Starting phenix.real_space_refine
on Mon Sep 23 23:34:47 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/09_2024/7vq5_32086.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/09_2024/7vq5_32086.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/09_2024/7vq5_32086.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/09_2024/7vq5_32086.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/09_2024/7vq5_32086.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/09_2024/7vq5_32086.cif"
  }
  resolution = 3.1
  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=   0.005
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      34      5.16       5
     C    4074      2.51       5
     N    1052      2.21       5
     O    1155      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6315
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3153
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3153
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'LMR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.07, per 1000 atoms: 0.64
  Number of scatterers: 6315
  At special positions: 0
  Unit cell: (83.148, 90.246, 112.554, 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      34     16.00
     O    1155      8.00
     N    1052      7.00
     C    4074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.69
  Conformation dependent library (CDL) restraints added in 831.8 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
      removed outlier: 3.609A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 3.942A  pdb=" N   GLY A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 66
    Processing helix  chain 'A' and resid 69 through 102
      removed outlier: 3.819A  pdb=" N   THR A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 125
      removed outlier: 4.587A  pdb=" N   ILE A 108 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 3.716A  pdb=" N   ILE A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 183
    Processing helix  chain 'A' and resid 187 through 214
    Processing helix  chain 'A' and resid 223 through 241
      removed outlier: 5.024A  pdb=" N   ARG A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   TYR A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP A 241 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 3.855A  pdb=" N   GLU A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A 251 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 256 " --> pdb=" O   TYR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 293
      removed outlier: 3.541A  pdb=" N   TYR A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 3.819A  pdb=" N   LYS A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 330
    Processing helix  chain 'A' and resid 335 through 357
      removed outlier: 4.400A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER A 344 " --> pdb=" O   HIS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 363
      removed outlier: 4.332A  pdb=" N   ASP A 362 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 359 through 363'
    Processing helix  chain 'A' and resid 364 through 398
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 3.518A  pdb=" N   ILE B   7 " --> pdb=" O   LYS B   3 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B  10 " --> pdb=" O   GLU B   6 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 39
      removed outlier: 3.543A  pdb=" N   ILE B  23 " --> pdb=" O   PRO B  19 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLY B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 66
      removed outlier: 3.523A  pdb=" N   VAL B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 102
      removed outlier: 3.893A  pdb=" N   THR B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   HIS B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG B  99 " --> pdb=" O   HIS B  95 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 125
      removed outlier: 4.046A  pdb=" N   VAL B 111 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 133
      removed outlier: 4.026A  pdb=" N   THR B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS B 133 " --> pdb=" O   TRP B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 149
      removed outlier: 3.549A  pdb=" N   ILE B 138 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE B 145 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 183
      removed outlier: 3.715A  pdb=" N   MET B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASP B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU B 163 " --> pdb=" O   MET B 159 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 171 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLY B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   CYS B 176 " --> pdb=" O   GLY B 172 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE B 179 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 215
