Starting phenix.real_space_refine
on Thu Nov 14 19:27:12 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8d_34543/11_2024/8h8d_34543.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8d_34543/11_2024/8h8d_34543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8d_34543/11_2024/8h8d_34543.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8d_34543/11_2024/8h8d_34543.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8d_34543/11_2024/8h8d_34543.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8d_34543/11_2024/8h8d_34543.cif"
  }
  resolution = 4.26
  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=  -0.002 sd=   0.054
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      39      5.16       5
     C    4587      2.51       5
     N    1179      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 7054
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2366
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 12, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2337
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 12, 'TRANS': 270}
    Chain: "C"
      Number of atoms: 2351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2351
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 12, 'TRANS': 272}
  Time building chain proxies: 5.05, per 1000 atoms: 0.72
  Number of scatterers: 7054
  At special positions: 0
  Unit cell: (80.438, 80.438, 140.223, 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      39     16.00
     O    1249      8.00
     N    1179      7.00
     C    4587      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 129 " - pdb=" SG  CYS C 151 " 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: 1.69
  Conformation dependent library (CDL) restraints added in 990.0 milliseconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1652

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      34.5% alpha, 28.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 99
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.655A  pdb=" N   PHE A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   CYS A 225 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 254
      No H-bonds generated for 'chain 'A' and resid 252 through 254'
    Processing helix  chain 'A' and resid 304 through 343
    Processing helix  chain 'B' and resid 61 through 97
      removed outlier: 3.689A  pdb=" N   MET B  79 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 215
      removed outlier: 3.716A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 213 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 223
    Processing helix  chain 'B' and resid 304 through 342
      removed outlier: 3.789A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 68
    Processing helix  chain 'C' and resid 69 through 99
      removed outlier: 4.051A  pdb=" N   TYR C  75 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 215
    Processing helix  chain 'C' and resid 217 through 229
      removed outlier: 3.521A  pdb=" N   CYS C 225 " --> pdb=" O   PHE C 221 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER C 227 " --> pdb=" O   GLN C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 344
      removed outlier: 3.575A  pdb=" N   ALA C 310 " --> pdb=" O   TRP C 306 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP C 324 " --> pdb=" O   PHE C 320 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 107
      removed outlier: 3.944A  pdb=" N   GLN A 295 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ASP A 299 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   HIS A 190 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   LEU A 126 " --> pdb=" O   HIS A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 107
      removed outlier: 3.944A  pdb=" N   GLN A 295 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ASP A 299 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG A 261 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155
      removed outlier: 3.716A  pdb=" N   ILE A 172 " --> pdb=" O   GLN A 154 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU A 119 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 201 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 108
      removed outlier: 8.167A  pdb=" N   TYR B 293 " --> pdb=" O   MET B 244 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   LEU B 246 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN B 295 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   ASP B 299 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 159
      removed outlier: 3.506A  pdb=" N   GLN B 154 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE B 156 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA B 170 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE B 117 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP B 202 " --> pdb=" O   TYR B 120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 131
      removed outlier: 3.640A  pdb=" N   HIS B 190 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   GLN B 188 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS B 129 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   PHE B 186 " --> pdb=" O   CYS B 129 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   PHE B 238 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE B 284 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 108
      removed outlier: 14.129A  pdb=" N   TYR C 293 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 10.813A  pdb=" N   MET C 244 " --> pdb=" O   TYR C 293 " (cutoff:3.500A)
      removed outlier: 9.958A  pdb=" N   GLN C 295 " --> pdb=" O   MET C 244 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   LEU C 246 " --> pdb=" O   GLN C 295 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   ILE C 297 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS C 248 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   THR C 240 " --> pdb=" O   PHE C 284 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN C 188 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER C 128 " --> pdb=" O   GLN C 188 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   HIS C 190 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   LEU C 126 " --> pdb=" O   HIS C 190 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 108
      removed outlier: 14.129A  pdb=" N   TYR C 293 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 10.813A  pdb=" N   MET C 244 " --> pdb=" O   TYR C 293 " (cutoff:3.500A)
      removed outlier: 9.958A  pdb=" N   GLN C 295 " --> pdb=" O   MET C 244 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   LEU C 246 " --> pdb=" O   GLN C 295 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   ILE C 297 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS C 248 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS C 243 " --> pdb=" O   GLU C 263 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 117 through 120
      removed outlier: 4.371A  pdb=" N   ASP C 202 " --> pdb=" O   TYR C 120 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155
    Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 159

    374 hydrogen bonds defined for protein.
