Starting phenix.real_space_refine
on Wed Mar 12 18:08:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rmg_24569/03_2025/7rmg_24569.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rmg_24569/03_2025/7rmg_24569.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rmg_24569/03_2025/7rmg_24569.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rmg_24569/03_2025/7rmg_24569.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rmg_24569/03_2025/7rmg_24569.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rmg_24569/03_2025/7rmg_24569.cif"
  }
  resolution = 3.0
  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=   0.004 sd=   0.412
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic.
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      53      5.16       5
     C    4737      2.51       5
     N    1226      2.21       5
     O    1300      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: 7316
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1510
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 188}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 71
    Chain: "R"
      Number of atoms: 2306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2306
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 14, 'TRANS': 274}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "S"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 8}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2319
          Classifications: {'peptide': 322}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 5, 'TRANS': 316}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 149
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 113
    Chain: "G"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 245
          Classifications: {'peptide': 38}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "N"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 851
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 5.08, per 1000 atoms: 0.69
  Number of scatterers: 7316
  At special positions: 0
  Unit cell: (70.14, 96.86, 131.93, 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      53     16.00
     O    1300      8.00
     N    1226      7.00
     C    4737      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 180 " 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=2.04

  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: 1.79
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1838

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 11 sheets defined
      39.4% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 38
      removed outlier: 3.515A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.626A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 4.080A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 350
      removed outlier: 3.587A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.553A  pdb=" N   ARG A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 60
      removed outlier: 3.988A  pdb=" N   ILE R  42 " --> pdb=" O   ALA R  38 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   HIS R  60 " --> pdb=" O   ILE R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 96
      removed outlier: 4.352A  pdb=" N   HIS R  95 " --> pdb=" O   THR R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 100 through 136
      removed outlier: 4.233A  pdb=" N   TYR R 104 " --> pdb=" O   TYR R 100 " (cutoff:3.500A)
      Proline residue:  R 112  - end of helix
    Processing helix  chain 'R' and resid 143 through 168
      Proline residue:  R 164  - end of helix
    Processing helix  chain 'R' and resid 190 through 225
      removed outlier: 5.024A  pdb=" N   LEU R 207 " --> pdb=" O   LEU R 203 " (cutoff:3.500A)
      Proline residue:  R 208  - end of helix
      removed outlier: 3.586A  pdb=" N   ALA R 225 " --> pdb=" O   ILE R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 239 through 270
      removed outlier: 3.646A  pdb=" N   LYS R 243 " --> pdb=" O   GLN R 239 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 271 through 273
      No H-bonds generated for 'chain 'R' and resid 271 through 273'
    Processing helix  chain 'R' and resid 274 through 280
      removed outlier: 3.907A  pdb=" N   LEU R 277 " --> pdb=" O   ASN R 274 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   TYR R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU R 279 " --> pdb=" O   ASP R 276 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS R 280 " --> pdb=" O   LEU R 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 274 through 280'
    Processing helix  chain 'R' and resid 281 through 296
    Processing helix  chain 'R' and resid 299 through 309
      removed outlier: 3.915A  pdb=" N   ILE R 303 " --> pdb=" O   MET R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 309 through 320
    Processing helix  chain 'B' and resid 15 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.832A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.577A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.768A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.389A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 174
