Starting phenix.real_space_refine
on Wed Feb 12 17:33:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rmg_24569/02_2025/7rmg_24569.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rmg_24569/02_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_24569/02_2025/7rmg_24569.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rmg_24569/02_2025/7rmg_24569.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rmg_24569/02_2025/7rmg_24569.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rmg_24569/02_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-5592/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: 4.86, per 1000 atoms: 0.66
  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: 1.72
  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: 0.78
  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: 2.01 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:             2.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.230
  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:13.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.710
-------------------------------------------------------------------------------
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  : 0.881 
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: 1.0217
  time to fit residues: 162.9836
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  : 0.844 
-------------------------------------------------------------------------------
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 = 15500.500|
|-----------------------------------------------------------------------------|
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: 4.96 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  22.438   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  : 0.843 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7781 (tp30)
REVERT: A  272 ASP cc_start: 0.8003 (m-30) cc_final: 0.7605 (m-30)
REVERT: A  339 TYR cc_start: 0.8701 (m-80) cc_final: 0.8373 (m-80)
REVERT: A  385 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8408 (tp-100)
REVERT: R  139 GLN cc_start: 0.9123 (tp40) cc_final: 0.8854 (mp10)
REVERT: R  172 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6627 (tm-30)
REVERT: R  186 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6906 (tm-30)
REVERT: N   50 ASP cc_start: 0.8240 (p0) cc_final: 0.7712 (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: 1.0259
  time to fit residues: 132.3885
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  : 0.868 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   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:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.109009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.096484 restraints weight = 16018.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.45
r_work: 0.3358 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2017

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= 0.191
  Angle     :  0.509   9.392  10226  Z= 0.276
  Chirality :  0.042   0.193   1194
  Planarity :  0.003   0.043   1275
  Dihedral  :  4.149  20.603   1034
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 10.99 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 942
  helix:  1.53 (0.27), residues: 367
  sheet:  0.79 (0.34), residues: 208
  loop : -0.57 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R  55 
 HIS   0.004   0.001   HIS R 197 
 PHE   0.013   0.001   PHE R 264 
 TYR   0.011   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
  138 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8557 (tp40) cc_final: 0.7808 (tm-30)
REVERT: A  268 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: A  272 ASP cc_start: 0.8026 (m-30) cc_final: 0.7359 (m-30)
REVERT: R  123 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8661 (ttp)
REVERT: R  139 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8881 (mp10)
REVERT: R  186 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6809 (tm-30)
REVERT: B  138 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8418 (mt-10)
REVERT: N   50 ASP cc_start: 0.8314 (p0) cc_final: 0.7801 (p0)
REVERT: N   53 GLN cc_start: 0.7258 (mp10) cc_final: 0.6856 (mp10)
  outliers start: 25
  outliers final: 8
  residues processed: 123
  average time/residue: 1.0534
  time to fit residues: 138.2404
Evaluate side-chains
  115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
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  123 MET
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 R residue  251 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  138 GLU
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:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0770
   chunk 1 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.1344

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.108527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.095918 restraints weight = 16094.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.47
r_work: 0.3345 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7492  Z= 0.194
  Angle     :  0.516   9.490  10226  Z= 0.279
  Chirality :  0.043   0.194   1194
  Planarity :  0.003   0.040   1275
  Dihedral  :  4.075  20.475   1034
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.19 %
    Favored  : 83.65 %
  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:  1.02 (0.28), residues: 942
  helix:  1.76 (0.28), residues: 367
  sheet:  0.77 (0.34), residues: 210
  loop : -0.45 (0.32), residues: 365