    1062 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: 1.92

  Time building geometry restraints manager: 1.99 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: 1833
        1.33 -     1.45: 1377
        1.45 -     1.57: 3970
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 7243
  Sorted by residual:
  bond pdb=" CE1 HIS B 340 "
       pdb=" NE2 HIS B 340 "
    ideal  model  delta    sigma   weight residual
    1.321  1.361 -0.040 1.00e-02 1.00e+04 1.60e+01
  bond pdb=" N   ILE B 300 "
       pdb=" CA  ILE B 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.14e-02 7.69e+03 1.04e+01
  bond pdb=" N   VAL B 330 "
       pdb=" CA  VAL B 330 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.87e+00
  bond pdb=" N   ILE B 301 "
       pdb=" CA  ILE B 301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.24e-02 6.50e+03 7.72e+00
  bond pdb=" N   ILE A 301 "
       pdb=" CA  ILE A 301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.27e-02 6.20e+03 7.71e+00
  ... (remaining 7238 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 9436
        2.16 -     4.31: 310
        4.31 -     6.47: 32
        6.47 -     8.62: 9
        8.62 -    10.78: 6
  Bond angle restraints: 9793
  Sorted by residual:
  angle pdb=" C   ILE A 159 "
        pdb=" N   ASP A 160 "
        pdb=" CA  ASP A 160 "
      ideal   model   delta    sigma   weight residual
     120.49  131.27  -10.78 1.42e+00 4.96e-01 5.76e+01
  angle pdb=" N   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" C   LYS A 321 "
      ideal   model   delta    sigma   weight residual
     111.36  105.92    5.44 1.09e+00 8.42e-01 2.49e+01
  angle pdb=" CA  ARG B 182 "
        pdb=" CB  ARG B 182 "
        pdb=" CG  ARG B 182 "
      ideal   model   delta    sigma   weight residual
     114.10  123.34   -9.24 2.00e+00 2.50e-01 2.13e+01
  angle pdb=" N   THR B 302 "
        pdb=" CA  THR B 302 "
        pdb=" C   THR B 302 "
      ideal   model   delta    sigma   weight residual
     111.28  115.55   -4.27 1.09e+00 8.42e-01 1.53e+01
  angle pdb=" N   ALA B 303 "
        pdb=" CA  ALA B 303 "
        pdb=" C   ALA B 303 "
      ideal   model   delta    sigma   weight residual
     109.07  115.28   -6.21 1.61e+00 3.86e-01 1.49e+01
  ... (remaining 9788 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3622
       17.90 -    35.81: 530
       35.81 -    53.71: 137
       53.71 -    71.62: 30
       71.62 -    89.52: 13
  Dihedral angle restraints: 4332
    sinusoidal: 1795
      harmonic: 2537
  Sorted by residual:
  dihedral pdb=" CD  ARG B 337 "
           pdb=" NE  ARG B 337 "
           pdb=" CZ  ARG B 337 "
           pdb=" NH1 ARG B 337 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.44   78.44     1      1.00e+01 1.00e-02 7.68e+01
  dihedral pdb=" CB  CYS B 129 "
           pdb=" SG  CYS B 129 "
           pdb=" SG  CYS B 151 "
           pdb=" CB  CYS B 151 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.68   51.32     1      1.00e+01 1.00e-02 3.60e+01
  dihedral pdb=" CD  ARG B 339 "
           pdb=" NE  ARG B 339 "
           pdb=" CZ  ARG B 339 "
           pdb=" NH1 ARG B 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -48.39   48.39     1      1.00e+01 1.00e-02 3.23e+01
  ... (remaining 4329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 765
       0.044 -    0.089: 192
       0.089 -    0.133: 76
       0.133 -    0.178: 14
       0.178 -    0.222: 17
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" CA  VAL B 315 "
            pdb=" N   VAL B 315 "
            pdb=" C   VAL B 315 "
            pdb=" CB  VAL B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  VAL A 318 "
            pdb=" N   VAL A 318 "
            pdb=" C   VAL A 318 "
            pdb=" CB  VAL A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CB  VAL B 318 "
