Starting phenix.real_space_refine
on Sat Dec 28 16:59:50 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xw9_33494/12_2024/7xw9_33494.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xw9_33494/12_2024/7xw9_33494.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xw9_33494/12_2024/7xw9_33494.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xw9_33494/12_2024/7xw9_33494.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xw9_33494/12_2024/7xw9_33494.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xw9_33494/12_2024/7xw9_33494.cif"
  }
  resolution = 2.7
  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=   0.033
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      63      5.16       5
     C    5729      2.51       5
     N    1533      2.21       5
     O    1663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8988
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2294
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1862
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "S"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 25
          Classifications: {'peptide': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.50, per 1000 atoms: 0.61
  Number of scatterers: 8988
  At special positions: 0
  Unit cell: (116.61, 111.54, 123.708, 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      63     16.00
     O    1663      8.00
     N    1533      7.00
     C    5729      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      37.9% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'R' and resid 23 through 53
    Processing helix  chain 'R' and resid 58 through 79
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.782A  pdb=" N   ILE R  83 " --> pdb=" O   GLY R  79 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR R  84 " --> pdb=" O   LEU R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
      removed outlier: 4.031A  pdb=" N   SER R 113 " --> pdb=" O   ILE R 109 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 162
      removed outlier: 3.837A  pdb=" N   TYR R 156 " --> pdb=" O   PHE R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 184 through 187
    Processing helix  chain 'R' and resid 188 through 220
      Proline residue:  R 203  - end of helix
      removed outlier: 3.553A  pdb=" N   LEU R 220 " --> pdb=" O   ARG R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 258 through 290
      removed outlier: 4.051A  pdb=" N   GLN R 263 " --> pdb=" O   SER R 259 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL R 264 " --> pdb=" O   SER R 260 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   THR R 265 " --> pdb=" O   ARG R 261 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS R 266 " --> pdb=" O   LYS R 262 " (cutoff:3.500A)
      Proline residue:  R 281  - end of helix
      removed outlier: 3.648A  pdb=" N   SER R 290 " --> pdb=" O   VAL R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 321
      Proline residue:  R 317  - end of helix
    Processing helix  chain 'R' and resid 325 through 335
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.143A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 4.236A  pdb=" N   GLY A  45 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 264
      removed outlier: 3.733A  pdb=" N   GLN A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASN A 264 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 293
    Processing helix  chain 'A' and resid 308 through 319
      removed outlier: 3.903A  pdb=" N   LEU A 312 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 327
      removed outlier: 4.067A  pdb=" N   TYR A 326 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
      removed outlier: 3.542A  pdb=" N   THR A 350 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 406
      removed outlier: 3.560A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.592A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.550A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.517A  pdb=" N   ASP S 211 " --> pdb=" O   GLU S 208 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 208 through 212'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 239
      removed outlier: 4.631A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 270 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.508A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.665A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.843A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.552A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.729A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.414A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.890A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.513A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.978A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.635A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.482A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    453 hydrogen bonds defined for protein.