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.988A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.653A  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: 3.652A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.813A  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: 3.600A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.993A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.759A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.789A  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: 6.953A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.356A  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: 3.596A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60
      removed outlier: 5.165A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1098 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: 2.14

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1362
        1.33 -     1.45: 2058
        1.45 -     1.58: 3997
        1.58 -     1.71: 0
        1.71 -     1.83: 75
  Bond restraints: 7492
  Sorted by residual:
  bond pdb=" C   ILE A 382 "
       pdb=" O   ILE A 382 "
    ideal  model  delta    sigma   weight residual
    1.237  1.202  0.035 1.19e-02 7.06e+03 8.43e+00
  bond pdb=" N   ILE B  58 "
       pdb=" CA  ILE B  58 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.66e+00
  bond pdb=" C   ASP A 381 "
       pdb=" O   ASP A 381 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.034 1.26e-02 6.30e+03 7.24e+00
  bond pdb=" N   ILE A 382 "
       pdb=" CA  ILE A 382 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 1.21e-02 6.83e+03 7.09e+00
  bond pdb=" C   ILE B  58 "
       pdb=" O   ILE B  58 "
    ideal  model  delta    sigma   weight residual
    1.237  1.206  0.031 1.20e-02 6.94e+03 6.84e+00
  ... (remaining 7487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 9839
        1.73 -     3.46: 313
        3.46 -     5.20: 55
        5.20 -     6.93: 11
        6.93 -     8.66: 8
  Bond angle restraints: 10226
  Sorted by residual:
  angle pdb=" CA  ILE A 382 "
        pdb=" C   ILE A 382 "
        pdb=" O   ILE A 382 "
      ideal   model   delta    sigma   weight residual
     120.85  116.82    4.03 1.06e+00 8.90e-01 1.45e+01
  angle pdb=" O   ILE A 382 "
        pdb=" C   ILE A 382 "
        pdb=" N   ILE A 383 "
      ideal   model   delta    sigma   weight residual
     121.83  125.41   -3.58 1.03e+00 9.43e-01 1.21e+01
  angle pdb=" O   LYS A 380 "
        pdb=" C   LYS A 380 "
        pdb=" N   ASP A 381 "
      ideal   model   delta    sigma   weight residual
     122.12  118.52    3.60 1.06e+00 8.90e-01 1.15e+01
  angle pdb=" N   PHE R 111 "
        pdb=" CA  PHE R 111 "
        pdb=" C   PHE R 111 "
      ideal   model   delta    sigma   weight residual
     109.81  117.17   -7.36 2.21e+00 2.05e-01 1.11e+01
  angle pdb=" CA  LYS A 380 "
        pdb=" C   LYS A 380 "
        pdb=" N   ASP A 381 "
      ideal   model   delta    sigma   weight residual
     117.30  121.10   -3.80 1.16e+00 7.43e-01 1.08e+01
  ... (remaining 10221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 3968
       16.21 -    32.41: 294
       32.41 -    48.61: 50
       48.61 -    64.82: 11
       64.82 -    81.02: 9
  Dihedral angle restraints: 4332
    sinusoidal: 1495
      harmonic: 2837
  Sorted by residual:
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.28  -25.72     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.50  -23.50     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  TYR R 205 "
           pdb=" C   TYR R 205 "
           pdb=" N   PHE R 206 "
           pdb=" CA  PHE R 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.45  -19.55     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 4329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 786
       0.041 -    0.082: 272
       0.082 -    0.123: 99
       0.123 -    0.165: 31
       0.165 -    0.206: 6
  Chirality restraints: 1194
  Sorted by residual:
  chirality pdb=" CB  ILE B  58 "
            pdb=" CA  ILE B  58 "
            pdb=" CG1 ILE B  58 "
            pdb=" CG2 ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  ILE A 382 "
            pdb=" CA  ILE A 382 "
            pdb=" CG1 ILE A 382 "
            pdb=" CG2 ILE A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  ILE A 383 "
            pdb=" CA  ILE A 383 "
            pdb=" CG1 ILE A 383 "
            pdb=" CG2 ILE A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1191 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.044 5.00e-02 4.00e+02   6.70e-02 7.17e+00
        pdb=" N   PRO B 236 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R  82 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.85e+00
        pdb=" C   ALA R  82 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ALA R  82 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA R  83 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 241 "    0.013 2.00e-02 2.50e+03   1.95e-02 6.62e+00
        pdb=" CG  PHE B 241 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 241 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 241 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 241 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 241 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 241 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2015
        2.81 -     3.33: 6111
        3.33 -     3.86: 12100
        3.86 -     4.38: 14013
        4.38 -     4.90: 25013
  Nonbonded interactions: 59252
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   ALA R  36 "
            pdb=" OG1 THR R  40 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.349 3.040
  ... (remaining 59247 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:             15.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.600
