight = 14078.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.061567 restraints weight = 11205.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.062482 restraints weight = 9390.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6784  Z= 0.103
  Angle     :  0.635  12.462   9192  Z= 0.308
  Chirality :  0.044   0.150    980
  Planarity :  0.003   0.045   1174
  Dihedral  :  4.885  40.205    901
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.37 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.26), residues: 822
  helix: -1.16 (0.35), residues: 164
  sheet: -1.35 (0.37), residues: 186
  loop : -2.44 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 336 
 TYR   0.019   0.001   TYR B 124 
 PHE   0.008   0.001   PHE A 141 
 TRP   0.014   0.001   TRP A 423 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 6776)
  covalent geometry    : angle       0.63476 ( 9176)
  SS BOND              : bond        0.00088 (    8)
  SS BOND              : angle       0.51864 (   16)
  hydrogen bonds       : bond        0.03202 (  172)
  hydrogen bonds       : angle       6.29084 (  468)

*********************** 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
  96 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8322 (mmt180)
REVERT: A  272 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8369 (mp0)
REVERT: A  333 LEU cc_start: 0.8904 (mt) cc_final: 0.8695 (mt)
REVERT: A  407 MET cc_start: 0.8860 (ppp) cc_final: 0.8054 (ppp)
REVERT: A  453 MET cc_start: 0.8031 (pmm) cc_final: 0.6634 (mmm)
REVERT: B  181 ARG cc_start: 0.8563 (mmm160) cc_final: 0.8285 (mmt180)
REVERT: B  407 MET cc_start: 0.8823 (ppp) cc_final: 0.8263 (ppp)
REVERT: B  453 MET cc_start: 0.8129 (pmm) cc_final: 0.6712 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 88
  average time/residue: 0.0790
  time to fit residues: 9.8022
Evaluate side-chains
  90 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  363 GLN
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  414 SER
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  331 MET
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  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 3 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0470
   chunk 11 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    2.1682

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.066984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.049337 restraints weight = 32219.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.051359 restraints weight = 21167.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.052860 restraints weight = 15821.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.053988 restraints weight = 12810.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.054813 restraints weight = 10909.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6784  Z= 0.209
  Angle     :  0.689  11.205   9192  Z= 0.352
  Chirality :  0.045   0.147    980
  Planarity :  0.004   0.029   1174
  Dihedral  :  5.250  39.138    901
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 18.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.70 (0.26), residues: 822
  helix: -0.45 (0.38), residues: 152
  sheet: -1.34 (0.40), residues: 160
  loop : -2.50 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 293 
 TYR   0.019   0.002   TYR A 124 
 PHE   0.016   0.002   PHE B 278 
 TRP   0.020   0.002   TRP A 412 
 HIS   0.005   0.001   HIS B 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6776)
  covalent geometry    : angle       0.68882 ( 9176)
  SS BOND              : bond        0.00206 (    8)
  SS BOND              : angle       0.70342 (   16)
  hydrogen bonds       : bond        0.03296 (  172)
  hydrogen bonds       : angle       6.26987 (  468)

*********************** 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
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8615 (mp0)
REVERT: A  407 MET cc_start: 0.9028 (ppp) cc_final: 0.8278 (ppp)
REVERT: A  453 MET cc_start: 0.8101 (pmm) cc_final: 0.6763 (mmm)
REVERT: B  407 MET cc_start: 0.8935 (ppp) cc_final: 0.8301 (ppp)
  outliers start: 36
  outliers final: 27
  residues processed: 93
  average time/residue: 0.0742
  time to fit residues: 9.9750
Evaluate side-chains
  93 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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  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  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  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  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0980
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 HIS
** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3861 r_free = 0.3861 target = 0.070068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.051956 restraints weight = 31142.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.054193 restraints weight = 19890.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.055857 restraints weight = 14635.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.057086 restraints weight = 11713.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.058009 restraints weight = 9881.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6784  Z= 0.101
  Angle     :  0.641  14.478   9192  Z= 0.308
  Chirality :  0.044   0.132    980
  Planarity :  0.003   0.025   1174
  Dihedral  :  4.761  28.168    901
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 20.19 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.59 (0.27), residues: 822
  helix: -0.20 (0.39), residues: 152
  sheet: -1.66 (0.38), residues: 172
  loop : -2.34 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.016   0.001   TYR A 124 
 PHE   0.010   0.001   PHE A  44 
 TRP   0.021   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 6776)
  covalent geometry    : angle       0.64114 ( 9176)
  SS BOND              : bond        0.00082 (    8)
  SS BOND              : angle       0.57688 (   16)
  hydrogen bonds       : bond        0.02800 (  172)
  hydrogen bonds       : angle       5.86048 (  468)