            pdb=" CA  VAL B 318 "
            pdb=" CG1 VAL B 318 "
            pdb=" CG2 VAL B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1061 not shown)

  Planarity restraints: 1229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 337 "    1.083 9.50e-02 1.11e+02   4.85e-01 1.42e+02
        pdb=" NE  ARG B 337 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 337 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 337 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 337 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 339 "    0.820 9.50e-02 1.11e+02   3.67e-01 8.20e+01
        pdb=" NE  ARG B 339 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 339 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 339 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 339 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 197 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.90e+00
        pdb=" CG  ASP A 197 "   -0.049 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 197 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 197 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1226 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 271
        2.70 -     3.25: 7641
        3.25 -     3.80: 11911
        3.80 -     4.35: 14178
        4.35 -     4.90: 21981
  Nonbonded interactions: 55982
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 197 "
            pdb=" N   PHE A 198 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   ARG B 181 "
            pdb=" NH1 ARG B 181 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" O   ALA B 211 "
            pdb=" OG  SER B 215 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG1 THR C 302 "
            pdb=" OD1 ASN C 304 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD1 ASN B 268 "
            pdb=" N   PHE B 269 "
     model   vdw
     2.232 3.120
  ... (remaining 55977 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' and resid 61 through 342)
  selection = (chain 'B' and (resid 61 through 72 or (resid 73 through 76 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 77 through 342))
  selection = (chain 'C' and (resid 61 through 72 or (resid 73 through 76 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 77 through 342))
}

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:                  0.010
  Normalize map: mean=0, sd=1:             2.480
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.000
  Find NCS groups from input model:        0.340
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
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      :  0.004   0.040   7243  Z= 0.288
  Angle     :  0.867  10.779   9793  Z= 0.539
  Chirality :  0.053   0.222   1064
  Planarity :  0.018   0.485   1229
  Dihedral  : 18.367  89.523   2671
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 30.45 %
    Favored  : 64.59 %
  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: -0.02 (0.30), residues: 850
  helix:  1.85 (0.30), residues: 288
  sheet: -0.45 (0.31), residues: 289
  loop : -1.49 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C 133 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.022   0.001   PHE A 320 
 TYR   0.014   0.001   TYR A 120 
 ARG   0.003   0.000   ARG C 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 MET cc_start: 0.8608 (ptm) cc_final: 0.8395 (ppp)
REVERT: B  325 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9100 (p90)
REVERT: B  338 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4702 (mmm160)
REVERT: B  340 HIS cc_start: -0.2636 (OUTLIER) cc_final: -0.2867 (t-90)
REVERT: C  154 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8426 (tm-30)
  outliers start: 39
  outliers final: 17