      removed outlier: 3.812A  pdb=" N   ASP B 201 " --> pdb=" O   ALA B 197 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE B 206 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASP B 212 " --> pdb=" O   GLN B 208 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B 215 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 241
      removed outlier: 4.884A  pdb=" N   ARG B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 240 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP B 241 " --> pdb=" O   LYS B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 256
      removed outlier: 3.657A  pdb=" N   GLU B 246 " --> pdb=" O   SER B 242 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLU B 254 " --> pdb=" O   ALA B 250 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   TRP B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU B 256 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 291
      removed outlier: 3.512A  pdb=" N   GLN B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.665A  pdb=" N   LYS B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 330
      removed outlier: 3.881A  pdb=" N   GLU B 323 " --> pdb=" O   ASN B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 357
      removed outlier: 4.307A  pdb=" N   ILE B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN B 343 " --> pdb=" O   ILE B 339 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   SER B 344 " --> pdb=" O   HIS B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 363
      removed outlier: 4.277A  pdb=" N   ASP B 362 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL B 363 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 359 through 363'
    Processing helix  chain 'B' and resid 364 through 396
      removed outlier: 4.667A  pdb=" N   SER B 370 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B 387 " --> pdb=" O   ASN B 383 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1446 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: 1.60

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1586
        1.33 -     1.45: 1178
        1.45 -     1.57: 3618
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" C1  LMR B 601 "
       pdb=" C2  LMR B 601 "
    ideal  model  delta    sigma   weight residual
    1.543  1.495  0.048 2.00e-02 2.50e+03 5.70e+00
  bond pdb=" C   ILE B  53 "
       pdb=" O   ILE B  53 "
    ideal  model  delta    sigma   weight residual
    1.236  1.212  0.025 1.19e-02 7.06e+03 4.27e+00
  bond pdb=" C   ILE A  53 "
       pdb=" O   ILE A  53 "
    ideal  model  delta    sigma   weight residual
    1.236  1.212  0.024 1.19e-02 7.06e+03 4.09e+00
  bond pdb=" CB  THR A 168 "
       pdb=" CG2 THR A 168 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.09e+00
  bond pdb=" C3  LMR B 601 "
       pdb=" C4  LMR B 601 "
    ideal  model  delta    sigma   weight residual
    1.538  1.503  0.035 2.00e-02 2.50e+03 3.07e+00
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8187
        1.47 -     2.94: 453
        2.94 -     4.42: 47
        4.42 -     5.89: 7
        5.89 -     7.36: 8
  Bond angle restraints: 8702
  Sorted by residual:
  angle pdb=" C   GLU A 307 "
        pdb=" N   THR A 308 "
        pdb=" CA  THR A 308 "
      ideal   model   delta    sigma   weight residual
     119.83  116.03    3.80 1.11e+00 8.12e-01 1.17e+01
  angle pdb=" N   TYR A  39 "
        pdb=" CA  TYR A  39 "
        pdb=" C   TYR A  39 "
      ideal   model   delta    sigma   weight residual
     111.36  114.89   -3.53 1.09e+00 8.42e-01 1.05e+01
  angle pdb=" C   GLU B   6 "
        pdb=" N   ILE B   7 "
        pdb=" CA  ILE B   7 "
      ideal   model   delta    sigma   weight residual
     122.35  118.75    3.60 1.18e+00 7.18e-01 9.31e+00
  angle pdb=" C   THR A 132 "
        pdb=" N   LYS A 133 "
        pdb=" CA  LYS A 133 "
      ideal   model   delta    sigma   weight residual
     122.42  118.05    4.37 1.55e+00 4.16e-01 7.96e+00
  angle pdb=" C   GLY B 260 "
        pdb=" N   GLN B 261 "
        pdb=" CA  GLN B 261 "
      ideal   model   delta    sigma   weight residual
     124.31  128.72   -4.41 1.67e+00 3.59e-01 6.98e+00
  ... (remaining 8697 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 3384
       17.98 -    35.95: 405
       35.95 -    53.93: 68
       53.93 -    71.91: 5
       71.91 -    89.89: 1
  Dihedral angle restraints: 3863
    sinusoidal: 1539
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CA  PRO A 299 "
           pdb=" C   PRO A 299 "
           pdb=" N   VAL A 300 "
           pdb=" CA  VAL A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.85  -23.15     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  TRP A 255 "
           pdb=" C   TRP A 255 "
           pdb=" N   GLU A 256 "
           pdb=" CA  GLU A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.40  -18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  LEU A 233 "
           pdb=" C   LEU A 233 "
           pdb=" N   GLU A 234 "
           pdb=" CA  GLU A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.11  -16.89     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 3860 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 783
       0.054 -    0.108: 197