  Find NCS groups from input model:        0.080
  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:12.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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   0.062   7492  Z= 0.251
  Angle     :  0.757   8.659  10226  Z= 0.432
  Chirality :  0.051   0.206   1194
  Planarity :  0.006   0.067   1275
  Dihedral  : 12.654  81.023   2485
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.41 %
    Favored  : 99.45 %
  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: -0.92 (0.25), residues: 942
  helix: -0.67 (0.24), residues: 352
  sheet:  0.38 (0.34), residues: 211
  loop : -0.97 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  99 
 HIS   0.015   0.002   HIS B  54 
 PHE   0.044   0.002   PHE B 241 
 TYR   0.020   0.002   TYR R  92 
 ARG   0.004   0.000   ARG B 314 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  272 ASP cc_start: 0.6554 (m-30) cc_final: 0.5659 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 1.0128
  time to fit residues: 161.4705
Evaluate side-chains
  108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
A 278 ASN
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  50 ASN
R  73 ASN
R 318 HIS
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.109066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.096398 restraints weight = 15500.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.54
r_work: 0.3315 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7492  Z= 0.207
  Angle     :  0.533   9.211  10226  Z= 0.291
  Chirality :  0.043   0.200   1194
  Planarity :  0.004   0.049   1275
  Dihedral  :  4.351  22.439   1034
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 10.03 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 942
  helix:  0.89 (0.26), residues: 366
  sheet:  0.59 (0.33), residues: 208
  loop : -0.75 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 197 
 PHE   0.014   0.001   PHE R 264 
 TYR   0.011   0.001   TYR G  40 
 ARG   0.007   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.529 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7779 (tp30)
REVERT: A  272 ASP cc_start: 0.8004 (m-30) cc_final: 0.7605 (m-30)
REVERT: A  339 TYR cc_start: 0.8701 (m-80) cc_final: 0.8375 (m-80)
REVERT: R  139 GLN cc_start: 0.9123 (tp40) cc_final: 0.8854 (mp10)
REVERT: R  172 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6628 (tm-30)
REVERT: R  186 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6908 (tm-30)
REVERT: N   50 ASP cc_start: 0.8238 (p0) cc_final: 0.7711 (p0)
REVERT: N   53 GLN cc_start: 0.7242 (mp10) cc_final: 0.6966 (mp10)
  outliers start: 15
  outliers final: 6
  residues processed: 121
  average time/residue: 1.2451
  time to fit residues: 160.4629
Evaluate side-chains
  106 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0670
   chunk 63 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0570
   chunk 23 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0470
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 GLN
R 318 HIS
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.111002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.098637 restraints weight = 15896.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.45
r_work: 0.3360 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7492  Z= 0.131
  Angle     :  0.485   8.355  10226  Z= 0.262
  Chirality :  0.041   0.196   1194
  Planarity :  0.003   0.044   1275
  Dihedral  :  3.984  20.034   1034
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.81 %
    Favored  : 85.71 %
  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:  0.85 (0.27), residues: 942
  helix:  1.57 (0.27), residues: 367
  sheet:  0.77 (0.34), residues: 208
  loop : -0.56 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 261 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.005   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8499 (tp40) cc_final: 0.7924 (tm-30)
REVERT: A  268 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A  272 ASP cc_start: 0.8039 (m-30) cc_final: 0.7423 (m-30)
REVERT: R  139 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8873 (mp10)
REVERT: R  186 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6882 (tm-30)
REVERT: B  243 THR cc_start: 0.8995 (p) cc_final: 0.8732 (p)
REVERT: N   50 ASP cc_start: 0.8098 (p0) cc_final: 0.7612 (p0)
REVERT: N   53 GLN cc_start: 0.7092 (mp10) cc_final: 0.6757 (mp10)
  outliers start: 18
  outliers final: 7
  residues processed: 126
  average time/residue: 0.9855
  time to fit residues: 132.8706
Evaluate side-chains
  116 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  139 GLN
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 43 optimal weight:    0.3980
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 318 HIS
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.109073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.096676 restraints weight = 16027.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.43
r_work: 0.3352 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7492  Z= 0.202
  Angle     :  0.504   9.440  10226  Z= 0.275
  Chirality :  0.043   0.201   1194
  Planarity :  0.003   0.041   1275
  Dihedral  :  4.059  20.306   1034
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.23 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.28), residues: 942
  helix:  1.80 (0.28), residues: 367
  sheet:  0.79 (0.34), residues: 210