    1272 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: 2.65

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 1449
        1.30 -     1.43: 2504
        1.43 -     1.57: 5132
        1.57 -     1.70: 0
        1.70 -     1.83: 91
  Bond restraints: 9176
  Sorted by residual:
  bond pdb=" CG  PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.517  1.420  0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" CA  HIS L   2 "
       pdb=" C   HIS L   2 "
    ideal  model  delta    sigma   weight residual
    1.525  1.424  0.101 2.10e-02 2.27e+03 2.29e+01
  bond pdb=" N   PCA L   1 "
       pdb=" CD  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.253  0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" N   PCA L   1 "
       pdb=" CA  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.379  0.079 1.90e-02 2.77e+03 1.73e+01
  bond pdb=" CA  PCA L   1 "
       pdb=" CB  PCA L   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.456  0.074 2.00e-02 2.50e+03 1.37e+01
  ... (remaining 9171 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 12332
        2.96 -     5.92: 88
        5.92 -     8.88: 12
        8.88 -    11.84: 1
       11.84 -    14.80: 1
  Bond angle restraints: 12434
  Sorted by residual:
  angle pdb=" N   SER A  44 "
        pdb=" CA  SER A  44 "
        pdb=" C   SER A  44 "
      ideal   model   delta    sigma   weight residual
     111.28  126.08  -14.80 1.09e+00 8.42e-01 1.84e+02
  angle pdb=" C   VAL R 201 "
        pdb=" N   VAL R 202 "
        pdb=" CA  VAL R 202 "
      ideal   model   delta    sigma   weight residual
     122.13  113.55    8.58 1.85e+00 2.92e-01 2.15e+01
  angle pdb=" C   GLU A  43 "
        pdb=" N   SER A  44 "
        pdb=" CA  SER A  44 "
      ideal   model   delta    sigma   weight residual
     120.28  126.31   -6.03 1.34e+00 5.57e-01 2.02e+01
  angle pdb=" N   TRP R 300 "
        pdb=" CA  TRP R 300 "
        pdb=" C   TRP R 300 "
      ideal   model   delta    sigma   weight residual
     114.56  109.00    5.56 1.27e+00 6.20e-01 1.92e+01
  angle pdb=" N   PCA L   1 "
        pdb=" CA  PCA L   1 "
        pdb=" CB  PCA L   1 "
      ideal   model   delta    sigma   weight residual
     110.50  103.75    6.75 1.70e+00 3.46e-01 1.58e+01
  ... (remaining 12429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 4916
       15.42 -    30.85: 426
       30.85 -    46.27: 85
       46.27 -    61.70: 18
       61.70 -    77.12: 6
  Dihedral angle restraints: 5451
    sinusoidal: 2129
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  LEU R  22 "
           pdb=" C   LEU R  22 "
           pdb=" N   GLU R  23 "
           pdb=" CA  GLU R  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.11   23.89     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  TYR S 101 "
           pdb=" C   TYR S 101 "
           pdb=" N   TYR S 102 "
           pdb=" CA  TYR S 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.82   20.18     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  GLU R 298 "
           pdb=" C   GLU R 298 "
           pdb=" N   ASN R 299 "
           pdb=" CA  ASN R 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 5448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1300
       0.092 -    0.184: 102
       0.184 -    0.276: 3
       0.276 -    0.369: 1
       0.369 -    0.461: 2
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  SER A  44 "
            pdb=" N   SER A  44 "
            pdb=" C   SER A  44 "
            pdb=" CB  SER A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.31e+00
  chirality pdb=" CA  PRO L   3 "
            pdb=" N   PRO L   3 "
            pdb=" C   PRO L   3 "
            pdb=" CB  PRO L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.30    0.42 2.00e-01 2.50e+01 4.38e+00
  chirality pdb=" CB  VAL R 202 "
            pdb=" CA  VAL R 202 "
            pdb=" CG1 VAL R 202 "
            pdb=" CG2 VAL R 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   PCA L   1 "   -0.064 2.00e-02 2.50e+03   4.54e-02 2.58e+01
        pdb=" CA  PCA L   1 "    0.057 2.00e-02 2.50e+03
        pdb=" CG  PCA L   1 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD  PCA L   1 "   -0.016 2.00e-02 2.50e+03
        pdb=" OE  PCA L   1 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 198 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   VAL R 198 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL R 198 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE R 199 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  40 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   GLY A  40 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   GLY A  40 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A  41 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 319
        2.71 -     3.26: 8460
        3.26 -     3.81: 14220
        3.81 -     4.35: 18140
        4.35 -     4.90: 31421