       0.108 -    0.163: 15
       0.163 -    0.217: 1
       0.217 -    0.271: 1
  Chirality restraints: 997
  Sorted by residual:
  chirality pdb=" CA  TYR A  39 "
            pdb=" N   TYR A  39 "
            pdb=" C   TYR A  39 "
            pdb=" CB  TYR A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  TYR A  40 "
            pdb=" N   TYR A  40 "
            pdb=" C   TYR A  40 "
            pdb=" CB  TYR A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CA  PRO B 258 "
            pdb=" N   PRO B 258 "
            pdb=" C   PRO B 258 "
            pdb=" CB  PRO B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.97e-01
  ... (remaining 994 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 257 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO B 258 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 258 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 258 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  18 "    0.028 5.00e-02 4.00e+02   4.17e-02 2.79e+00
        pdb=" N   PRO A  19 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A  19 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  19 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 200 "   -0.013 2.00e-02 2.50e+03   1.02e-02 1.81e+00
        pdb=" CG  PHE B 200 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 200 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 200 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 200 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 200 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 200 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 97
        2.67 -     3.23: 6464
        3.23 -     3.78: 9458
        3.78 -     4.34: 12794
        4.34 -     4.90: 21454
  Nonbonded interactions: 50267
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 236 "
            pdb=" OD1 ASP B 286 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" OE1 GLU B 246 "
            pdb=" NH2 ARG B 279 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" O   ILE B 369 "
            pdb=" OG1 THR B 373 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NH2 ARG B  80 "
            pdb=" O4A LMR B 601 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" NZ  LYS B 133 "
            pdb=" OE1 GLU B 254 "
     model   vdw
     2.247 3.120
  ... (remaining 50262 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' and resid 1 through 405)
}

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 individual isotropic
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:             0.290
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.170
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
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      :  0.009   0.067   6442  Z= 0.599
  Angle     :  0.766   7.360   8702  Z= 0.446
  Chirality :  0.046   0.271    997
  Planarity :  0.004   0.043   1092
  Dihedral  : 14.845  89.886   2359
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 12.36 %
    Favored  : 87.50 %
  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: -3.56 (0.25), residues: 792
  helix: -1.79 (0.17), residues: 664
  sheet:  None (None), residues: 0
  loop : -4.38 (0.42), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 255 
 HIS   0.006   0.002   HIS B 259 
 PHE   0.023   0.002   PHE B 200 
 TYR   0.015   0.002   TYR A 271 
 ARG   0.005   0.001   ARG B 312 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.6907 (t-90)
REVERT: A  228 LYS cc_start: 0.7209 (pttt) cc_final: 0.6790 (pttt)
REVERT: A  368 MET cc_start: 0.7920 (mmm) cc_final: 0.7591 (mmm)
REVERT: A  372 MET cc_start: 0.8479 (mmm) cc_final: 0.8169 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2053
  time to fit residues: 25.1216
Evaluate side-chains
  77 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 266 HIS
A 293 ASN
A 340 HIS
A 383 ASN
B 266 HIS
B 289 ASN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6442  Z= 0.184
  Angle     :  0.506   5.599   8702  Z= 0.282
  Chirality :  0.038   0.143    997
  Planarity :  0.004   0.035   1092
  Dihedral  :  4.795  53.246    867
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.65 %
    Favored  : 84.91 %
  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: -0.40 (0.29), residues: 792
  helix:  0.41 (0.19), residues: 674
  sheet:  None (None), residues: 0
  loop : -3.94 (0.47), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 255 
 HIS   0.004   0.001   HIS B 193 
 PHE   0.015   0.001   PHE A 206 
 TYR   0.017   0.002   TYR A  39 
 ARG   0.003   0.000   ARG A 400 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.6732 (t-90)
REVERT: A  228 LYS cc_start: 0.7107 (pttt) cc_final: 0.6734 (pttt)
REVERT: A  331 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7518 (mpp)
REVERT: A  372 MET cc_start: 0.8579 (mmm) cc_final: 0.8197 (mmm)
REVERT: B   10 GLU cc_start: 0.8247 (tp30) cc_final: 0.8040 (tp30)
REVERT: B   17 GLU cc_start: 0.7675 (tt0) cc_final: 0.7426 (tt0)
REVERT: B  209 ASP cc_start: 0.7476 (m-30) cc_final: 0.7224 (m-30)
