Starting phenix.real_space_refine
on Wed Mar 12 13:35:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8itl_35706/03_2025/8itl_35706.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8itl_35706/03_2025/8itl_35706.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8itl_35706/03_2025/8itl_35706.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8itl_35706/03_2025/8itl_35706.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8itl_35706/03_2025/8itl_35706.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8itl_35706/03_2025/8itl_35706.cif"
  }
  resolution = 3.23
  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=   0.093
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      43      5.16       5
     C    5024      2.51       5
     N    1421      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7954
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2139
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 6, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 199
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 96
    Chain: "A"
      Number of atoms: 1875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1875
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "B"
      Number of atoms: 2567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2567
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 33
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 417
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "N"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 956
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 4.77, per 1000 atoms: 0.60
  Number of scatterers: 7954
  At special positions: 0
  Unit cell: (76.041, 102.816, 125.307, 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      43     16.00
     O    1466      8.00
     N    1421      7.00
     C    5024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 180 " - pdb=" SG  CYS R 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.00

  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1942

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      43.4% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'R' and resid 88 through 126
    Processing helix  chain 'R' and resid 131 through 158
      removed outlier: 3.890A  pdb=" N   LEU R 152 " --> pdb=" O   ALA R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 211
      removed outlier: 3.854A  pdb=" N   TYR R 195 " --> pdb=" O   VAL R 191 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 245
      Proline residue:  R 231  - end of helix
      Proline residue:  R 237  - end of helix
    Processing helix  chain 'R' and resid 256 through 293
      removed outlier: 3.987A  pdb=" N   ILE R 262 " --> pdb=" O   ALA R 258 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ILE R 263 " --> pdb=" O   ILE R 259 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      removed outlier: 3.597A  pdb=" N   ARG R 292 " --> pdb=" O   LYS R 288 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 321
      removed outlier: 3.525A  pdb=" N   ARG R 302 " --> pdb=" O   ASP R 298 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 332 through 356
      removed outlier: 3.792A  pdb=" N   ILE R 342 " --> pdb=" O   LEU R 338 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 360 through 379
    Processing helix  chain 'A' and resid 10 through 40
      removed outlier: 3.767A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.678A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.647A  pdb=" N   SER A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.284A  pdb=" N   ASP A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.528A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 4.430A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.788A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.867A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223
      removed outlier: 7.219A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.639A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.046A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.581A  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: 3.621A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150
      removed outlier: 5.008A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.775A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.510A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.097A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1221 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: 2.08

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2652
        1.34 -     1.46: 1957
        1.46 -     1.58: 3446
        1.58 -     1.70: 0
        1.70 -     1.83: 56
  Bond restraints: 8111
  Sorted by residual:
  bond pdb=" CA  PHE N 108 "
       pdb=" C   PHE N 108 "
    ideal  model  delta    sigma   weight residual
    1.528  1.490  0.037 1.35e-02 5.49e+03 7.71e+00
  bond pdb=" CA  MET A 221 "
       pdb=" C   MET A 221 "
    ideal  model  delta    sigma   weight residual
    1.523  1.498  0.025 1.21e-02 6.83e+03 4.15e+00
  bond pdb=" CA  GLU B 260 "
       pdb=" C   GLU B 260 "
    ideal  model  delta    sigma   weight residual
    1.526  1.504  0.023 1.37e-02 5.33e+03 2.76e+00
  bond pdb=" C   VAL R 311 "
       pdb=" N   PRO R 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.357 -0.023 1.44e-02 4.82e+03 2.64e+00
  bond pdb=" CA  ASN B 293 "
       pdb=" C   ASN B 293 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.017 1.08e-02 8.57e+03 2.57e+00
  ... (remaining 8106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 10759
        1.65 -     3.30: 201
        3.30 -     4.95: 35
        4.95 -     6.59: 11
