Starting phenix.real_space_refine
on Tue Sep 24 03:00:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/09_2024/8erl_28554.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/09_2024/8erl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/09_2024/8erl_28554.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/09_2024/8erl_28554.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/09_2024/8erl_28554.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/09_2024/8erl_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-5461/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: 4.92, per 1000 atoms: 0.75
  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 999.4 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: 0.74
  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: 1.95

  Time building geometry restraints manager: 1.85 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: 0.00
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:             1.570
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.280
  Find NCS groups from input model:        0.170
  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:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.080
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   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: 0.1680
  time to fit residues: 21.3953
Evaluate side-chains
  87 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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 fitting.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8498 (mp0)
REVERT: A  407 MET cc_start: 0.8860 (ppp) cc_final: 0.8399 (ppp)
REVERT: A  453 MET cc_start: 0.8100 (pmm) cc_final: 0.6570 (mmm)
REVERT: B  181 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8359 (mmt-90)
REVERT: B  407 MET cc_start: 0.8832 (ppp) cc_final: 0.8478 (ppp)
REVERT: B  409 LYS cc_start: 0.8373 (tptm) cc_final: 0.8038 (tptt)
REVERT: B  453 MET cc_start: 0.8117 (pmm) cc_final: 0.6641 (mmm)
  outliers start: 19
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1885
  time to fit residues: 22.5042
Evaluate side-chains
  83 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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 41 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0980
   chunk 50 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5782

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6776  Z= 0.144
  Angle     :  0.637  13.025   9176  Z= 0.308
  Chirality :  0.044   0.136    980
  Planarity :  0.003   0.042   1174
  Dihedral  :  4.880  40.223    901
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.96 %
    Favored  : 77.88 %
  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: -2.81 (0.26), residues: 822
  helix: -1.14 (0.35), residues: 164
  sheet: -1.34 (0.37), residues: 186
  loop : -2.43 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 423 
 HIS   0.003   0.001   HIS B 123 
 PHE   0.006   0.001   PHE A 300 
 TYR   0.019   0.001   TYR B 124 
 ARG   0.004   0.000   ARG B  38 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8646 (mmm160) cc_final: 0.8358 (mmt180)
REVERT: A  272 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8522 (mp0)
REVERT: A  407 MET cc_start: 0.8909 (ppp) cc_final: 0.8065 (ppp)
REVERT: A  453 MET cc_start: 0.8009 (pmm) cc_final: 0.6638 (mmm)
REVERT: B  181 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8351 (mmt180)
REVERT: B  407 MET cc_start: 0.8886 (ppp) cc_final: 0.8317 (ppp)
REVERT: B  409 LYS cc_start: 0.8380 (tptm) cc_final: 0.8076 (tppt)
REVERT: B  453 MET cc_start: 0.8088 (pmm) cc_final: 0.6715 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 90
  average time/residue: 0.1689
  time to fit residues: 21.2325
Evaluate side-chains
  91 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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  272 GLU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  363 GLN
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    2.7986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6776  Z= 0.326
  Angle     :  0.715   9.431   9176  Z= 0.370
  Chirality :  0.046   0.153    980
  Planarity :  0.004   0.033   1174
  Dihedral  :  5.423  40.346    901
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 20.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 17.45 %
    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: -2.70 (0.26), residues: 822
  helix: -0.36 (0.39), residues: 152
  sheet: -1.39 (0.40), residues: 160
  loop : -2.51 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 412 
 HIS   0.005   0.001   HIS B 271 
 PHE   0.018   0.002   PHE A 278 
 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
  110 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 67
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9026 (ppp) cc_final: 0.8247 (ppp)
REVERT: B  142 MET cc_start: 0.9767 (mmm) cc_final: 0.9546 (ppp)
REVERT: B  407 MET cc_start: 0.8941 (ppp) cc_final: 0.8275 (ppp)
  outliers start: 43
  outliers final: 30
  residues processed: 99
  average time/residue: 0.1617
  time to fit residues: 22.7630
Evaluate side-chains
  92 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 62
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   chunk 32 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   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 469 HIS
B 469 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6776  Z= 0.270
  Angle     :  0.693  11.524   9176  Z= 0.351
  Chirality :  0.044   0.149    980
  Planarity :  0.004   0.031   1174
  Dihedral  :  5.310  31.828    901
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 19.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 19.23 %
    Favored  : 75.41 %
  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: -0.07 (0.41), residues: 152
  sheet: -1.55 (0.38), residues: 174
  loop : -2.36 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 412 
 HIS   0.004   0.001   HIS B 271 
 PHE   0.015   0.002   PHE A  44 
 TYR   0.016   0.002   TYR A 124 
 ARG   0.003   0.001   ARG B 273 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 71
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9100 (ppp) cc_final: 0.8318 (ppp)
REVERT: B  407 MET cc_start: 0.9013 (ppp) cc_final: 0.8241 (ppp)
  outliers start: 39
  outliers final: 28
  residues processed: 100
  average time/residue: 0.2051
  time to fit residues: 28.5005
Evaluate side-chains
  92 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 64
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  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 26 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0030
   chunk 36 optimal weight:    0.1980
   chunk 6 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.9994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6776  Z= 0.176
  Angle     :  0.691  14.274   9176  Z= 0.334
  Chirality :  0.044   0.135    980
  Planarity :  0.003   0.029   1174
  Dihedral  :  4.934  19.617    898
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 20.74 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.27), residues: 822
  helix:  0.06 (0.41), residues: 152
  sheet: -1.79 (0.38), residues: 174
  loop : -2.20 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.016   0.001   TYR A 124 
 ARG   0.002   0.000   ARG B 181 