*********************** 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
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.292 
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: 0.8954 (ppp) cc_final: 0.8086 (ppp)
REVERT: A  453 MET cc_start: 0.7867 (pmm) cc_final: 0.6571 (mmm)
REVERT: B  407 MET cc_start: 0.8941 (ppp) cc_final: 0.8191 (ppp)
REVERT: B  409 LYS cc_start: 0.8540 (tptm) cc_final: 0.8298 (tptp)
REVERT: B  453 MET cc_start: 0.7829 (pmm) cc_final: 0.6652 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 93
  average time/residue: 0.0851
  time to fit residues: 10.8567
Evaluate side-chains
  97 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 68 optimal weight:    0.4980
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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 469 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.066541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.048939 restraints weight = 32258.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.050952 restraints weight = 21341.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.052424 restraints weight = 16046.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.053481 restraints weight = 13046.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.054300 restraints weight = 11213.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6784  Z= 0.186
  Angle     :  0.664  12.404   9192  Z= 0.334
  Chirality :  0.044   0.137    980
  Planarity :  0.003   0.028   1174
  Dihedral  :  4.891  18.457    898
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 19.64 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.27), residues: 822
  helix:  0.04 (0.41), residues: 152
  sheet: -1.73 (0.38), residues: 170
  loop : -2.22 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.016   0.001   TYR B 124 
 PHE   0.013   0.001   PHE A 278 
 TRP   0.019   0.002   TRP A 412 
 HIS   0.004   0.001   HIS B 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6776)
  covalent geometry    : angle       0.66366 ( 9176)
  SS BOND              : bond        0.00172 (    8)
  SS BOND              : angle       0.66973 (   16)
  hydrogen bonds       : bond        0.02998 (  172)
  hydrogen bonds       : angle       6.09462 (  468)

*********************** 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
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 70
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9040 (ppp) cc_final: 0.8240 (ppp)
REVERT: A  453 MET cc_start: 0.7987 (pmm) cc_final: 0.6567 (mmm)
REVERT: B  407 MET cc_start: 0.8979 (ppp) cc_final: 0.8229 (ppp)
REVERT: B  409 LYS cc_start: 0.8603 (tptm) cc_final: 0.8352 (tptp)
  outliers start: 38
  outliers final: 29
  residues processed: 98
  average time/residue: 0.0801
  time to fit residues: 10.7046
Evaluate side-chains
  98 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  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  373 VAL
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   37 PHE
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   overall best weight:    2.3986

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.064776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.047484 restraints weight = 32460.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.049377 restraints weight = 21697.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.050795 restraints weight = 16477.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.051727 restraints weight = 13466.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.052382 restraints weight = 11707.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4020

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= 0.211
  Angle     :  0.713  11.971   9192  Z= 0.359
  Chirality :  0.044   0.127    980
  Planarity :  0.004   0.031   1174
  Dihedral  :  5.160  19.242    898
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 21.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 19.78 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.27), residues: 822
  helix:  0.12 (0.43), residues: 152
  sheet: -1.98 (0.39), residues: 144
  loop : -2.28 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.015   0.002   TYR B 124 
 PHE   0.013   0.002   PHE A 278 
 TRP   0.027   0.002   TRP A 412 
 HIS   0.004   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6776)
  covalent geometry    : angle       0.71277 ( 9176)
  SS BOND              : bond        0.00193 (    8)
  SS BOND              : angle       0.74747 (   16)
  hydrogen bonds       : bond        0.03080 (  172)
  hydrogen bonds       : angle       6.28412 (  468)