  Nonbonded interactions: 72560
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" NZ  LYS A 308 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OE1 GLU A 234 "
            pdb=" NE2 HIS A 245 "
     model   vdw
     2.326 3.120
  ... (remaining 72555 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.410
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:12.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104   9176  Z= 0.329
  Angle     :  0.680  14.803  12434  Z= 0.390
  Chirality :  0.050   0.461   1408
  Planarity :  0.005   0.064   1573
  Dihedral  : 12.265  77.123   3305
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.37 (0.25), residues: 1124
  helix:  0.43 (0.26), residues: 384
  sheet:  1.23 (0.32), residues: 272
  loop : -0.41 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R  91 
 HIS   0.011   0.001   HIS L   2 
 PHE   0.021   0.002   PHE R 161 
 TYR   0.021   0.002   TYR R  24 
 ARG   0.016   0.001   ARG B  22 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.894 
Fit side-chains
REVERT: R  139 PHE cc_start: 0.8130 (t80) cc_final: 0.7129 (t80)
REVERT: R  147 ILE cc_start: 0.8123 (pt) cc_final: 0.7897 (mt)
REVERT: A   32 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6502 (mmt90)
REVERT: A  314 GLU cc_start: 0.6772 (mp0) cc_final: 0.6408 (mp0)
REVERT: A  329 GLU cc_start: 0.6658 (mp0) cc_final: 0.6429 (mp0)
REVERT: A  396 ASP cc_start: 0.6708 (m-30) cc_final: 0.6473 (m-30)
REVERT: B  175 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7294 (mm-40)
REVERT: B  258 ASP cc_start: 0.6670 (t70) cc_final: 0.6390 (t70)
REVERT: S   57 THR cc_start: 0.8332 (p) cc_final: 0.8104 (t)
  outliers start: 0
  outliers final: 1
  residues processed: 242
  average time/residue: 1.2288
  time to fit residues: 317.0924
Evaluate side-chains
  227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0170
   chunk 52 optimal weight:    0.0050
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.9836

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

Flipped N/Q/H residues before XYZ refinement:
R  61 ASN
A 400 GLN
A 402 ASN
B 176 GLN
B 259 GLN
B 293 ASN
B 340 ASN
S 167 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9176  Z= 0.235
  Angle     :  0.588   9.846  12434  Z= 0.313
  Chirality :  0.044   0.204   1408
  Planarity :  0.004   0.051   1573
  Dihedral  :  4.644  37.579   1254
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  7.96 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.02 (0.26), residues: 1124
  helix:  1.43 (0.26), residues: 383
  sheet:  1.22 (0.31), residues: 304
  loop : -0.35 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.017   0.001   PHE R 161 
 TYR   0.014   0.002   TYR R  24 
 ARG   0.008   0.001   ARG B  22 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
REVERT: R  141 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7479 (ttt180)
REVERT: R  146 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8112 (mp)
REVERT: R  202 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7764 (t)
REVERT: R  315 ILE cc_start: 0.8213 (mt) cc_final: 0.8002 (mp)
REVERT: A  243 ASN cc_start: 0.8583 (m-40) cc_final: 0.8165 (m110)
REVERT: A  329 GLU cc_start: 0.6709 (mp0) cc_final: 0.6311 (mp0)
REVERT: A  375 TYR cc_start: 0.8333 (m-80) cc_final: 0.8015 (m-80)
REVERT: A  396 ASP cc_start: 0.6713 (m-30) cc_final: 0.6477 (m-30)
REVERT: B   22 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6568 (mpt180)
REVERT: B  175 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7268 (mm-40)
REVERT: B  258 ASP cc_start: 0.6752 (t70) cc_final: 0.5778 (t70)
REVERT: S  180 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7425 (ptp)
  outliers start: 21
  outliers final: 6
  residues processed: 230
  average time/residue: 1.3797
  time to fit residues: 335.8933
Evaluate side-chains
  222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 213
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0980
   chunk 109 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
A 400 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9176  Z= 0.301
  Angle     :  0.610  10.998  12434  Z= 0.322
  Chirality :  0.045   0.208   1408
  Planarity :  0.005   0.050   1573
  Dihedral  :  4.864  47.751   1254
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 11.33 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.07 (0.26), residues: 1124
  helix:  1.64 (0.27), residues: 384
  sheet:  1.17 (0.31), residues: 307
  loop : -0.45 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.018   0.002   PHE R 139 
 TYR   0.019   0.002   TYR B 105 
 ARG   0.008   0.001   ARG B  19 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 222
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: R  141 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.7605 (ttt180)
REVERT: R  202 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (t)
REVERT: A  243 ASN cc_start: 0.8553 (m-40) cc_final: 0.8130 (m-40)