  residues processed: 130
  average time/residue: 0.2119
  time to fit residues: 36.3370
Evaluate side-chains
  118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0010
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 GLN
** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7243  Z= 0.266
  Angle     :  0.657   8.383   9793  Z= 0.347
  Chirality :  0.044   0.184   1064
  Planarity :  0.005   0.087   1229
  Dihedral  :  4.878  20.204    928
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  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: -0.25 (0.30), residues: 850
  helix:  1.34 (0.29), residues: 293
  sheet: -0.43 (0.31), residues: 295
  loop : -1.45 (0.42), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 232 
 HIS   0.006   0.001   HIS C 190 
 PHE   0.024   0.002   PHE A 320 
 TYR   0.017   0.002   TYR B 158 
 ARG   0.020   0.001   ARG B 337 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   96 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9070 (mmmm)
REVERT: B  158 TYR cc_start: 0.8588 (m-10) cc_final: 0.8379 (m-10)
REVERT: B  222 MET cc_start: 0.8318 (tmm) cc_final: 0.7982 (tmm)
REVERT: B  244 MET cc_start: 0.8996 (ttp) cc_final: 0.8673 (ttt)
REVERT: B  333 MET cc_start: 0.6653 (tpp) cc_final: 0.6253 (tmm)
REVERT: C   79 MET cc_start: 0.8735 (mmp) cc_final: 0.8505 (mmm)
REVERT: C  112 TYR cc_start: 0.7652 (p90) cc_final: 0.7309 (p90)
REVERT: C  169 HIS cc_start: 0.7726 (t-170) cc_final: 0.7410 (t-90)
REVERT: C  222 MET cc_start: 0.8584 (ppp) cc_final: 0.8364 (ppp)
REVERT: C  233 LYS cc_start: 0.8964 (tptt) cc_final: 0.8744 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1831
  time to fit residues: 33.8554
Evaluate side-chains
  91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 82 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7243  Z= 0.292
  Angle     :  0.635   7.358   9793  Z= 0.335
  Chirality :  0.041   0.153   1064
  Planarity :  0.005   0.077   1229
  Dihedral  :  5.001  23.432    928
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  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: -0.26 (0.30), residues: 850
  helix:  1.42 (0.29), residues: 287
  sheet: -0.49 (0.30), residues: 300
  loop : -1.47 (0.44), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 232 
 HIS   0.006   0.001   HIS C 132 
 PHE   0.025   0.002   PHE C  93 
 TYR   0.021   0.002   TYR C 203 
 ARG   0.008   0.001   ARG C 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LEU cc_start: 0.9570 (tt) cc_final: 0.9327 (tt)
REVERT: A  253 ASP cc_start: 0.8864 (m-30) cc_final: 0.8578 (t0)
REVERT: A  308 MET cc_start: 0.9349 (tmm) cc_final: 0.9129 (tmm)
REVERT: B  222 MET cc_start: 0.8330 (tmm) cc_final: 0.7941 (tmm)
REVERT: B  244 MET cc_start: 0.9111 (ttp) cc_final: 0.8564 (ttt)
REVERT: B  333 MET cc_start: 0.6672 (tpp) cc_final: 0.6274 (tmm)
REVERT: C   79 MET cc_start: 0.8799 (mmp) cc_final: 0.8459 (mmm)
REVERT: C  178 ASP cc_start: 0.8598 (t0) cc_final: 0.8395 (p0)
REVERT: C  321 LYS cc_start: 0.9809 (tttm) cc_final: 0.9576 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1861
  time to fit residues: 26.4503
Evaluate side-chains
  84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7243  Z= 0.170
  Angle     :  0.590   8.752   9793  Z= 0.302
  Chirality :  0.042   0.141   1064
  Planarity :  0.005   0.119   1229
  Dihedral  :  4.747  21.018    928
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  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: -0.16 (0.30), residues: 850
  helix:  1.47 (0.28), residues: 287
  sheet: -0.40 (0.30), residues: 302
  loop : -1.40 (0.44), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 232 
 HIS   0.010   0.001   HIS C 132 
 PHE   0.025   0.001   PHE A 316 
 TYR   0.015   0.001   TYR C 203 