        6.59 -     8.24: 3
  Bond angle restraints: 11009
  Sorted by residual:
  angle pdb=" C   PHE A 312 "
        pdb=" N   PRO A 313 "
        pdb=" CA  PRO A 313 "
      ideal   model   delta    sigma   weight residual
     119.28  115.02    4.26 1.10e+00 8.26e-01 1.50e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     113.15  108.61    4.54 1.19e+00 7.06e-01 1.46e+01
  angle pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
        pdb=" C   ASP N 109 "
      ideal   model   delta    sigma   weight residual
     112.47  116.75   -4.28 1.24e+00 6.50e-01 1.19e+01
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     121.54  126.51   -4.97 1.91e+00 2.74e-01 6.78e+00
  angle pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
        pdb=" CB  THR B  87 "
      ideal   model   delta    sigma   weight residual
     113.65  109.88    3.77 1.47e+00 4.63e-01 6.58e+00
  ... (remaining 11004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4343
       17.85 -    35.69: 370
       35.69 -    53.54: 76
       53.54 -    71.39: 3
       71.39 -    89.23: 17
  Dihedral angle restraints: 4809
    sinusoidal: 1805
      harmonic: 3004
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -9.28  -76.72     1      1.00e+01 1.00e-02 7.39e+01
  dihedral pdb=" CB  CYS R 180 "
           pdb=" SG  CYS R 180 "
           pdb=" SG  CYS R 250 "
           pdb=" CB  CYS R 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.32  -71.32     1      1.00e+01 1.00e-02 6.53e+01
  dihedral pdb=" CB  GLU B 215 "
           pdb=" CG  GLU B 215 "
           pdb=" CD  GLU B 215 "
           pdb=" OE1 GLU B 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.04  -88.04     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 4806 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 794
       0.034 -    0.068: 323
       0.068 -    0.102: 92
       0.102 -    0.135: 40
       0.135 -    0.169: 1
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CA  ASP N 109 "
            pdb=" N   ASP N 109 "
            pdb=" C   ASP N 109 "
            pdb=" CB  ASP N 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CA  VAL B 112 "
            pdb=" N   VAL B 112 "
            pdb=" C   VAL B 112 "
            pdb=" CB  VAL B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 1247 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 220 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   HIS A 220 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   HIS A 220 "    0.018 2.00e-02 2.50e+03
        pdb=" N   MET A 221 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 352 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   VAL R 352 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL R 352 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER R 353 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 311 "   -0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO R 312 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO R 312 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 312 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 46
        2.47 -     3.08: 5482
        3.08 -     3.68: 11942
        3.68 -     4.29: 17092
        4.29 -     4.90: 29573
  Nonbonded interactions: 64135
  Sorted by model distance:
  nonbonded pdb=" CZ  PHE B 292 "
            pdb=" OD1 ASN B 313 "
     model   vdw
     1.862 3.340
  nonbonded pdb=" CD1 PHE B 292 "
            pdb=" C   ASN B 313 "
     model   vdw
     2.018 2.856
  nonbonded pdb=" CD2 PHE B 292 "
            pdb=" O   ASP B 312 "
     model   vdw
     2.125 3.340
  nonbonded pdb=" NZ  LYS B  57 "
            pdb=" OH  TYR B  59 "
     model   vdw
     2.128 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.157 3.040
  ... (remaining 64130 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:                     20.600
  Find NCS groups from input model:        0.070
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
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   0.038   8111  Z= 0.264
  Angle     :  0.608   8.243  11009  Z= 0.350
  Chirality :  0.042   0.169   1250
  Planarity :  0.003   0.044   1416
  Dihedral  : 14.366  89.234   2858
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -0.13 (0.27), residues: 1019
  helix:  1.82 (0.26), residues: 410
  sheet: -1.08 (0.36), residues: 228
  loop : -1.55 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B 241 
 TYR   0.025   0.002   TYR N 115 
 ARG   0.002   0.000   ARG R  95 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.797 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: A  209 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6818 (mm-30)
REVERT: B  246 ASP cc_start: 0.7715 (m-30) cc_final: 0.7459 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1993
  time to fit residues: 35.0902
Evaluate side-chains
  102 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0010
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    0.4980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
R 373 HIS
A 371 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.197241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.155972 restraints weight = 9193.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.20
r_work: 0.3580 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8111  Z= 0.191
  Angle     :  0.532   9.610  11009  Z= 0.280
  Chirality :  0.041   0.156   1250
  Planarity :  0.004   0.060   1416
  Dihedral  :  4.062  19.212   1132
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.37 %
    Favored  : 90.89 %
  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:  0.36 (0.28), residues: 1019
  helix:  2.38 (0.26), residues: 408