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   0.014   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
  127 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8495 (tp40) cc_final: 0.7984 (tm-30)
REVERT: A  268 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7664 (tm-30)
REVERT: A  272 ASP cc_start: 0.8071 (m-30) cc_final: 0.7406 (m-30)
REVERT: R  123 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8682 (ttp)
REVERT: R  139 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8881 (mp10)
REVERT: R  186 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6814 (tm-30)
REVERT: N   50 ASP cc_start: 0.8353 (p0) cc_final: 0.7849 (p0)
REVERT: N   53 GLN cc_start: 0.7283 (mp10) cc_final: 0.6895 (mp10)
  outliers start: 23
  outliers final: 10
  residues processed: 116
  average time/residue: 0.9429
  time to fit residues: 117.3147
Evaluate side-chains
  110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
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  123 MET
Chi-restraints excluded: chain R residue  139 GLN
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  186 GLU
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 G residue   38 MET
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:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 79 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.108829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.096295 restraints weight = 16068.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.44
r_work: 0.3354 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7492  Z= 0.178
  Angle     :  0.509   8.942  10226  Z= 0.273
  Chirality :  0.042   0.201   1194
  Planarity :  0.003   0.040   1275
  Dihedral  :  3.979  19.626   1034
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.42 %
    Favored  : 83.10 %
  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:  1.15 (0.28), residues: 942
  helix:  1.88 (0.28), residues: 368
  sheet:  0.89 (0.34), residues: 208
  loop : -0.44 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 197 
 PHE   0.014   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
  127 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8497 (tp40) cc_final: 0.7950 (tm-30)
REVERT: A   42 ARG cc_start: 0.8263 (mpp80) cc_final: 0.7765 (mtm180)
REVERT: A  268 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7658 (tm-30)
REVERT: A  272 ASP cc_start: 0.8062 (m-30) cc_final: 0.7446 (m-30)
REVERT: R  139 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8898 (mp10)
REVERT: R  186 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6789 (tm-30)
REVERT: B  243 THR cc_start: 0.8992 (p) cc_final: 0.8744 (p)
REVERT: N   50 ASP cc_start: 0.8353 (p0) cc_final: 0.7852 (p0)
REVERT: N   53 GLN cc_start: 0.7312 (mp10) cc_final: 0.6909 (mp10)
  outliers start: 18
  outliers final: 10
  residues processed: 117
  average time/residue: 0.9419
  time to fit residues: 118.2227
Evaluate side-chains
  114 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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  139 GLN
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 G residue   38 MET
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:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3648 r_free = 0.3648 target = 0.108900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.096275 restraints weight = 16016.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.47
r_work: 0.3364 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7492  Z= 0.165
  Angle     :  0.506   7.974  10226  Z= 0.271
  Chirality :  0.042   0.200   1194
  Planarity :  0.003   0.039   1275
  Dihedral  :  3.969  21.432   1034
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.15 %
    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:  1.24 (0.28), residues: 942
  helix:  1.94 (0.28), residues: 369
  sheet:  0.87 (0.34), residues: 209
  loop : -0.33 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 197 
 PHE   0.013   0.001   PHE R 264 
 TYR   0.011   0.001   TYR R 278 
 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
  129 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8485 (tp40) cc_final: 0.7895 (tm-30)
REVERT: A   42 ARG cc_start: 0.8257 (mpp80) cc_final: 0.7794 (mtm110)
REVERT: A  268 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7618 (tm-30)
REVERT: A  272 ASP cc_start: 0.8095 (m-30) cc_final: 0.7463 (m-30)
REVERT: R  174 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7052 (mpt)
REVERT: R  186 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6801 (tm-30)
REVERT: B  243 THR cc_start: 0.9001 (p) cc_final: 0.8746 (p)
REVERT: N   50 ASP cc_start: 0.8307 (p0) cc_final: 0.7781 (p0)
REVERT: N   53 GLN cc_start: 0.7285 (mp10) cc_final: 0.6854 (mp10)
  outliers start: 22
  outliers final: 9
  residues processed: 119
  average time/residue: 0.9769
  time to fit residues: 124.3981
Evaluate side-chains
  109 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
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  174 MET
Chi-restraints excluded: chain R residue  186 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.107867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.095268 restraints weight = 15905.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.45
r_work: 0.3347 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2426

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= 0.194
  Angle     :  0.528   8.745  10226  Z= 0.283
  Chirality :  0.043   0.215   1194
  Planarity :  0.003   0.038   1275
  Dihedral  :  4.037  20.900   1034
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.84 %
    Favored  : 82.55 %
  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:  1.25 (0.28), residues: 942
  helix:  1.94 (0.28), residues: 369
  sheet:  0.85 (0.34), residues: 213
  loop : -0.30 (0.33), residues: 360