 ARG   0.028   0.001   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 LEU cc_start: 0.9522 (tt) cc_final: 0.9316 (tt)
REVERT: A  308 MET cc_start: 0.9305 (tmm) cc_final: 0.9062 (tmm)
REVERT: A  316 PHE cc_start: 0.9513 (m-80) cc_final: 0.9284 (m-80)
REVERT: B  222 MET cc_start: 0.8285 (tmm) cc_final: 0.7877 (tmm)
REVERT: B  244 MET cc_start: 0.9096 (ttp) cc_final: 0.8734 (ttt)
REVERT: B  333 MET cc_start: 0.6709 (tpp) cc_final: 0.6345 (tmm)
REVERT: C   79 MET cc_start: 0.8761 (mmp) cc_final: 0.8426 (mmm)
REVERT: C  233 LYS cc_start: 0.8910 (tptt) cc_final: 0.8676 (tptt)
REVERT: C  238 PHE cc_start: 0.8727 (m-10) cc_final: 0.8504 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1818
  time to fit residues: 27.4805
Evaluate side-chains
  85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 56 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.1990

-------------------------------------------------------------------------------
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: 0.7909
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7243  Z= 0.195
  Angle     :  0.592   7.458   9793  Z= 0.306
  Chirality :  0.041   0.151   1064
  Planarity :  0.005   0.116   1229
  Dihedral  :  4.678  20.595    928
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  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: -0.04 (0.30), residues: 850
  helix:  1.57 (0.29), residues: 285
  sheet: -0.27 (0.31), residues: 293
  loop : -1.38 (0.42), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 232 
 HIS   0.009   0.001   HIS C 132 
 PHE   0.020   0.001   PHE B 316 
 TYR   0.018   0.001   TYR C 203 
 ARG   0.012   0.000   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9316 (tmm) cc_final: 0.9060 (tmm)
REVERT: A  316 PHE cc_start: 0.9537 (m-80) cc_final: 0.9321 (m-80)
REVERT: A  318 VAL cc_start: 0.9502 (t) cc_final: 0.9301 (t)
REVERT: B  111 MET cc_start: 0.8653 (tmm) cc_final: 0.8256 (tmm)
REVERT: B  222 MET cc_start: 0.8331 (tmm) cc_final: 0.7851 (tmm)
REVERT: B  244 MET cc_start: 0.9150 (ttp) cc_final: 0.8744 (ttt)
REVERT: B  333 MET cc_start: 0.6698 (tpp) cc_final: 0.6353 (tmm)
REVERT: C   79 MET cc_start: 0.8755 (mmp) cc_final: 0.8399 (mmm)
REVERT: C  233 LYS cc_start: 0.8917 (tptt) cc_final: 0.8675 (tptt)
REVERT: C  244 MET cc_start: 0.9081 (ptt) cc_final: 0.8646 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1684
  time to fit residues: 25.6615
Evaluate side-chains
  82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0770
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6142

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

Flipped N/Q/H residues before XYZ refinement:
C 136 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7243  Z= 0.151
  Angle     :  0.587   7.527   9793  Z= 0.297
  Chirality :  0.041   0.151   1064
  Planarity :  0.004   0.087   1229
  Dihedral  :  4.539  21.340    928
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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:  0.04 (0.30), residues: 850
  helix:  1.61 (0.29), residues: 286
  sheet: -0.23 (0.31), residues: 292
  loop : -1.32 (0.42), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 232 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.015   0.001   PHE A 316 
 TYR   0.015   0.001   TYR C 203 
 ARG   0.007   0.000   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9323 (tmm) cc_final: 0.9070 (tmm)
REVERT: A  316 PHE cc_start: 0.9544 (m-80) cc_final: 0.9307 (m-80)
REVERT: B  110 ASN cc_start: 0.8940 (t0) cc_final: 0.8717 (p0)
REVERT: B  222 MET cc_start: 0.8388 (tmm) cc_final: 0.7909 (tmm)
REVERT: B  244 MET cc_start: 0.9104 (ttp) cc_final: 0.8700 (ttt)
REVERT: B  333 MET cc_start: 0.6765 (tpp) cc_final: 0.6414 (tmm)
REVERT: C   79 MET cc_start: 0.8760 (mmp) cc_final: 0.8360 (mmm)
REVERT: C  233 LYS cc_start: 0.8929 (tptt) cc_final: 0.8687 (tptt)