REVERT: B  228 LYS cc_start: 0.7685 (mttm) cc_final: 0.7093 (pttt)
REVERT: B  312 ARG cc_start: 0.8853 (tpp-160) cc_final: 0.8583 (tpp80)
  outliers start: 10
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1628
  time to fit residues: 22.4620
Evaluate side-chains
  92 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain B residue  331 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 72 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0030
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.1196

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

Flipped N/Q/H residues before XYZ refinement:
A 289 ASN
A 393 HIS
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6442  Z= 0.185
  Angle     :  0.469   5.179   8702  Z= 0.256
  Chirality :  0.037   0.146    997
  Planarity :  0.003   0.037   1092
  Dihedral  :  4.558  54.633    867
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.24 %
    Favored  : 82.33 %
  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:  0.94 (0.30), residues: 792
  helix:  1.29 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -3.50 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 255 
 HIS   0.007   0.001   HIS A 393 
 PHE   0.015   0.001   PHE A 206 
 TYR   0.017   0.002   TYR A  39 
 ARG   0.004   0.000   ARG B 229 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.6770 (t-90)
REVERT: A  228 LYS cc_start: 0.7075 (pttt) cc_final: 0.6738 (pttt)
REVERT: A  331 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7633 (mpp)
REVERT: A  372 MET cc_start: 0.8499 (mmm) cc_final: 0.8108 (mmm)
REVERT: B  209 ASP cc_start: 0.7477 (m-30) cc_final: 0.7220 (m-30)
REVERT: B  228 LYS cc_start: 0.7506 (mttm) cc_final: 0.6998 (pttt)
  outliers start: 10
  outliers final: 5
  residues processed: 103
  average time/residue: 0.1765
  time to fit residues: 24.4927
Evaluate side-chains
  94 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0570
   chunk 20 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.1702

-------------------------------------------------------------------------------
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: 0.8015
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6442  Z= 0.178
  Angle     :  0.460   5.312   8702  Z= 0.251
  Chirality :  0.037   0.145    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.472  56.050    867
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.39 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.53 (0.31), residues: 792
  helix:  1.71 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -3.31 (0.51), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 255 
 HIS   0.004   0.001   HIS A 193 
 PHE   0.013   0.001   PHE B 264 
 TYR   0.014   0.001   TYR A  39 
 ARG   0.004   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.6830 (t-90)
REVERT: A  228 LYS cc_start: 0.7057 (pttt) cc_final: 0.6737 (pttt)
REVERT: A  246 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: A  331 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.7701 (mpp)
REVERT: A  368 MET cc_start: 0.7907 (mmm) cc_final: 0.7380 (mmm)
REVERT: A  372 MET cc_start: 0.8481 (mmm) cc_final: 0.7962 (mmm)
REVERT: B  154 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6529 (mmm160)
REVERT: B  209 ASP cc_start: 0.7449 (m-30) cc_final: 0.7182 (m-30)
REVERT: B  228 LYS cc_start: 0.7581 (mttm) cc_final: 0.7083 (pttt)
REVERT: B  368 MET cc_start: 0.7625 (tpp) cc_final: 0.7252 (tpp)
  outliers start: 13
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1690
  time to fit residues: 23.2765
Evaluate side-chains
  97 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0770
   chunk 69 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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: 0.7964
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6442  Z= 0.141
  Angle     :  0.430   5.036   8702  Z= 0.233
  Chirality :  0.036   0.145    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.294  55.830    867
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.68 %
    Favored  : 79.74 %
  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:  1.99 (0.30), residues: 792
  helix:  1.99 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -3.10 (0.51), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.014   0.001   PHE B 264 
 TYR   0.012   0.001   TYR B  50 
 ARG   0.005   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.6660 (t-90)
REVERT: A  153 PHE cc_start: 0.7851 (m-80) cc_final: 0.7597 (m-10)
REVERT: A  228 LYS cc_start: 0.7056 (pttt) cc_final: 0.6757 (pttt)
REVERT: A  246 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7474 (mt-10)
REVERT: A  331 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.7568 (mpp)
REVERT: A  372 MET cc_start: 0.8396 (mmm) cc_final: 0.8071 (mmm)
REVERT: B  154 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6581 (mmm160)
REVERT: B  209 ASP cc_start: 0.7435 (m-30) cc_final: 0.7137 (m-30)
REVERT: B  228 LYS cc_start: 0.7508 (mttm) cc_final: 0.7084 (pttt)
  outliers start: 11
  outliers final: 7
  residues processed: 107