REVERT: A  273 VAL cc_start: 0.8669 (t) cc_final: 0.8453 (p)
REVERT: A  329 GLU cc_start: 0.6759 (mp0) cc_final: 0.6331 (mp0)
REVERT: A  375 TYR cc_start: 0.8369 (m-80) cc_final: 0.8076 (m-80)
REVERT: A  389 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7716 (mtm180)
REVERT: A  396 ASP cc_start: 0.6746 (m-30) cc_final: 0.6482 (m-30)
REVERT: B   22 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6829 (mtt90)
REVERT: B  258 ASP cc_start: 0.6820 (t70) cc_final: 0.6272 (t70)
REVERT: S   18 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7594 (ttt180)
REVERT: S  180 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7495 (ptp)
  outliers start: 29
  outliers final: 16
  residues processed: 235
  average time/residue: 1.3708
  time to fit residues: 340.9488
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 211
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    0.2980
   chunk 52 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 89 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9176  Z= 0.304
  Angle     :  0.601  11.507  12434  Z= 0.319
  Chirality :  0.045   0.211   1408
  Planarity :  0.005   0.050   1573
  Dihedral  :  4.888  47.415   1254
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.06 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.05 (0.26), residues: 1124
  helix:  1.70 (0.27), residues: 384
  sheet:  1.06 (0.31), residues: 308
  loop : -0.45 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.015   0.002   PHE R 296 
 TYR   0.016   0.002   TYR B 105 
 ARG   0.006   0.001   ARG B 251 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 215
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: R  141 ARG cc_start: 0.7860 (ttt-90) cc_final: 0.7614 (ttt180)
REVERT: R  202 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7813 (t)
REVERT: A    8 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7112 (mt-10)
REVERT: A  243 ASN cc_start: 0.8569 (m-40) cc_final: 0.8121 (m110)
REVERT: A  329 GLU cc_start: 0.6777 (mp0) cc_final: 0.6521 (mp0)
REVERT: A  375 TYR cc_start: 0.8374 (m-80) cc_final: 0.8057 (m-80)
REVERT: A  389 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7489 (mtt180)
REVERT: A  396 ASP cc_start: 0.6747 (m-30) cc_final: 0.6499 (m-30)
REVERT: B   22 ARG cc_start: 0.7232 (mtt90) cc_final: 0.6699 (mmm-85)
REVERT: B   45 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8026 (mtm)
REVERT: B  258 ASP cc_start: 0.6882 (t70) cc_final: 0.6390 (t70)
REVERT: S  180 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7485 (ptp)
  outliers start: 30
  outliers final: 19
  residues processed: 226
  average time/residue: 1.4228
  time to fit residues: 339.9549
Evaluate side-chains
  235 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 213
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  204 MET
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9176  Z= 0.271
  Angle     :  0.584  11.190  12434  Z= 0.309
  Chirality :  0.044   0.208   1408
  Planarity :  0.005   0.048   1573
  Dihedral  :  4.795  46.239   1254
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.10 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.06 (0.26), residues: 1124
  helix:  1.78 (0.27), residues: 384
  sheet:  1.02 (0.30), residues: 307
  loop : -0.47 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.014   0.001   PHE R 139 
 TYR   0.012   0.002   TYR S 178 
 ARG   0.005   0.000   ARG B  19 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 219
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: R  202 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7820 (t)
REVERT: A    8 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7095 (mt-10)
REVERT: A  243 ASN cc_start: 0.8589 (m-40) cc_final: 0.8208 (m-40)
REVERT: A  329 GLU cc_start: 0.6785 (mp0) cc_final: 0.6539 (mp0)
REVERT: A  375 TYR cc_start: 0.8378 (m-80) cc_final: 0.8023 (m-80)
REVERT: A  396 ASP cc_start: 0.6745 (m-30) cc_final: 0.6492 (m-30)
REVERT: B   22 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6829 (mtt90)
REVERT: B  258 ASP cc_start: 0.6878 (t70) cc_final: 0.6424 (t70)
REVERT: S   18 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7569 (ttt180)
REVERT: S  167 GLN cc_start: 0.8452 (tt0) cc_final: 0.8211 (tt0)
REVERT: S  180 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7487 (ptp)
  outliers start: 30
  outliers final: 18
  residues processed: 232
  average time/residue: 1.4229
  time to fit residues: 349.2448
Evaluate side-chains
  235 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 215
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  245 HIS
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 107 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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: 0.7423
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9176  Z= 0.201
  Angle     :  0.555  10.852  12434  Z= 0.294
  Chirality :  0.043   0.203   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.589  42.610   1252