REVERT: C  244 MET cc_start: 0.9015 (ptt) cc_final: 0.8489 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1628
  time to fit residues: 24.9942
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
B 340 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7243  Z= 0.288
  Angle     :  0.639   8.561   9793  Z= 0.326
  Chirality :  0.042   0.232   1064
  Planarity :  0.005   0.130   1229
  Dihedral  :  4.756  19.465    928
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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: -0.02 (0.30), residues: 850
  helix:  1.62 (0.29), residues: 285
  sheet: -0.37 (0.31), residues: 292
  loop : -1.26 (0.42), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 232 
 HIS   0.008   0.001   HIS C 132 
 PHE   0.022   0.002   PHE B 316 
 TYR   0.026   0.002   TYR B  75 
 ARG   0.013   0.001   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9318 (tmm) cc_final: 0.9074 (tmm)
REVERT: A  316 PHE cc_start: 0.9559 (m-80) cc_final: 0.9304 (m-80)
REVERT: B  222 MET cc_start: 0.8490 (tmm) cc_final: 0.8013 (tmm)
REVERT: B  244 MET cc_start: 0.9180 (ttp) cc_final: 0.8679 (ttt)
REVERT: B  333 MET cc_start: 0.6774 (tpp) cc_final: 0.6434 (tmm)
REVERT: C   79 MET cc_start: 0.8790 (mmp) cc_final: 0.8425 (mmm)
REVERT: C  244 MET cc_start: 0.9040 (ptt) cc_final: 0.8626 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1627
  time to fit residues: 23.3996
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 73 optimal weight:    0.4980
   chunk 77 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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: 0.7926
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7243  Z= 0.200
  Angle     :  0.610   7.891   9793  Z= 0.311
  Chirality :  0.042   0.267   1064
  Planarity :  0.004   0.098   1229
  Dihedral  :  4.686  20.101    928
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  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:  0.00 (0.30), residues: 850
  helix:  1.67 (0.29), residues: 285
  sheet: -0.36 (0.30), residues: 294
  loop : -1.29 (0.42), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 232 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.014   0.001   PHE C 234 
 TYR   0.020   0.001   TYR C 203 
 ARG   0.009   0.000   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9299 (tmm) cc_final: 0.9047 (tmm)
REVERT: A  316 PHE cc_start: 0.9550 (m-80) cc_final: 0.9283 (m-80)
REVERT: B  222 MET cc_start: 0.8453 (tmm) cc_final: 0.7996 (tmm)
REVERT: B  232 TRP cc_start: 0.8100 (m-10) cc_final: 0.7777 (m-10)
REVERT: B  244 MET cc_start: 0.9172 (ttp) cc_final: 0.8749 (ttt)
REVERT: B  333 MET cc_start: 0.6776 (tpp) cc_final: 0.6440 (tmm)
REVERT: C   79 MET cc_start: 0.8796 (mmp) cc_final: 0.8382 (mmm)
REVERT: C  202 ASP cc_start: 0.8533 (t0) cc_final: 0.8289 (t0)
REVERT: C  233 LYS cc_start: 0.9000 (tptt) cc_final: 0.8709 (tptt)
REVERT: C  244 MET cc_start: 0.8969 (ptt) cc_final: 0.8586 (ppp)
REVERT: C  333 MET cc_start: 0.7907 (ttm) cc_final: 0.7406 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1535
  time to fit residues: 22.3577
Evaluate side-chains
  77 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.3980
   chunk 77 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 79 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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: 0.7913
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7243  Z= 0.171
  Angle     :  0.612   8.087   9793  Z= 0.305
  Chirality :  0.042   0.252   1064
  Planarity :  0.004   0.090   1229
  Dihedral  :  4.616  24.061    928
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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:  0.09 (0.30), residues: 850
  helix:  1.67 (0.29), residues: 285
