Starting phenix.real_space_refine
on Tue Feb 11 21:48:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erl_28554/02_2025/8erl_28554.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erl_28554/02_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_28554/02_2025/8erl_28554.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erl_28554/02_2025/8erl_28554.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erl_28554/02_2025/8erl_28554.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erl_28554/02_2025/8erl_28554.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4208      2.51       5
     N    1130      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6600
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3300
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3300
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Chain breaks: 1
  Time building chain proxies: 4.47, per 1000 atoms: 0.68
  Number of scatterers: 6600
  At special positions: 0
  Unit cell: (76.56, 157.52, 58.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1226      8.00
     N    1130      7.00
     C    4208      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.55
  Conformation dependent library (CDL) restraints added in 922.6 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 6 sheets defined
      23.7% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  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: 1.74

  Time building geometry restraints manager: 1.82 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1885
        2.82 -     3.34: 5895
        3.34 -     3.86: 11272
        3.86 -     4.38: 12283
        4.38 -     4.90: 20881
  Nonbonded interactions: 52216
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 457 "
            pdb=" O   GLY B 459 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NE2 GLN A 457 "
            pdb=" O   GLY A 459 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   ALA B 128 "
            pdb=" OG1 THR B 131 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ALA A 128 "
            pdb=" OG1 THR A 131 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASN B  73 "
            pdb=" OG  SER B  76 "
     model   vdw
     2.337 3.040
  ... (remaining 52211 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.600
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6776  Z= 0.358
  Angle     :  1.277  18.484   9176  Z= 0.623
  Chirality :  0.065   0.311    980
  Planarity :  0.006   0.042   1174
  Dihedral  : 15.420  88.923   2466
  Min Nonbonded Distance : 2.296

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

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

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

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.776 
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: 0.1751
  time to fit residues: 22.3324
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  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  272 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.074433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.056695 restraints weight = 30070.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.058917 restraints weight = 19743.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.060560 restraints weight = 14678.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1440

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

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

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

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

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8431 (mp0)
REVERT: A  407 MET cc_start: 0.8812 (ppp) cc_final: 0.8391 (ppp)
REVERT: A  453 MET cc_start: 0.8187 (pmm) cc_final: 0.6636 (mmm)
REVERT: B  181 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8280 (mmt-90)
REVERT: B  407 MET cc_start: 0.8798 (ppp) cc_final: 0.8484 (ppp)
REVERT: B  409 LYS cc_start: 0.8513 (tptm) cc_final: 0.8131 (tptt)
REVERT: B  453 MET cc_start: 0.8239 (pmm) cc_final: 0.6762 (mmm)
  outliers start: 19
  outliers final: 10
  residues processed: 88
  average time/residue: 0.2124
  time to fit residues: 25.2492
Evaluate side-chains
  83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.5586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.069551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.051836 restraints weight = 30803.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.053897 restraints weight = 19962.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.055504 restraints weight = 14907.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6776  Z= 0.212
  Angle     :  0.657  10.890   9176  Z= 0.331
  Chirality :  0.044   0.147    980
  Planarity :  0.004   0.038   1174
  Dihedral  :  5.118  41.937    901
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 18.13 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.26), residues: 822
  helix: -0.80 (0.37), residues: 152
  sheet: -1.53 (0.37), residues: 192
  loop : -2.50 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 412 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.010   0.001   PHE A 278 
 TYR   0.019   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 293 

*********************** 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
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 71
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8455 (m)
REVERT: A  272 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8572 (mp0)
REVERT: A  331 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7472 (mtp)
REVERT: A  333 LEU cc_start: 0.8970 (mt) cc_final: 0.8712 (mt)
REVERT: A  407 MET cc_start: 0.8990 (ppp) cc_final: 0.8102 (ppp)
REVERT: A  453 MET cc_start: 0.8138 (pmm) cc_final: 0.6775 (mmm)
REVERT: A  464 ILE cc_start: 0.9124 (pt) cc_final: 0.8898 (mm)
REVERT: B  333 LEU cc_start: 0.9006 (mt) cc_final: 0.8758 (mt)
REVERT: B  407 MET cc_start: 0.8917 (ppp) cc_final: 0.8356 (ppp)
REVERT: B  409 LYS cc_start: 0.8591 (tptm) cc_final: 0.8270 (tptt)
  outliers start: 35
  outliers final: 23
  residues processed: 94
  average time/residue: 0.1364
  time to fit residues: 18.8711
Evaluate side-chains
  94 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  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 A residue  436 VAL
Chi-restraints excluded: chain A residue  466 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  363 GLN
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
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    2.5588