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.51 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.14 (0.26), residues: 1124
  helix:  1.93 (0.27), residues: 384
  sheet:  1.03 (0.30), residues: 302
  loop : -0.49 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.013   0.001   PHE R 304 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.005   0.000   ARG B  19 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 220
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7498 (mt) cc_final: 0.7233 (mm)
REVERT: R  122 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6545 (mt-10)
REVERT: R  202 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7812 (t)
REVERT: A  329 GLU cc_start: 0.6772 (mp0) cc_final: 0.6515 (mp0)
REVERT: A  375 TYR cc_start: 0.8385 (m-80) cc_final: 0.8076 (m-80)
REVERT: A  396 ASP cc_start: 0.6721 (m-30) cc_final: 0.6465 (m-30)
REVERT: B   22 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6758 (mtt90)
REVERT: B   45 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8025 (mtm)
REVERT: B  184 THR cc_start: 0.8088 (p) cc_final: 0.7799 (m)
REVERT: B  258 ASP cc_start: 0.6878 (t70) cc_final: 0.6352 (t70)
REVERT: S   18 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7564 (ttt180)
REVERT: S  167 GLN cc_start: 0.8447 (tt0) cc_final: 0.8180 (tt0)
REVERT: S  180 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7486 (ptp)
  outliers start: 36
  outliers final: 21
  residues processed: 237
  average time/residue: 1.3845
  time to fit residues: 347.8056
Evaluate side-chains
  240 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 215
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 SER
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 42 optimal weight:    0.2980
   chunk 63 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
R 297 GLN
A 400 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9176  Z= 0.164
  Angle     :  0.538  11.110  12434  Z= 0.283
  Chirality :  0.042   0.204   1408
  Planarity :  0.004   0.043   1573
  Dihedral  :  4.408  41.826   1252
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.22 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.27 (0.26), residues: 1124
  helix:  2.17 (0.27), residues: 378
  sheet:  1.04 (0.30), residues: 300
  loop : -0.46 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.003   0.001   HIS L   2 
 PHE   0.015   0.001   PHE R 304 
 TYR   0.015   0.001   TYR S 101 
 ARG   0.004   0.000   ARG B  19 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: R   30 LEU cc_start: 0.7489 (mt) cc_final: 0.7280 (mm)
REVERT: R  122 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6505 (mt-10)
REVERT: A  329 GLU cc_start: 0.6737 (mp0) cc_final: 0.6487 (mp0)
REVERT: A  375 TYR cc_start: 0.8385 (m-80) cc_final: 0.8055 (m-80)
REVERT: A  379 THR cc_start: 0.8200 (p) cc_final: 0.7968 (m)
REVERT: A  396 ASP cc_start: 0.6702 (m-30) cc_final: 0.6437 (m-30)
REVERT: B   22 ARG cc_start: 0.7116 (mtt90) cc_final: 0.6677 (mtt90)
REVERT: B   45 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8028 (mtm)
REVERT: B  184 THR cc_start: 0.8026 (p) cc_final: 0.7764 (m)
REVERT: B  212 ASP cc_start: 0.7701 (p0) cc_final: 0.7365 (p0)
REVERT: B  258 ASP cc_start: 0.6835 (t70) cc_final: 0.6276 (t70)
REVERT: S   18 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7561 (ttt180)
REVERT: S  167 GLN cc_start: 0.8437 (tt0) cc_final: 0.8123 (tt0)
REVERT: S  180 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7410 (ptp)
  outliers start: 31
  outliers final: 17
  residues processed: 224
  average time/residue: 1.2915
  time to fit residues: 307.3977
Evaluate side-chains
  225 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue  180 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   9176  Z= 0.287
  Angle     :  0.579  11.311  12434  Z= 0.307
  Chirality :  0.044   0.160   1408
  Planarity :  0.005   0.056   1573
  Dihedral  :  4.697  43.837   1252
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.73 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.11 (0.26), residues: 1124
  helix:  1.93 (0.27), residues: 385
  sheet:  0.97 (0.30), residues: 304
  loop : -0.50 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.015   0.001   PHE R 304 
 TYR   0.017   0.002   TYR S 101 
 ARG   0.006   0.000   ARG R 306 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 219
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: R  122 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6514 (mt-10)
REVERT: A  329 GLU cc_start: 0.6779 (mp0) cc_final: 0.6521 (mp0)
REVERT: A  375 TYR cc_start: 0.8371 (m-80) cc_final: 0.8010 (m-80)
REVERT: A  396 ASP cc_start: 0.6739 (m-30) cc_final: 0.6473 (m-30)
REVERT: B   22 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6821 (mmm-85)
REVERT: S   18 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7590 (ttt180)
REVERT: S  167 GLN cc_start: 0.8464 (tt0) cc_final: 0.8164 (tt0)
REVERT: S  180 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7528 (ptp)