*********************** 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
  116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 70
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.9750 (mt0) cc_final: 0.9523 (mp10)
REVERT: A  407 MET cc_start: 0.9085 (ppp) cc_final: 0.8344 (ppp)
REVERT: B  342 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8686 (tptp)
REVERT: B  407 MET cc_start: 0.8992 (ppp) cc_final: 0.8237 (ppp)
REVERT: B  409 LYS cc_start: 0.8624 (tptm) cc_final: 0.8406 (tptp)
  outliers start: 46
  outliers final: 35
  residues processed: 103
  average time/residue: 0.0819
  time to fit residues: 11.5234
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  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 A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  342 LYS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 78 optimal weight:    8.9990
   chunk 73 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 60 optimal weight:    0.2980
   chunk 81 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:    0.0270
   overall best weight:    0.5838

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.067743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.050084 restraints weight = 30970.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.052206 restraints weight = 19964.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.053786 restraints weight = 14725.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.054964 restraints weight = 11747.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.055806 restraints weight = 9934.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6784  Z= 0.111
  Angle     :  0.720  15.497   9192  Z= 0.339
  Chirality :  0.046   0.143    980
  Planarity :  0.003   0.029   1174
  Dihedral  :  4.755  19.287    898
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.39 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.42 (0.28), residues: 822
  helix:  0.16 (0.42), residues: 152
  sheet: -1.96 (0.37), residues: 170
  loop : -2.13 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 336 
 TYR   0.017   0.001   TYR A 124 
 PHE   0.010   0.001   PHE B  44 
 TRP   0.029   0.002   TRP A 412 
 HIS   0.004   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6776)
  covalent geometry    : angle       0.72031 ( 9176)
  SS BOND              : bond        0.00107 (    8)
  SS BOND              : angle       0.58179 (   16)
  hydrogen bonds       : bond        0.02767 (  172)
  hydrogen bonds       : angle       5.82655 (  468)

*********************** 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
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7950 (t-100) cc_final: 0.7536 (t-100)
REVERT: A  136 GLN cc_start: 0.9772 (mt0) cc_final: 0.9487 (mt0)
REVERT: A  181 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8315 (mmt-90)
REVERT: A  407 MET cc_start: 0.9003 (ppp) cc_final: 0.8164 (ppp)
REVERT: A  453 MET cc_start: 0.7861 (pmm) cc_final: 0.6603 (mmm)
REVERT: B  116 TRP cc_start: 0.7978 (t-100) cc_final: 0.7731 (t-100)
REVERT: B  407 MET cc_start: 0.8902 (ppp) cc_final: 0.8051 (ppp)
  outliers start: 29
  outliers final: 25
  residues processed: 97
  average time/residue: 0.0712
  time to fit residues: 9.7352
Evaluate side-chains
  98 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  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  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
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  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  362 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0020
   chunk 59 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.0192

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.066727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.049389 restraints weight = 30701.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.051493 restraints weight = 19842.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.053007 restraints weight = 14620.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.054102 restraints weight = 11697.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.054952 restraints weight = 9915.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3893

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= 0.124
  Angle     :  0.720  15.251   9192  Z= 0.341
  Chirality :  0.045   0.135    980
  Planarity :  0.003   0.040   1174
  Dihedral  :  4.743  19.065    898
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 23.63 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.28), residues: 822
  helix:  0.13 (0.41), residues: 152
  sheet: -2.11 (0.36), residues: 176
  loop : -2.02 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 336 
 TYR   0.016   0.001   TYR A 124 
 PHE   0.010   0.001   PHE B  44 
 TRP   0.028   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6776)
  covalent geometry    : angle       0.72046 ( 9176)
  SS BOND              : bond        0.00123 (    8)
  SS BOND              : angle       0.58132 (   16)
  hydrogen bonds       : bond        0.02825 (  172)
  hydrogen bonds       : angle       5.84636 (  468)