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.064711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.047333 restraints weight = 33330.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.049286 restraints weight = 22122.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.050687 restraints weight = 16712.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6776  Z= 0.312
  Angle     :  0.717   9.657   9176  Z= 0.369
  Chirality :  0.046   0.178    980
  Planarity :  0.004   0.033   1174
  Dihedral  :  5.567  38.365    901
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 22.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 17.31 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.26), residues: 822
  helix: -0.19 (0.40), residues: 152
  sheet: -1.79 (0.41), residues: 140
  loop : -2.48 (0.24), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 412 
 HIS   0.005   0.001   HIS B 271 
 PHE   0.017   0.002   PHE A  44 
 TYR   0.017   0.002   TYR A 124 
 ARG   0.004   0.001   ARG B 293 

*********************** 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
  114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 66
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 TRP cc_start: 0.7907 (t-100) cc_final: 0.7413 (t-100)
REVERT: A  407 MET cc_start: 0.9031 (ppp) cc_final: 0.8294 (ppp)
REVERT: A  409 LYS cc_start: 0.8660 (tptm) cc_final: 0.8401 (tptt)
REVERT: B  407 MET cc_start: 0.8956 (ppp) cc_final: 0.8322 (ppp)
REVERT: B  409 LYS cc_start: 0.8643 (tptm) cc_final: 0.8374 (tptp)
  outliers start: 48
  outliers final: 36
  residues processed: 101
  average time/residue: 0.1589
  time to fit residues: 22.8708
Evaluate side-chains
  102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 66
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  210 ASP
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  396 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 43 optimal weight:    0.2980
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 110 ASN
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 GLN
A 469 HIS
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 469 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.066810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.049048 restraints weight = 31745.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.051112 restraints weight = 20626.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.052631 restraints weight = 15380.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6776  Z= 0.182
  Angle     :  0.674  13.342   9176  Z= 0.327
  Chirality :  0.044   0.146    980
  Planarity :  0.003   0.030   1174
  Dihedral  :  5.093  28.545    901
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 18.82 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.27), residues: 822
  helix: -0.01 (0.41), residues: 152
  sheet: -1.80 (0.38), residues: 174
  loop : -2.27 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 412 
 HIS   0.003   0.001   HIS B 271 
 PHE   0.012   0.001   PHE A  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.005   0.000   ARG B 336 