*********************** 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
  107 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 71
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9713 (pmm) cc_final: 0.9510 (pmm)
REVERT: A  407 MET cc_start: 0.9166 (ppp) cc_final: 0.8041 (ppp)
REVERT: B  407 MET cc_start: 0.9017 (ppp) cc_final: 0.8085 (ppp)
  outliers start: 36
  outliers final: 32
  residues processed: 96
  average time/residue: 0.1737
  time to fit residues: 22.8385
Evaluate side-chains
  100 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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  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 B residue   37 PHE
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  414 SER
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6776  Z= 0.195
  Angle     :  0.688  14.316   9176  Z= 0.333
  Chirality :  0.044   0.143    980
  Planarity :  0.003   0.029   1174
  Dihedral  :  4.883  19.115    898
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 20.74 %
    Favored  : 73.76 %
  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: -2.39 (0.28), residues: 822
  helix:  0.15 (0.42), residues: 152
  sheet: -1.89 (0.37), residues: 174
  loop : -2.12 (0.27), 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   0.011   0.001   PHE A  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 72
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7969 (t-100) cc_final: 0.7556 (t-100)
REVERT: A  136 GLN cc_start: 0.9788 (mt0) cc_final: 0.9549 (mp10)
REVERT: A  407 MET cc_start: 0.9105 (ppp) cc_final: 0.8178 (ppp)
REVERT: B  116 TRP cc_start: 0.8041 (t-100) cc_final: 0.7606 (t-100)
REVERT: B  407 MET cc_start: 0.9040 (ppp) cc_final: 0.8034 (ppp)
  outliers start: 40
  outliers final: 35
  residues processed: 99
  average time/residue: 0.1583
  time to fit residues: 21.8979
Evaluate side-chains
  105 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 70
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   94 TRP
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0770
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.3544

-------------------------------------------------------------------------------
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
B 362 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6776  Z= 0.193
  Angle     :  0.698  13.408   9176  Z= 0.335
  Chirality :  0.044   0.126    980
  Planarity :  0.003   0.030   1174
  Dihedral  :  4.838  18.621    898
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 21.29 %
    Favored  : 73.21 %
  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: -2.44 (0.28), residues: 822
  helix:  0.20 (0.42), residues: 152
  sheet: -2.14 (0.39), residues: 156
  loop : -2.11 (0.26), residues: 514

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   0.011   0.001   PHE A  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.002   0.000   ARG A  47 

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

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 72
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7976 (t-100) cc_final: 0.7577 (t-100)
REVERT: A  136 GLN cc_start: 0.9798 (mt0) cc_final: 0.9564 (mp10)
REVERT: A  407 MET cc_start: 0.9108 (ppp) cc_final: 0.8215 (ppp)
REVERT: B  116 TRP cc_start: 0.8034 (t-100) cc_final: 0.7615 (t-100)
REVERT: B  136 GLN cc_start: 0.9787 (mt0) cc_final: 0.9546 (mp10)
  outliers start: 40
  outliers final: 34
  residues processed: 101
  average time/residue: 0.1585
  time to fit residues: 22.7470
Evaluate side-chains
  106 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 72
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  194 TYR
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  362 ASN
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  398 THR
Chi-restraints excluded: chain B residue  405 LEU
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 75 optimal weight:    0.7980
   chunk 44 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0770
   chunk 48 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.5938