  sheet: -0.27 (0.31), residues: 292
  loop : -1.19 (0.42), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 232 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.021   0.001   PHE B 316 
 TYR   0.013   0.001   TYR B  75 
 ARG   0.007   0.000   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9273 (tmm) cc_final: 0.8982 (tmm)
REVERT: A  316 PHE cc_start: 0.9533 (m-80) cc_final: 0.9260 (m-80)
REVERT: B  222 MET cc_start: 0.8422 (tmm) cc_final: 0.8013 (tmm)
REVERT: B  232 TRP cc_start: 0.7977 (m-10) cc_final: 0.7641 (m-10)
REVERT: B  233 LYS cc_start: 0.9303 (ttpt) cc_final: 0.9090 (tttt)
REVERT: B  244 MET cc_start: 0.9153 (ttp) cc_final: 0.8737 (ttt)
REVERT: B  268 ASN cc_start: 0.8792 (t0) cc_final: 0.8493 (t0)
REVERT: B  333 MET cc_start: 0.6810 (tpp) cc_final: 0.6434 (tmm)
REVERT: C   79 MET cc_start: 0.8793 (mmp) cc_final: 0.8379 (mmm)
REVERT: C  202 ASP cc_start: 0.8358 (t0) cc_final: 0.7964 (t0)
REVERT: C  244 MET cc_start: 0.8947 (ptt) cc_final: 0.8573 (ppp)
REVERT: C  291 ASP cc_start: 0.7941 (t0) cc_final: 0.7692 (t0)
REVERT: C  333 MET cc_start: 0.7858 (ttm) cc_final: 0.7364 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1541
  time to fit residues: 22.3794
Evaluate side-chains
  80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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: 0.7972
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7243  Z= 0.320
  Angle     :  0.655   8.987   9793  Z= 0.338
  Chirality :  0.042   0.246   1064
  Planarity :  0.005   0.132   1229
  Dihedral  :  4.992  26.164    928
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -0.19 (0.30), residues: 850
  helix:  1.54 (0.29), residues: 285
  sheet: -0.51 (0.30), residues: 294
  loop : -1.37 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 232 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.016   0.002   PHE B 260 
 TYR   0.017   0.002   TYR C 203 
 ARG   0.012   0.001   ARG B 181 

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9300 (tmm) cc_final: 0.9034 (tmm)
REVERT: A  316 PHE cc_start: 0.9543 (m-80) cc_final: 0.9244 (m-80)
REVERT: B  244 MET cc_start: 0.9226 (ttp) cc_final: 0.8715 (ttt)
REVERT: B  333 MET cc_start: 0.6763 (tpp) cc_final: 0.6415 (tmm)
REVERT: C   79 MET cc_start: 0.8848 (mmp) cc_final: 0.8440 (mmm)
REVERT: C  244 MET cc_start: 0.8978 (ptt) cc_final: 0.8708 (ppp)
REVERT: C  291 ASP cc_start: 0.8018 (t0) cc_final: 0.7748 (t0)
REVERT: C  306 TRP cc_start: 0.7912 (m100) cc_final: 0.7591 (m100)
REVERT: C  333 MET cc_start: 0.7913 (ttm) cc_final: 0.7433 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1503
  time to fit residues: 21.4827
Evaluate side-chains
  79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   chunk 27 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.089359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.066183 restraints weight = 26615.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.066761 restraints weight = 19952.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.067362 restraints weight = 14067.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7243  Z= 0.199
  Angle     :  0.634   8.527   9793  Z= 0.322
  Chirality :  0.043   0.246   1064
  Planarity :  0.005   0.101   1229
  Dihedral  :  4.855  24.347    928
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -0.08 (0.30), residues: 850
  helix:  1.58 (0.29), residues: 285
  sheet: -0.45 (0.30), residues: 302
  loop : -1.25 (0.43), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 232 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.025   0.002   PHE B 229 
 TYR   0.014   0.001   TYR C 203 
 ARG   0.009   0.000   ARG B 181 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1711.73 seconds
wall clock time: 32 minutes 7.89 seconds (1927.89 seconds total)