*********************** 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
  102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7920 (t-100) cc_final: 0.7497 (t-100)
REVERT: A  136 GLN cc_start: 0.9764 (mt0) cc_final: 0.9523 (mp10)
REVERT: A  316 MET cc_start: 0.8882 (tmm) cc_final: 0.8648 (tmm)
REVERT: A  407 MET cc_start: 0.9003 (ppp) cc_final: 0.8088 (ppp)
REVERT: A  417 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7740 (m-80)
REVERT: B  316 MET cc_start: 0.8929 (tmm) cc_final: 0.8709 (tmm)
REVERT: B  407 MET cc_start: 0.8932 (ppp) cc_final: 0.8044 (ppp)
REVERT: B  417 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7844 (m-80)
  outliers start: 25
  outliers final: 19
  residues processed: 93
  average time/residue: 0.0760
  time to fit residues: 9.9043
Evaluate side-chains
  96 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue  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  376 SER
Chi-restraints excluded: chain B residue  379 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 13 optimal weight:    9.9990
   chunk 67 optimal weight:    0.4980
   chunk 7 optimal weight:    0.1980
   chunk 81 optimal weight:    9.9990
   chunk 61 optimal weight:    0.3980
   chunk 41 optimal weight:   10.0000
   chunk 73 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3832 r_free = 0.3832 target = 0.068689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.051051 restraints weight = 29829.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.053247 restraints weight = 19002.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.054845 restraints weight = 13881.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.055971 restraints weight = 11031.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.056869 restraints weight = 9314.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6784  Z= 0.106
  Angle     :  0.716  15.833   9192  Z= 0.332
  Chirality :  0.045   0.136    980
  Planarity :  0.003   0.038   1174
  Dihedral  :  4.516  18.527    898
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 24.18 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.34 (0.28), residues: 822
  helix:  0.16 (0.41), residues: 152
  sheet: -2.04 (0.37), residues: 170
  loop : -1.99 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 336 
 TYR   0.017   0.001   TYR B 124 
 PHE   0.008   0.001   PHE B  44 
 TRP   0.019   0.002   TRP B 412 
 HIS   0.004   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6776)
  covalent geometry    : angle       0.71644 ( 9176)
  SS BOND              : bond        0.00097 (    8)
  SS BOND              : angle       0.59166 (   16)
  hydrogen bonds       : bond        0.02871 (  172)
  hydrogen bonds       : angle       5.69542 (  468)

********************** 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
  96 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7846 (t-100) cc_final: 0.7420 (t-100)
REVERT: A  136 GLN cc_start: 0.9780 (mt0) cc_final: 0.9507 (mt0)
REVERT: A  316 MET cc_start: 0.8894 (tmm) cc_final: 0.8662 (tmm)
REVERT: A  409 LYS cc_start: 0.7749 (tptp) cc_final: 0.7465 (tppt)
REVERT: A  453 MET cc_start: 0.7789 (pmm) cc_final: 0.6598 (mmm)
REVERT: B  116 TRP cc_start: 0.7952 (t-100) cc_final: 0.7565 (t-100)
REVERT: B  316 MET cc_start: 0.8955 (tmm) cc_final: 0.8734 (tmm)
REVERT: B  407 MET cc_start: 0.8872 (ppp) cc_final: 0.7909 (ppp)
REVERT: B  417 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7689 (m-80)
REVERT: B  453 MET cc_start: 0.7334 (pmm) cc_final: 0.6450 (mmm)
  outliers start: 18
  outliers final: 15
  residues processed: 90
  average time/residue: 0.0761
  time to fit residues: 9.7195
Evaluate side-chains
  94 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
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  331 MET
Chi-restraints excluded: chain B residue  379 ILE
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 26 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0020
   chunk 69 optimal weight:    0.0980
   chunk 73 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4790

-------------------------------------------------------------------------------
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 ** 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 = 0.3836 r_free = 0.3836 target = 0.068730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.051016 restraints weight = 29651.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.053203 restraints weight = 18959.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.054775 restraints weight = 13888.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.055903 restraints weight = 11049.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.056832 restraints weight = 9347.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6784  Z= 0.108
  Angle     :  0.744  15.173   9192  Z= 0.343
  Chirality :  0.046   0.201    980
  Planarity :  0.003   0.033   1174
  Dihedral  :  4.464  18.516    898
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 24.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.28), residues: 822
  helix:  0.15 (0.42), residues: 152
  sheet: -2.01 (0.37), residues: 170
  loop : -1.94 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 336 
 TYR   0.016   0.001   TYR B 124 
 PHE   0.008   0.001   PHE B 365 
 TRP   0.021   0.002   TRP B 412 
 HIS   0.004   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6776)
  covalent geometry    : angle       0.74448 ( 9176)
  SS BOND              : bond        0.00103 (    8)
  SS BOND              : angle       0.59993 (   16)
  hydrogen bonds       : bond        0.02831 (  172)
  hydrogen bonds       : angle       5.92990 (  468)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1327.73 seconds
wall clock time: 23 minutes 48.38 seconds (1428.38 seconds total)