*********************** 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
  115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 77
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.9761 (mt0) cc_final: 0.9479 (mt0)
REVERT: A  407 MET cc_start: 0.9105 (ppp) cc_final: 0.8289 (ppp)
REVERT: A  409 LYS cc_start: 0.8570 (tptm) cc_final: 0.8366 (tptt)
REVERT: B  336 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7276 (ptt180)
REVERT: B  407 MET cc_start: 0.8940 (ppp) cc_final: 0.8162 (ppp)
REVERT: B  409 LYS cc_start: 0.8619 (tptm) cc_final: 0.8326 (tptp)
  outliers start: 38
  outliers final: 28
  residues processed: 105
  average time/residue: 0.1803
  time to fit residues: 25.6198
Evaluate side-chains
  104 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  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 39 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.8786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.064799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.047503 restraints weight = 31327.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.049491 restraints weight = 20417.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.050889 restraints weight = 15151.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6776  Z= 0.236
  Angle     :  0.696  13.047   9176  Z= 0.342
  Chirality :  0.045   0.143    980
  Planarity :  0.003   0.031   1174
  Dihedral  :  5.068  19.266    898
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 20.74 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.27), residues: 822
  helix:  0.18 (0.42), residues: 152
  sheet: -1.93 (0.40), residues: 144
  loop : -2.28 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B 271 
 PHE   0.012   0.001   PHE A 278 
 TYR   0.028   0.002   TYR A 360 
 ARG   0.003   0.000   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 73
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.9755 (mt0) cc_final: 0.9517 (mp10)
REVERT: A  407 MET cc_start: 0.9117 (ppp) cc_final: 0.8203 (ppp)
REVERT: A  409 LYS cc_start: 0.8588 (tptm) cc_final: 0.8370 (tptp)
REVERT: B  336 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6884 (ptt180)
REVERT: B  407 MET cc_start: 0.9013 (ppp) cc_final: 0.8147 (ppp)
REVERT: B  409 LYS cc_start: 0.8640 (tptm) cc_final: 0.8422 (tptt)
  outliers start: 38
  outliers final: 32
  residues processed: 100
  average time/residue: 0.1949
  time to fit residues: 26.1253
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  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  336 ARG
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 60 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 ASN
B 363 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.065196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.047735 restraints weight = 31055.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.049787 restraints weight = 19967.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.051277 restraints weight = 14736.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6776  Z= 0.200
  Angle     :  0.692  13.696   9176  Z= 0.334
  Chirality :  0.044   0.134    980
  Planarity :  0.003   0.030   1174
  Dihedral  :  4.961  19.182    898
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 17.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 21.29 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.28), residues: 822
  helix:  0.27 (0.42), residues: 152
  sheet: -2.10 (0.40), residues: 156
  loop : -2.22 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.023   0.002   TYR A 360 
 ARG   0.002   0.000   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 74
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.9754 (mt0) cc_final: 0.9483 (mt0)
REVERT: A  407 MET cc_start: 0.9123 (ppp) cc_final: 0.8206 (ppp)
REVERT: A  409 LYS cc_start: 0.8571 (tptm) cc_final: 0.8351 (tptp)
REVERT: B  116 TRP cc_start: 0.7973 (t-100) cc_final: 0.7592 (t-100)
REVERT: B  136 GLN cc_start: 0.9742 (mt0) cc_final: 0.9464 (mt0)
REVERT: B  407 MET cc_start: 0.9050 (ppp) cc_final: 0.8162 (ppp)
REVERT: B  409 LYS cc_start: 0.8638 (tptm) cc_final: 0.8421 (tptt)
  outliers start: 38
  outliers final: 32
  residues processed: 103
  average time/residue: 0.1735
  time to fit residues: 24.3996
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 73
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  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  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  336 ARG
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.3588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.065328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.047992 restraints weight = 30885.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.050002 restraints weight = 20055.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.051463 restraints weight = 14915.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6776  Z= 0.192
  Angle     :  0.712  14.202   9176  Z= 0.340
  Chirality :  0.045   0.181    980
  Planarity :  0.003   0.030   1174
  Dihedral  :  4.898  19.125    898
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 22.12 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.28), residues: 822
  helix:  0.24 (0.42), residues: 152
  sheet: -1.95 (0.39), residues: 174
  loop : -2.17 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.010   0.001   PHE B  44 
 TYR   0.020   0.001   TYR A 360 
 ARG   0.002   0.000   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.9756 (mt0) cc_final: 0.9521 (mp10)
REVERT: A  407 MET cc_start: 0.9123 (ppp) cc_final: 0.8194 (ppp)
REVERT: A  409 LYS cc_start: 0.8574 (tptm) cc_final: 0.8343 (tptp)
REVERT: B  116 TRP cc_start: 0.7977 (t-100) cc_final: 0.7611 (t-100)
REVERT: B  136 GLN cc_start: 0.9751 (mt0) cc_final: 0.9479 (mt0)
REVERT: B  272 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8442 (mp0)
REVERT: B  407 MET cc_start: 0.9002 (ppp) cc_final: 0.7997 (ppp)
REVERT: B  409 LYS cc_start: 0.8645 (tptm) cc_final: 0.8390 (tptp)
  outliers start: 36
  outliers final: 35
  residues processed: 104