  loop : -0.43 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  55 
 HIS   0.004   0.001   HIS R 197 
 PHE   0.014   0.001   PHE R 264 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.004   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8556 (tp40) cc_final: 0.7664 (tm-30)
REVERT: A   33 ASP cc_start: 0.8970 (m-30) cc_final: 0.8558 (m-30)
REVERT: A  268 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: A  272 ASP cc_start: 0.8046 (m-30) cc_final: 0.7427 (m-30)
REVERT: R  186 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6834 (tm-30)
REVERT: N   50 ASP cc_start: 0.8337 (p0) cc_final: 0.7825 (p0)
REVERT: N   53 GLN cc_start: 0.7255 (mp10) cc_final: 0.6939 (mp10)
  outliers start: 23
  outliers final: 8
  residues processed: 117
  average time/residue: 0.9520
  time to fit residues: 119.2744
Evaluate side-chains
  105 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 318 HIS
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.106888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.094531 restraints weight = 16028.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.44
r_work: 0.3323 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7492  Z= 0.242
  Angle     :  0.542   9.858  10226  Z= 0.292
  Chirality :  0.044   0.181   1194
  Planarity :  0.003   0.040   1275
  Dihedral  :  4.167  21.262   1034
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.60 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 942
  helix:  1.84 (0.28), residues: 366
  sheet:  0.80 (0.34), residues: 210
  loop : -0.44 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 197 
 PHE   0.016   0.001   PHE R 264 
 TYR   0.012   0.001   TYR R 278 
 ARG   0.003   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8527 (tp40) cc_final: 0.7990 (tm-30)
REVERT: A  268 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7664 (tm-30)
REVERT: A  272 ASP cc_start: 0.8095 (m-30) cc_final: 0.7398 (m-30)
REVERT: R  186 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6771 (tm-30)
REVERT: N   50 ASP cc_start: 0.8431 (p0) cc_final: 0.7895 (p0)
  outliers start: 21
  outliers final: 9
  residues processed: 115
  average time/residue: 0.9585
  time to fit residues: 118.1233
Evaluate side-chains
  107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   42 ILE
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0050
   chunk 2 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    1.3600

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.106561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094050 restraints weight = 16073.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.44
r_work: 0.3324 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7492  Z= 0.222
  Angle     :  0.536   8.527  10226  Z= 0.288
  Chirality :  0.043   0.167   1194
  Planarity :  0.003   0.039   1275
  Dihedral  :  4.193  22.759   1034
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.29 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.28), residues: 942
  helix:  1.81 (0.28), residues: 367
  sheet:  0.83 (0.34), residues: 212
  loop : -0.37 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 197 
 PHE   0.015   0.001   PHE R 264 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.003   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8545 (tp40) cc_final: 0.7696 (tm-30)
REVERT: A   33 ASP cc_start: 0.9012 (m-30) cc_final: 0.8479 (m-30)
REVERT: A  268 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: A  272 ASP cc_start: 0.8127 (m-30) cc_final: 0.7477 (m-30)
REVERT: R  186 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6754 (tm-30)
REVERT: B  101 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8143 (mmm)
REVERT: N   50 ASP cc_start: 0.8423 (p0) cc_final: 0.7892 (p0)
  outliers start: 21
  outliers final: 9
  residues processed: 116
  average time/residue: 0.9640
  time to fit residues: 119.7614
Evaluate side-chains
  108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.102748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.090243 restraints weight = 15869.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.47
r_work: 0.3216 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7492  Z= 0.348
  Angle     :  0.607   9.572  10226  Z= 0.327
  Chirality :  0.046   0.168   1194
  Planarity :  0.004   0.038   1275
  Dihedral  :  4.512  25.579   1034
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.29 %
    Favored  : 82.42 %
  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:  1.06 (0.27), residues: 942
  helix:  1.70 (0.27), residues: 366
  sheet:  1.02 (0.34), residues: 209
  loop : -0.47 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 197 
 PHE   0.018   0.002   PHE R 264 
 TYR   0.016   0.001   TYR A 339 
 ARG   0.003   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8581 (tp40) cc_final: 0.7990 (tm-30)
REVERT: A  272 ASP cc_start: 0.8147 (m-30) cc_final: 0.7942 (m-30)
REVERT: R  186 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6736 (tm-30)
REVERT: B  101 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8161 (mmm)
REVERT: N   50 ASP cc_start: 0.8518 (p0) cc_final: 0.7966 (p0)
  outliers start: 24
  outliers final: 13
  residues processed: 108
  average time/residue: 1.0455
  time to fit residues: 121.0970
Evaluate side-chains
  108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   42 ILE
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  273 ILE
Chi-restraints excluded: chain R residue  306 CYS