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6776  Z= 0.158
  Angle     :  0.732  15.948   9176  Z= 0.340
  Chirality :  0.045   0.131    980
  Planarity :  0.003   0.052   1174
  Dihedral  :  4.709  19.400    898
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.21 %
    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: -2.39 (0.28), residues: 822
  helix:  0.08 (0.41), residues: 152
  sheet: -2.01 (0.37), residues: 176
  loop : -2.04 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.010   0.001   PHE A  44 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.012   0.000   ARG A 336 

*********************** 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
  107 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7943 (t-100) cc_final: 0.7547 (t-100)
REVERT: A  136 GLN cc_start: 0.9801 (mt0) cc_final: 0.9538 (mt0)
REVERT: A  407 MET cc_start: 0.9073 (ppp) cc_final: 0.8154 (ppp)
REVERT: A  453 MET cc_start: 0.7322 (pmm) cc_final: 0.6389 (mmm)
REVERT: B  116 TRP cc_start: 0.7987 (t-100) cc_final: 0.7562 (t-100)
REVERT: B  136 GLN cc_start: 0.9789 (mt0) cc_final: 0.9525 (mt0)
REVERT: B  417 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7944 (m-80)
REVERT: B  453 MET cc_start: 0.7205 (pmm) cc_final: 0.6272 (mmm)
  outliers start: 28
  outliers final: 24
  residues processed: 99
  average time/residue: 0.1530
  time to fit residues: 21.4662
Evaluate side-chains
  102 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  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  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  417 TYR
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0270
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.8640

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6776  Z= 0.167
  Angle     :  0.731  15.866   9176  Z= 0.341
  Chirality :  0.045   0.142    980
  Planarity :  0.003   0.045   1174
  Dihedral  :  4.677  19.075    898
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.63 %
    Favored  : 73.08 %
  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: -2.39 (0.28), residues: 822
  helix:  0.09 (0.41), residues: 152
  sheet: -2.09 (0.36), residues: 176
  loop : -2.00 (0.27), residues: 494

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 A  44 
 TYR   0.016   0.001   TYR A 124 
 ARG   0.010   0.000   ARG A 336 

********************** 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
  102 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 TRP cc_start: 0.7960 (t-100) cc_final: 0.7555 (t-100)
REVERT: A  136 GLN cc_start: 0.9803 (mt0) cc_final: 0.9543 (mt0)
REVERT: A  316 MET cc_start: 0.8803 (tmm) cc_final: 0.8596 (tmm)
REVERT: A  407 MET cc_start: 0.9074 (ppp) cc_final: 0.8138 (ppp)
REVERT: A  417 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7871 (m-80)
REVERT: A  453 MET cc_start: 0.7296 (pmm) cc_final: 0.6401 (mmm)
REVERT: B   90 MET cc_start: 0.8060 (ppp) cc_final: 0.7106 (ppp)
REVERT: B  116 TRP cc_start: 0.8005 (t-100) cc_final: 0.7577 (t-100)
REVERT: B  136 GLN cc_start: 0.9790 (mt0) cc_final: 0.9549 (mp10)
REVERT: B  316 MET cc_start: 0.8858 (tmm) cc_final: 0.8652 (tmm)
REVERT: B  407 MET cc_start: 0.8981 (ppp) cc_final: 0.7991 (ppp)
REVERT: B  453 MET cc_start: 0.7190 (pmm) cc_final: 0.6284 (mmm)
  outliers start: 24
  outliers final: 22
  residues processed: 93
  average time/residue: 0.1617
  time to fit residues: 20.9657
Evaluate side-chains
  100 residues out of total 728 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  166 HIS
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  417 TYR
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  161 TYR
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  405 LEU
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 59 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 3 optimal weight:    9.9990
   chunk 47 optimal weight:    0.0980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.066663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.049429 restraints weight = 30208.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.051426 restraints weight = 19946.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.052878 restraints weight = 14926.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.4115

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= 0.181
  Angle     :  0.737  15.589   9176  Z= 0.346
  Chirality :  0.045   0.134    980
  Planarity :  0.003   0.038   1174
  Dihedral  :  4.684  18.457    898
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.63 %
    Favored  : 73.21 %
  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: -2.38 (0.28), residues: 822
  helix:  0.10 (0.42), residues: 152
  sheet: -2.06 (0.36), residues: 176
  loop : -2.00 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 412 
 HIS   0.003   0.001   HIS A  83 
 PHE   0.011   0.001   PHE A  44 
 TYR   0.016   0.001   TYR A 124 
 ARG   0.009   0.000   ARG A 336 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1533.02 seconds
wall clock time: 28 minutes 48.99 seconds (1728.99 seconds total)