  average time/residue: 0.1806
  time to fit residues: 25.6119
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 TYR
Chi-restraints excluded: chain A residue  363 GLN
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  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  272 GLU
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  373 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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**
** 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 = 0.3738 r_free = 0.3738 target = 0.065190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.047649 restraints weight = 32622.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.049666 restraints weight = 21211.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.051090 restraints weight = 15862.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6776  Z= 0.227
  Angle     :  0.722  13.830   9176  Z= 0.348
  Chirality :  0.045   0.196    980
  Planarity :  0.003   0.031   1174
  Dihedral  :  4.954  19.597    898
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 19.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 22.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.28), residues: 822
  helix:  0.19 (0.42), residues: 152
  sheet: -2.04 (0.41), residues: 144
  loop : -2.26 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 412 
 HIS   0.003   0.001   HIS B 276 
 PHE   0.011   0.001   PHE A 278 
 TYR   0.019   0.001   TYR A 360 
 ARG   0.003   0.000   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.9755 (mt0) cc_final: 0.9534 (mp10)
REVERT: A  407 MET cc_start: 0.9112 (ppp) cc_final: 0.8197 (ppp)
REVERT: A  409 LYS cc_start: 0.8591 (tptm) cc_final: 0.8363 (tptp)
REVERT: B  116 TRP cc_start: 0.7996 (t-100) cc_final: 0.7630 (t-100)
REVERT: B  136 GLN cc_start: 0.9743 (mt0) cc_final: 0.9521 (mp10)
REVERT: B  272 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8474 (mp0)
REVERT: B  407 MET cc_start: 0.8972 (ppp) cc_final: 0.7951 (ppp)
REVERT: B  409 LYS cc_start: 0.8660 (tptm) cc_final: 0.8400 (tptp)
REVERT: B  417 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7923 (m-80)
  outliers start: 34
  outliers final: 29
  residues processed: 101
  average time/residue: 0.1855
  time to fit residues: 25.5389
Evaluate side-chains
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 TYR
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   37 PHE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  272 GLU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
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**
B 110 ASN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.064165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.047046 restraints weight = 33167.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.048972 restraints weight = 21733.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.050356 restraints weight = 16387.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6776  Z= 0.278
  Angle     :  0.777  13.291   9176  Z= 0.376
  Chirality :  0.046   0.197    980
  Planarity :  0.004   0.032   1174
  Dihedral  :  5.278  19.759    898
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 22.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 23.21 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.28), residues: 822
  helix:  0.08 (0.43), residues: 152
  sheet: -2.13 (0.41), residues: 144
  loop : -2.33 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 412 
 HIS   0.005   0.001   HIS B 276 
 PHE   0.012   0.002   PHE A  44 
 TYR   0.020   0.002   TYR A 360 
 ARG   0.004   0.001   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 73
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8198 (ppp) cc_final: 0.7331 (ppp)
REVERT: A  407 MET cc_start: 0.9108 (ppp) cc_final: 0.8208 (ppp)
REVERT: B   90 MET cc_start: 0.8128 (ppp) cc_final: 0.7216 (ppp)
REVERT: B  116 TRP cc_start: 0.8137 (t-100) cc_final: 0.7799 (t-100)
REVERT: B  136 GLN cc_start: 0.9748 (mt0) cc_final: 0.9547 (mp10)
REVERT: B  272 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8492 (mp0)
REVERT: B  407 MET cc_start: 0.9014 (ppp) cc_final: 0.7987 (ppp)
REVERT: B  409 LYS cc_start: 0.8658 (tptm) cc_final: 0.8436 (tptt)
REVERT: B  417 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7947 (m-80)
  outliers start: 33
  outliers final: 30
  residues processed: 98
  average time/residue: 0.1854
  time to fit residues: 24.4731
Evaluate side-chains
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 TYR
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 A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  272 GLU
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  398 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0060
   chunk 17 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.7400

-------------------------------------------------------------------------------
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**
** 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 = 0.3769 r_free = 0.3769 target = 0.066453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.048647 restraints weight = 31729.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.050715 restraints weight = 20450.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.052233 restraints weight = 15259.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6776  Z= 0.171
  Angle     :  0.758  15.205   9176  Z= 0.354
  Chirality :  0.045   0.179    980
  Planarity :  0.003   0.031   1174
  Dihedral  :  4.872  19.742    898
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.18 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.28), residues: 822
  helix:  0.13 (0.42), residues: 152
  sheet: -2.06 (0.38), residues: 176
  loop : -2.20 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 412 
 HIS   0.005   0.001   HIS A  83 
 PHE   0.009   0.001   PHE A  44 
 TYR   0.019   0.001   TYR A 318 
 ARG   0.002   0.000   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2236.13 seconds
wall clock time: 41 minutes 20.02 seconds (2480.02 seconds total)