  sheet: -1.02 (0.36), residues: 215
  loop : -1.33 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.025   0.002   PHE B 292 
 TYR   0.013   0.001   TYR R 195 
 ARG   0.004   0.000   ARG B 197 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.155 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8312 (mt-10)
REVERT: B  118 ASP cc_start: 0.7924 (t0) cc_final: 0.7706 (t0)
REVERT: B  246 ASP cc_start: 0.8087 (m-30) cc_final: 0.7840 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 106
  average time/residue: 0.2182
  time to fit residues: 31.1265
Evaluate side-chains
  97 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   90 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.197682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157125 restraints weight = 9425.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 2.33
r_work: 0.3541 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8111  Z= 0.206
  Angle     :  0.515  10.155  11009  Z= 0.270
  Chirality :  0.041   0.159   1250
  Planarity :  0.004   0.058   1416
  Dihedral  :  3.957  19.113   1132
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.82 %
    Favored  : 86.70 %
  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:  0.37 (0.27), residues: 1019
  helix:  2.37 (0.26), residues: 414
  sheet: -0.81 (0.36), residues: 214
  loop : -1.50 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.021   0.002   PHE B 292 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.767 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8334 (mt-10)
REVERT: R  113 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6572 (mp)
REVERT: R  335 PHE cc_start: 0.5938 (p90) cc_final: 0.5407 (p90)
REVERT: R  341 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7397 (mt-10)
REVERT: A  221 MET cc_start: 0.7407 (tpp) cc_final: 0.7144 (mmm)
REVERT: B  175 GLN cc_start: 0.7958 (pm20) cc_final: 0.7697 (pm20)
REVERT: N   87 LYS cc_start: 0.8223 (mtmm) cc_final: 0.8016 (mttm)
  outliers start: 12
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1852
  time to fit residues: 26.6004
Evaluate side-chains
  101 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  279 ILE
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0770
   chunk 97 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.4267 r_free = 0.4267 target = 0.199893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.157718 restraints weight = 9289.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.21
r_work: 0.3550 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8111  Z= 0.166
  Angle     :  0.490  10.824  11009  Z= 0.256
  Chirality :  0.040   0.154   1250
  Planarity :  0.004   0.057   1416
  Dihedral  :  3.814  18.941   1132
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.55 %
    Favored  : 84.36 %
  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:  0.48 (0.27), residues: 1019
  helix:  2.48 (0.26), residues: 414
  sheet: -0.72 (0.36), residues: 214
  loop : -1.50 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.020   0.001   PHE R 335 
 TYR   0.012   0.001   TYR R 195 
 ARG   0.005   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.784 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: R  335 PHE cc_start: 0.5881 (p90) cc_final: 0.5343 (p90)
REVERT: R  341 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7564 (mt-10)
REVERT: R  358 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5915 (m-10)
REVERT: A   21 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6887 (mt-10)
REVERT: A   60 MET cc_start: 0.6730 (ptt) cc_final: 0.6309 (ptt)
REVERT: A  221 MET cc_start: 0.7395 (tpp) cc_final: 0.7157 (mmm)
REVERT: A  311 TYR cc_start: 0.6991 (m-80) cc_final: 0.6718 (m-80)
REVERT: B  175 GLN cc_start: 0.7919 (pm20) cc_final: 0.7598 (pm20)
REVERT: N   87 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8032 (mttm)
  outliers start: 17
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1960
  time to fit residues: 30.2162
Evaluate side-chains
  104 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 77 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.200340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.159012 restraints weight = 9310.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 2.27
r_work: 0.3548 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8111  Z= 0.209
  Angle     :  0.552  13.362  11009  Z= 0.278
  Chirality :  0.041   0.156   1250
  Planarity :  0.004   0.057   1416
  Dihedral  :  3.861  18.699   1132
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.78 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.27), residues: 1019
  helix:  2.44 (0.26), residues: 414
  sheet: -0.85 (0.36), residues: 219
  loop : -1.46 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.019   0.002   PHE R 335 
 TYR   0.011   0.001   TYR R 195 
 ARG   0.005   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.807 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8331 (mt-10)
REVERT: R  335 PHE cc_start: 0.5833 (p90) cc_final: 0.5285 (p90)
REVERT: R  341 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: R  358 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5941 (m-10)
REVERT: A  221 MET cc_start: 0.7363 (tpp) cc_final: 0.7124 (mmm)
REVERT: B   59 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7894 (m-80)
REVERT: B   90 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8548 (m)
REVERT: B  175 GLN cc_start: 0.7895 (pm20) cc_final: 0.7589 (pm20)
REVERT: N   87 LYS cc_start: 0.8286 (mtmm) cc_final: 0.8047 (mttm)
  outliers start: 20
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1909
  time to fit residues: 28.3382
Evaluate side-chains