  outliers start: 31
  outliers final: 20
  residues processed: 235
  average time/residue: 1.4018
  time to fit residues: 348.5308
Evaluate side-chains
  241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 220
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  280 MET
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 99 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9176  Z= 0.209
  Angle     :  0.565  12.181  12434  Z= 0.295
  Chirality :  0.043   0.157   1408
  Planarity :  0.004   0.048   1573
  Dihedral  :  4.525  41.061   1252
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.65 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.16 (0.26), residues: 1124
  helix:  2.07 (0.27), residues: 379
  sheet:  0.96 (0.30), residues: 302
  loop : -0.50 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.015   0.001   PHE R 304 
 TYR   0.020   0.001   TYR S 101 
 ARG   0.004   0.000   ARG B 314 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: R  122 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6633 (mt-10)
REVERT: A   46 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7286 (pttt)
REVERT: A  329 GLU cc_start: 0.6750 (mp0) cc_final: 0.6490 (mp0)
REVERT: A  375 TYR cc_start: 0.8374 (m-80) cc_final: 0.8044 (m-80)
REVERT: A  396 ASP cc_start: 0.6726 (m-30) cc_final: 0.6472 (m-30)
REVERT: B   22 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6742 (mmm-85)
REVERT: S   18 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7583 (ttt180)
REVERT: S  167 GLN cc_start: 0.8468 (tt0) cc_final: 0.8139 (tt0)
REVERT: S  180 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7480 (ptp)
  outliers start: 25
  outliers final: 19
  residues processed: 219
  average time/residue: 1.3666
  time to fit residues: 317.1204
Evaluate side-chains
  227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  198 VAL
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  280 MET
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 101 optimal weight:    0.3980
   chunk 88 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0060
   chunk 69 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9176  Z= 0.170
  Angle     :  0.547  11.990  12434  Z= 0.285
  Chirality :  0.042   0.208   1408
  Planarity :  0.004   0.042   1573
  Dihedral  :  4.357  38.841   1252
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.76 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.23 (0.26), residues: 1124
  helix:  2.16 (0.27), residues: 379
  sheet:  0.96 (0.30), residues: 302
  loop : -0.46 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.014   0.001   PHE R 304 
 TYR   0.022   0.001   TYR S 101 
 ARG   0.004   0.000   ARG B 314 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: R  315 ILE cc_start: 0.8200 (mt) cc_final: 0.7988 (mp)
REVERT: A   46 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7292 (pttt)
REVERT: A  329 GLU cc_start: 0.6722 (mp0) cc_final: 0.6474 (mp0)
REVERT: A  375 TYR cc_start: 0.8376 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  396 ASP cc_start: 0.6703 (m-30) cc_final: 0.6440 (m-30)
REVERT: B   22 ARG cc_start: 0.7025 (mtt90) cc_final: 0.6798 (mmm-85)
REVERT: B  184 THR cc_start: 0.8099 (p) cc_final: 0.7808 (m)
REVERT: B  212 ASP cc_start: 0.7708 (p0) cc_final: 0.7372 (p0)
REVERT: B  258 ASP cc_start: 0.6779 (t70) cc_final: 0.6419 (t70)
REVERT: S   18 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7569 (ttt180)
REVERT: S  167 GLN cc_start: 0.8459 (tt0) cc_final: 0.8138 (tt0)
REVERT: S  180 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7439 (ptp)
  outliers start: 22
  outliers final: 15
  residues processed: 215
  average time/residue: 1.3930
  time to fit residues: 318.8375
Evaluate side-chains
  222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  179 CYS
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  280 MET
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   48 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  192 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 88 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113865 restraints weight = 11778.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.75
r_work: 0.3341 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9176  Z= 0.263
  Angle     :  0.594  12.074  12434  Z= 0.310
  Chirality :  0.045   0.352   1408
  Planarity :  0.004   0.053   1573
  Dihedral  :  4.604  41.635   1252
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.86 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.11 (0.26), residues: 1124
  helix:  1.98 (0.27), residues: 379
  sheet:  0.91 (0.30), residues: 304
  loop : -0.47 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 372 
 PHE   0.015   0.001   PHE R 304 
 TYR   0.012   0.002   TYR S 178 
 ARG   0.006   0.000   ARG R 306 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4915.18 seconds
wall clock time: 88 minutes 18.31 seconds (5298.31 seconds total)