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 A 212 
 TYR   0.012   0.001   TYR R 278 
 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: 19
    poor density    : 103
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8522 (tp40) cc_final: 0.7920 (tm-30)
REVERT: A   42 ARG cc_start: 0.8317 (mpp80) cc_final: 0.7841 (mtm110)
REVERT: A  268 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A  272 ASP cc_start: 0.8086 (m-30) cc_final: 0.7455 (m-30)
REVERT: R  186 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6767 (tm-30)
REVERT: N   50 ASP cc_start: 0.8357 (p0) cc_final: 0.7835 (p0)
  outliers start: 19
  outliers final: 11
  residues processed: 114
  average time/residue: 0.9490
  time to fit residues: 115.8756
Evaluate side-chains
  112 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.106773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.094254 restraints weight = 16051.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.43
r_work: 0.3331 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7492  Z= 0.218
  Angle     :  0.545   9.452  10226  Z= 0.293
  Chirality :  0.043   0.182   1194
  Planarity :  0.003   0.038   1275
  Dihedral  :  4.108  21.623   1034
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.25 %
    Favored  : 82.14 %
  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:  1.24 (0.28), residues: 942
  helix:  1.90 (0.28), residues: 369
  sheet:  0.87 (0.34), residues: 215
  loop : -0.31 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 197 
 PHE   0.015   0.001   PHE R 264 
 TYR   0.016   0.001   TYR R 278 
 ARG   0.002   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
  116 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8564 (tp40) cc_final: 0.7964 (tm-30)
REVERT: A   42 ARG cc_start: 0.8350 (mpp80) cc_final: 0.7849 (mtm180)
REVERT: A  268 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: A  272 ASP cc_start: 0.8103 (m-30) cc_final: 0.7463 (m-30)
REVERT: R  186 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6732 (tm-30)
REVERT: N   50 ASP cc_start: 0.8410 (p0) cc_final: 0.7908 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 108
  average time/residue: 0.9540
  time to fit residues: 110.8770
Evaluate side-chains
  108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
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   18 LEU
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:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 91 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.108298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.095816 restraints weight = 16127.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.46
r_work: 0.3355 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2516

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= 0.175
  Angle     :  0.525   8.439  10226  Z= 0.281
  Chirality :  0.042   0.173   1194
  Planarity :  0.003   0.038   1275
  Dihedral  :  3.987  20.934   1034
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.93 %
    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:  1.34 (0.28), residues: 942
  helix:  2.02 (0.28), residues: 368
  sheet:  1.02 (0.34), residues: 209
  loop : -0.33 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 197 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.017   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: 15
    poor density    : 101
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8529 (tp40) cc_final: 0.7909 (tm-30)
REVERT: A   42 ARG cc_start: 0.8317 (mpp80) cc_final: 0.7827 (mtm180)
REVERT: A  268 GLU cc_start: 0.8633 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: A  272 ASP cc_start: 0.8167 (m-30) cc_final: 0.7524 (m-30)
REVERT: R  186 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6750 (tm-30)
REVERT: R  272 TYR cc_start: 0.8247 (m-80) cc_final: 0.8040 (m-80)
REVERT: B  243 THR cc_start: 0.8989 (p) cc_final: 0.8742 (p)
REVERT: N   50 ASP cc_start: 0.8340 (p0) cc_final: 0.7823 (p0)
  outliers start: 15
  outliers final: 12
  residues processed: 110
  average time/residue: 0.9714
  time to fit residues: 114.5946
Evaluate side-chains
  112 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
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   18 LEU
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:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.104953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.092377 restraints weight = 16348.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.46
r_work: 0.3295 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7492  Z= 0.291
  Angle     :  0.589  10.415  10226  Z= 0.317
  Chirality :  0.045   0.224   1194
  Planarity :  0.003   0.039   1275
  Dihedral  :  4.299  23.778   1034
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.80 %
    Favored  : 81.87 %
  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:  1.22 (0.28), residues: 942
  helix:  1.89 (0.28), residues: 366
  sheet:  0.96 (0.33), residues: 211
  loop : -0.37 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 197 
 PHE   0.016   0.001   PHE R 264 
 TYR   0.017   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: 17
    poor density    : 98
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8613 (tp40) cc_final: 0.8006 (tm-30)
REVERT: A   42 ARG cc_start: 0.8400 (mpp80) cc_final: 0.7900 (mtm180)
REVERT: A  268 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: A  272 ASP cc_start: 0.8169 (m-30) cc_final: 0.7478 (m-30)
REVERT: R  186 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6718 (tm-30)
REVERT: N   50 ASP cc_start: 0.8499 (p0) cc_final: 0.7969 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 106
  average time/residue: 0.9131
  time to fit residues: 104.0092
Evaluate side-chains
  107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
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 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  245 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   18 LEU
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:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3625 r_free = 0.3625 target = 0.107177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.094705 restraints weight = 16016.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.44
r_work: 0.3341 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7492  Z= 0.188
  Angle     :  0.546  10.214  10226  Z= 0.293
  Chirality :  0.043   0.226   1194
  Planarity :  0.003   0.038   1275
  Dihedral  :  4.100  21.648   1034
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.62 %
    Favored  : 81.46 %
  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:  1.32 (0.28), residues: 942
  helix:  2.01 (0.27), residues: 365
  sheet:  1.02 (0.33), residues: 210
  loop : -0.34 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 261 
 HIS   0.004   0.001   HIS R 318 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.021   0.001   TYR R 278 
 ARG   0.002   0.000   ARG R 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4870.06 seconds
wall clock time: 86 minutes 55.25 seconds (5215.25 seconds total)