  105 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.197561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.156772 restraints weight = 9281.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.22
r_work: 0.3551 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8111  Z= 0.209
  Angle     :  0.532  11.481  11009  Z= 0.272
  Chirality :  0.041   0.188   1250
  Planarity :  0.004   0.056   1416
  Dihedral  :  3.857  18.957   1132
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.64 %
    Favored  : 81.53 %
  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:  0.44 (0.27), residues: 1019
  helix:  2.45 (0.26), residues: 413
  sheet: -0.85 (0.35), residues: 219
  loop : -1.44 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.019   0.002   PHE R 335 
 TYR   0.011   0.001   TYR R 356 
 ARG   0.005   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.813 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8320 (mt-10)
REVERT: R  341 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7716 (mt-10)
REVERT: R  358 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.5972 (m-10)
REVERT: A   21 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6747 (mt-10)
REVERT: A  221 MET cc_start: 0.7332 (tpp) cc_final: 0.7108 (mmm)
REVERT: B   59 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7979 (m-80)
REVERT: B   90 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8547 (m)
REVERT: B  175 GLN cc_start: 0.7873 (pm20) cc_final: 0.7579 (pm20)
REVERT: N   87 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8056 (mttm)
  outliers start: 23
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1881
  time to fit residues: 29.1398
Evaluate side-chains
  109 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0020
   chunk 74 optimal weight:    0.7980
   chunk 13 optimal weight:    0.2980
   chunk 0 optimal weight:   30.0000
   chunk 42 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.4247 r_free = 0.4247 target = 0.198591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.157461 restraints weight = 9289.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 2.19
r_work: 0.3573 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8111  Z= 0.176
  Angle     :  0.516  12.179  11009  Z= 0.263
  Chirality :  0.041   0.218   1250
  Planarity :  0.003   0.055   1416
  Dihedral  :  3.783  18.517   1132
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.52 %
    Favored  : 81.53 %
  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:  0.50 (0.27), residues: 1019
  helix:  2.46 (0.26), residues: 415
  sheet: -0.77 (0.35), residues: 219
  loop : -1.41 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 197 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 335 
 TYR   0.012   0.001   TYR R 105 
 ARG   0.005   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: R   99 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8326 (mt-10)
REVERT: R  335 PHE cc_start: 0.5828 (p90) cc_final: 0.5244 (p90)
REVERT: R  341 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7696 (mt-10)
REVERT: R  358 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5964 (m-10)
REVERT: A   21 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6755 (mt-10)
REVERT: A  221 MET cc_start: 0.7310 (tpp) cc_final: 0.7093 (mmm)
REVERT: A  311 TYR cc_start: 0.6938 (m-80) cc_final: 0.6692 (m-80)
REVERT: B   55 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8744 (pp)
REVERT: B   59 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8021 (m-80)
REVERT: B   90 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (m)
REVERT: B  175 GLN cc_start: 0.7838 (pm20) cc_final: 0.7534 (pm20)
REVERT: B  234 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.7901 (m-80)
REVERT: N   87 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8090 (mttm)
  outliers start: 24
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1875
  time to fit residues: 29.0815
Evaluate side-chains
  112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4244 r_free = 0.4244 target = 0.198179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.157074 restraints weight = 9378.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.30
r_work: 0.3553 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8111  Z= 0.202
  Angle     :  0.532  12.231  11009  Z= 0.269
  Chirality :  0.041   0.242   1250
  Planarity :  0.003   0.055   1416
  Dihedral  :  3.824  19.142   1132
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.76 %
    Favored  : 81.03 %
  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:  0.49 (0.27), residues: 1019
  helix:  2.43 (0.26), residues: 415
  sheet: -0.76 (0.35), residues: 219
  loop : -1.39 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 335 
 TYR   0.011   0.001   TYR R 195 
 ARG   0.006   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: R   99 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8328 (mt-10)
REVERT: R  335 PHE cc_start: 0.5713 (p90) cc_final: 0.5176 (p90)
REVERT: R  341 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7697 (mt-10)
REVERT: R  358 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5958 (m-10)
REVERT: A   21 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6776 (mt-10)
REVERT: A   60 MET cc_start: 0.7008 (ptt) cc_final: 0.6659 (ptt)
REVERT: A  221 MET cc_start: 0.7314 (tpp) cc_final: 0.7096 (mmm)
REVERT: B   59 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8016 (m-80)
REVERT: B   90 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8540 (m)
REVERT: B  175 GLN cc_start: 0.7883 (pm20) cc_final: 0.7576 (pm20)
REVERT: B  234 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7895 (m-80)
REVERT: N   87 LYS cc_start: 0.8347 (mtmm) cc_final: 0.8095 (mttm)