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.105068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.092696 restraints weight = 16131.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.43
r_work: 0.3302 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7492  Z= 0.250
  Angle     :  0.569   8.620  10226  Z= 0.307
  Chirality :  0.044   0.168   1194
  Planarity :  0.003   0.037   1275
  Dihedral  :  4.356  24.348   1034
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.66 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 942
  helix:  1.85 (0.27), residues: 364
  sheet:  1.04 (0.34), residues: 208
  loop : -0.50 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 197 
 PHE   0.016   0.001   PHE R 264 
 TYR   0.017   0.001   TYR R 278 
 ARG   0.003   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8555 (tp40) cc_final: 0.7675 (tm-30)
REVERT: A   33 ASP cc_start: 0.9013 (m-30) cc_final: 0.8538 (m-30)
REVERT: A  268 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8113 (tp30)
REVERT: R  186 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6741 (tm-30)
REVERT: G   48 ASP cc_start: 0.7725 (t0) cc_final: 0.7511 (t0)
REVERT: N   50 ASP cc_start: 0.8487 (p0) cc_final: 0.7961 (p0)
  outliers start: 17
  outliers final: 11
  residues processed: 108
  average time/residue: 0.9876
  time to fit residues: 115.5873
Evaluate side-chains
  111 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  273 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** R  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 318 HIS
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.107128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.094764 restraints weight = 16153.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.43
r_work: 0.3338 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7492  Z= 0.179
  Angle     :  0.545   9.682  10226  Z= 0.293
  Chirality :  0.043   0.185   1194
  Planarity :  0.003   0.036   1275
  Dihedral  :  4.126  22.306   1034
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.21 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.28), residues: 942
  helix:  1.98 (0.28), residues: 366
  sheet:  0.93 (0.34), residues: 211
  loop : -0.38 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R  98 
 HIS   0.003   0.001   HIS R 197 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.020   0.001   TYR R 278 
 ARG   0.002   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8516 (tp40) cc_final: 0.7899 (tm-30)
REVERT: R  186 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6735 (tm-30)
REVERT: B  243 THR cc_start: 0.8995 (p) cc_final: 0.8746 (p)
REVERT: N   50 ASP cc_start: 0.8410 (p0) cc_final: 0.7902 (p0)
  outliers start: 13
  outliers final: 10
  residues processed: 110
  average time/residue: 1.0121
  time to fit residues: 120.1961
Evaluate side-chains
  110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
R 318 HIS
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.104825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.092611 restraints weight = 16445.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.42
r_work: 0.3291 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7492  Z= 0.299
  Angle     :  0.610  11.471  10226  Z= 0.329
  Chirality :  0.045   0.201   1194
  Planarity :  0.003   0.036   1275
  Dihedral  :  4.384  24.223   1034
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.62 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.28), residues: 942
  helix:  1.87 (0.28), residues: 365
  sheet:  1.00 (0.34), residues: 209
  loop : -0.43 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 197 
 PHE   0.017   0.001   PHE R 264 
 TYR   0.020   0.001   TYR R 278 
 ARG   0.002   0.000   ARG R 313 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 1.305 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8548 (tp40) cc_final: 0.7649 (tm-30)
REVERT: A   33 ASP cc_start: 0.9007 (m-30) cc_final: 0.8512 (m-30)
REVERT: R  186 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6691 (tm-30)
REVERT: R  272 TYR cc_start: 0.8285 (m-80) cc_final: 0.8035 (m-80)
REVERT: G   48 ASP cc_start: 0.7729 (t0) cc_final: 0.7522 (t0)
REVERT: N   50 ASP cc_start: 0.8535 (p0) cc_final: 0.8004 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 110
  average time/residue: 1.1719
  time to fit residues: 138.5572
Evaluate side-chains
  108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  186 GLU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
R 318 HIS
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.106830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.094490 restraints weight = 16042.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.42
r_work: 0.3334 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7492  Z= 0.193
  Angle     :  0.561  10.635  10226  Z= 0.302
  Chirality :  0.043   0.196   1194
  Planarity :  0.003   0.036   1275
  Dihedral  :  4.154  21.642   1034
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.03 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.28), residues: 942
  helix:  2.04 (0.27), residues: 364
  sheet:  0.94 (0.34), residues: 211
  loop : -0.37 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R  98 
 HIS   0.004   0.001   HIS R 318 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.021   0.001   TYR R 278 
 ARG   0.002   0.000   ARG A 232 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5309.01 seconds
wall clock time: 94 minutes 33.47 seconds (5673.47 seconds total)