  average time/residue: 0.1555
  time to fit residues: 22.9397
Evaluate side-chains
  103 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    0.0970
   chunk 15 optimal weight:    0.0470
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0030
   chunk 40 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.4286

-------------------------------------------------------------------------------
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: 0.7929
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6442  Z= 0.129
  Angle     :  0.427   6.140   8702  Z= 0.228
  Chirality :  0.036   0.146    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.162  55.798    867
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.54 %
    Favored  : 78.74 %
  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:  2.27 (0.30), residues: 792
  helix:  2.17 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -2.87 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 129 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.011   0.001   PHE A 206 
 TYR   0.013   0.001   TYR A  41 
 ARG   0.004   0.000   ARG A 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.652 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.6649 (t-90)
REVERT: A  228 LYS cc_start: 0.6979 (pttt) cc_final: 0.6704 (pttt)
REVERT: A  246 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7392 (mt-10)
REVERT: A  254 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6631 (tt0)
REVERT: A  331 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7485 (mpp)
REVERT: A  368 MET cc_start: 0.7776 (mmm) cc_final: 0.7255 (mmm)
REVERT: A  372 MET cc_start: 0.8279 (mmm) cc_final: 0.7743 (mmm)
REVERT: B  154 ARG cc_start: 0.7044 (mtp85) cc_final: 0.6564 (mmm160)
REVERT: B  228 LYS cc_start: 0.7452 (mttm) cc_final: 0.7083 (pttt)
  outliers start: 12
  outliers final: 5
  residues processed: 109
  average time/residue: 0.1505
  time to fit residues: 22.8274
Evaluate side-chains
  107 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 340 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6442  Z= 0.161
  Angle     :  0.446   6.039   8702  Z= 0.237
  Chirality :  0.036   0.144    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.210  56.822    867
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 20.40 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.30), residues: 792
  helix:  2.27 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -2.80 (0.51), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.015   0.001   PHE A 206 
 TYR   0.017   0.002   TYR A  41 
 ARG   0.003   0.000   ARG A 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.6721 (t-90)
REVERT: A  153 PHE cc_start: 0.7827 (m-80) cc_final: 0.7579 (m-80)
REVERT: A  228 LYS cc_start: 0.7090 (pttt) cc_final: 0.6792 (pttt)
REVERT: A  246 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7431 (mt-10)
REVERT: A  254 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6675 (tt0)
REVERT: A  331 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7564 (mpp)
REVERT: A  368 MET cc_start: 0.7799 (mmm) cc_final: 0.7187 (mmm)
REVERT: A  372 MET cc_start: 0.8276 (mmm) cc_final: 0.7801 (mmm)
REVERT: A  405 MET cc_start: 0.4859 (mmm) cc_final: 0.4646 (mmt)
REVERT: B  154 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6607 (mmm160)
REVERT: B  228 LYS cc_start: 0.7406 (mttm) cc_final: 0.7020 (pttt)
REVERT: B  368 MET cc_start: 0.7618 (tpt) cc_final: 0.7205 (tpt)
REVERT: B  405 MET cc_start: 0.4934 (mmt) cc_final: 0.4449 (mmp)
  outliers start: 13
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1801
  time to fit residues: 25.6120
Evaluate side-chains
  105 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0770
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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: 0.7955
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6442  Z= 0.151
  Angle     :  0.443   5.696   8702  Z= 0.236
  Chirality :  0.036   0.145    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.181  57.066    867
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 21.26 %
    Favored  : 77.16 %
  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 (0.30), residues: 792
  helix:  2.31 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.83 (0.51), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.016   0.001   PHE B 153 
 TYR   0.019   0.001   TYR B  41 
 ARG   0.002   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.6772 (t-90)
REVERT: A  153 PHE cc_start: 0.7757 (m-80) cc_final: 0.7523 (m-80)
REVERT: A  228 LYS cc_start: 0.7108 (pttt) cc_final: 0.6821 (pttt)
REVERT: A  246 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: A  254 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6645 (tt0)
REVERT: A  331 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.7666 (mpp)
REVERT: A  368 MET cc_start: 0.7754 (mmm) cc_final: 0.7162 (mmm)
REVERT: A  372 MET cc_start: 0.8263 (mmm) cc_final: 0.7779 (mmm)
REVERT: A  405 MET cc_start: 0.5023 (mmm) cc_final: 0.4758 (mmt)