  outliers start: 26
  outliers final: 18
  residues processed: 114
  average time/residue: 0.1822
  time to fit residues: 29.1302
Evaluate side-chains
  113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0570
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0030
   chunk 3 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5108

-------------------------------------------------------------------------------
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 = 0.4254 r_free = 0.4254 target = 0.199371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.158553 restraints weight = 9497.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.32
r_work: 0.3571 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8111  Z= 0.167
  Angle     :  0.531  12.390  11009  Z= 0.265
  Chirality :  0.041   0.311   1250
  Planarity :  0.003   0.053   1416
  Dihedral  :  3.739  18.490   1132
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.00 %
    Favored  : 80.42 %
  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:  0.57 (0.27), residues: 1019
  helix:  2.50 (0.26), residues: 415
  sheet: -0.66 (0.35), residues: 218
  loop : -1.39 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 197 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 335 
 TYR   0.014   0.001   TYR R 105 
 ARG   0.006   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   99 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8332 (mt-10)
REVERT: R  252 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6556 (pt0)
REVERT: R  335 PHE cc_start: 0.5623 (p90) cc_final: 0.5094 (p90)
REVERT: R  341 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7684 (mt-10)
REVERT: R  358 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6017 (m-80)
REVERT: A   21 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6831 (mt-10)
REVERT: A   60 MET cc_start: 0.6952 (ptt) cc_final: 0.6631 (ptt)
REVERT: A  311 TYR cc_start: 0.6925 (m-80) cc_final: 0.6693 (m-80)
REVERT: B   59 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8024 (m-80)
REVERT: B   61 MET cc_start: 0.8330 (ppp) cc_final: 0.7962 (ppp)
REVERT: B  234 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.7954 (m-80)
REVERT: N   87 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8070 (mttm)
  outliers start: 21
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1969
  time to fit residues: 30.6637
Evaluate side-chains
  113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.198348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.157658 restraints weight = 9316.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.25
r_work: 0.3576 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8111  Z= 0.197
  Angle     :  0.543  12.832  11009  Z= 0.272
  Chirality :  0.041   0.211   1250
  Planarity :  0.003   0.055   1416
  Dihedral  :  3.802  18.928   1132
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.00 %
    Favored  : 80.17 %
  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:  0.55 (0.27), residues: 1019
  helix:  2.46 (0.26), residues: 415
  sheet: -0.69 (0.35), residues: 218
  loop : -1.37 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 335 
 TYR   0.011   0.001   TYR R 195 
 ARG   0.006   0.000   ARG N  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: R   99 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8378 (mt-10)
REVERT: R  134 ASN cc_start: 0.7580 (m-40) cc_final: 0.7301 (m110)
REVERT: R  252 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6459 (pt0)
REVERT: R  335 PHE cc_start: 0.5617 (p90) cc_final: 0.5082 (p90)
REVERT: R  341 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7732 (mt-10)
REVERT: R  358 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6004 (m-80)
REVERT: A   21 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6812 (mt-10)
REVERT: A   60 MET cc_start: 0.6653 (ptt) cc_final: 0.6363 (ptt)
REVERT: A  311 TYR cc_start: 0.6953 (m-80) cc_final: 0.6709 (m-80)
REVERT: B   55 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8747 (pp)
REVERT: B   59 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8020 (m-80)
REVERT: B  175 GLN cc_start: 0.7805 (pm20) cc_final: 0.7500 (pm20)
REVERT: B  234 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.7883 (m-80)
REVERT: N   87 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8116 (mttm)
  outliers start: 23
  outliers final: 17
  residues processed: 112
  average time/residue: 0.1892
  time to fit residues: 29.4332
Evaluate side-chains
  115 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 34 optimal weight:    0.2980
   chunk 70 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0060
   chunk 26 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.196909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.157137 restraints weight = 9337.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.40
r_work: 0.3564 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8111  Z= 0.173
  Angle     :  0.541  12.736  11009  Z= 0.268
  Chirality :  0.041   0.240   1250
  Planarity :  0.003   0.054   1416
  Dihedral  :  3.726  18.400   1132
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.24 %
    Favored  : 80.05 %
  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:  0.58 (0.27), residues: 1019
  helix:  2.49 (0.26), residues: 415
  sheet: -0.64 (0.35), residues: 218
  loop : -1.37 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 197 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 335 
 TYR   0.012   0.001   TYR R 195 
 ARG   0.004   0.000   ARG N  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3817.46 seconds
wall clock time: 66 minutes 18.45 seconds (3978.45 seconds total)