REVERT: B  154 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6615 (mmm160)
REVERT: B  209 ASP cc_start: 0.7315 (m-30) cc_final: 0.7035 (m-30)
REVERT: B  228 LYS cc_start: 0.7366 (mttm) cc_final: 0.7010 (pttt)
REVERT: B  368 MET cc_start: 0.7513 (tpt) cc_final: 0.7165 (tpt)
  outliers start: 11
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1281
  time to fit residues: 17.8349
Evaluate side-chains
  102 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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: 0.8003
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6442  Z= 0.190
  Angle     :  0.459   5.390   8702  Z= 0.246
  Chirality :  0.037   0.142    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.356  58.878    867
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.26 %
    Favored  : 77.01 %
  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:  2.55 (0.30), residues: 792
  helix:  2.32 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -2.53 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A 193 
 PHE   0.018   0.001   PHE A 206 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.002   0.000   ARG B 312 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.6909 (t-90)
REVERT: A  153 PHE cc_start: 0.7785 (m-80) cc_final: 0.7571 (m-80)
REVERT: A  228 LYS cc_start: 0.7207 (pttt) cc_final: 0.6890 (pttt)
REVERT: A  246 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7395 (mt-10)
REVERT: A  254 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6715 (tt0)
REVERT: A  331 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.7766 (mpp)
REVERT: A  368 MET cc_start: 0.7821 (mmm) cc_final: 0.7178 (mmm)
REVERT: A  372 MET cc_start: 0.8314 (mmm) cc_final: 0.7791 (mmm)
REVERT: A  405 MET cc_start: 0.5040 (mmm) cc_final: 0.4773 (mmt)
REVERT: B   95 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7174 (t70)
REVERT: B  154 ARG cc_start: 0.7110 (mtp85) cc_final: 0.6644 (mmm160)
REVERT: B  228 LYS cc_start: 0.7425 (mttm) cc_final: 0.7031 (pttt)
REVERT: B  368 MET cc_start: 0.7561 (tpt) cc_final: 0.7065 (tpt)
  outliers start: 12
  outliers final: 8
  residues processed: 98
  average time/residue: 0.1797
  time to fit residues: 24.5689
Evaluate side-chains
  104 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 340 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6442  Z= 0.202
  Angle     :  0.472   6.155   8702  Z= 0.251
  Chirality :  0.037   0.142    997
  Planarity :  0.003   0.038   1092
  Dihedral  :  4.392  59.898    867
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.69 %
    Favored  : 77.30 %
  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:  2.56 (0.30), residues: 792
  helix:  2.32 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -2.46 (0.55), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A 193 
 PHE   0.018   0.001   PHE A 206 
 TYR   0.015   0.002   TYR B  41 
 ARG   0.001   0.000   ARG A  80 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7014 (t-90)
REVERT: A  153 PHE cc_start: 0.7790 (m-80) cc_final: 0.7583 (m-80)
REVERT: A  228 LYS cc_start: 0.7039 (pttt) cc_final: 0.6773 (pttt)
REVERT: A  246 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7408 (mt-10)
REVERT: A  254 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6718 (tt0)
REVERT: A  331 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7808 (mpp)
REVERT: A  368 MET cc_start: 0.7831 (mmm) cc_final: 0.7195 (mmm)
REVERT: A  372 MET cc_start: 0.8349 (mmm) cc_final: 0.7791 (mmm)
REVERT: A  405 MET cc_start: 0.5157 (mmm) cc_final: 0.4845 (mmt)
REVERT: B   95 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7170 (t70)
REVERT: B  154 ARG cc_start: 0.7123 (mtp85) cc_final: 0.6647 (mmm160)
REVERT: B  228 LYS cc_start: 0.7432 (mttm) cc_final: 0.7038 (pttt)
REVERT: B  368 MET cc_start: 0.7612 (tpt) cc_final: 0.7256 (tpt)
REVERT: B  404 LYS cc_start: 0.7519 (tptt) cc_final: 0.7305 (tptt)
REVERT: B  405 MET cc_start: 0.4450 (mmp) cc_final: 0.3653 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1556
  time to fit residues: 21.2086
Evaluate side-chains
  102 residues out of total 696 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.144485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.106769 restraints weight = 8282.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.25
r_work: 0.3224 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6442  Z= 0.151
  Angle     :  0.467  12.599   8702  Z= 0.243
  Chirality :  0.036   0.145    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.296  59.740    867
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 21.84 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.30), residues: 792
  helix:  2.39 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.67 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 129 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.017   0.001   PHE A 206 
 TYR   0.015   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 235 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1480.24 seconds
wall clock time: 35 minutes 25.45 seconds (2125.45 seconds total)