Starting phenix.real_space_refine
on Mon Jul 28 13:15:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v6a_31740/07_2025/7v6a_31740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v6a_31740/07_2025/7v6a_31740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2025/7v6a_31740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2025/7v6a_31740.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2025/7v6a_31740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2025/7v6a_31740.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.024
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 2132 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      65      5.16       5
     C    5497      2.51       5
     N    1460      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8584
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1646
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 2562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2562
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2168
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 10, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'5XI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.83, per 1000 atoms: 0.56
  Number of scatterers: 8584
  At special positions: 0
  Unit cell: (94.2936, 123.414, 123.414, 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      65     16.00
     O    1562      8.00
     N    1460      7.00
     C    5497      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      35.9% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.087A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.887A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.124A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 34 through 42
      removed outlier: 3.558A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 55
    Processing helix  chain 'R' and resid 55 through 60
    Processing helix  chain 'R' and resid 65 through 67
      No H-bonds generated for 'chain 'R' and resid 65 through 67'
    Processing helix  chain 'R' and resid 68 through 91
      removed outlier: 5.378A  pdb=" N   MET R  86 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   ASN R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 101 through 136
      removed outlier: 4.149A  pdb=" N   TYR R 113 " --> pdb=" O   LEU R 109 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN R 117 " --> pdb=" O   TYR R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 144
    Processing helix  chain 'R' and resid 145 through 165
    Processing helix  chain 'R' and resid 165 through 176
      removed outlier: 4.291A  pdb=" N   LEU R 169 " --> pdb=" O   ALA R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 204
      removed outlier: 3.929A  pdb=" N   THR R 196 " --> pdb=" O   ASN R 192 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ALA R 202 " --> pdb=" O   GLY R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 222
    Processing helix  chain 'R' and resid 392 through 413
      removed outlier: 3.654A  pdb=" N   LEU R 406 " --> pdb=" O   ILE R 402 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 415 through 420
    Processing helix  chain 'R' and resid 431 through 441
    Processing helix  chain 'R' and resid 443 through 455
      Proline residue:  R 450  - end of helix
    Processing helix  chain 'R' and resid 457 through 463
    Processing helix  chain 'R' and resid 465 through 470
      removed outlier: 3.823A  pdb=" N   CYS R 470 " --> pdb=" O   HIS R 466 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.503A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226
      removed outlier: 7.147A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.731A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.435A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.084A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.796A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.881A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.648A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 275
      removed outlier: 6.322A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7
      removed outlier: 3.513A  pdb=" N   ARG S  18 " --> pdb=" O   MET S  83 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU S  81 " --> pdb=" O   LEU S  20 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU S  79 " --> pdb=" O   CYS S  22 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.691A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 146
      removed outlier: 3.599A  pdb=" N   VAL S 143 " --> pdb=" O   ILE S 204 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177
      removed outlier: 6.782A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1050 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: 2.15

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2252
        1.33 -     1.45: 1739
        1.45 -     1.57: 4685
        1.57 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 8770
  Sorted by residual:
  bond pdb=" C19 5XI R 601 "
       pdb=" N4  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.351  1.479 -0.128 2.00e-02 2.50e+03 4.10e+01
  bond pdb=" C19 5XI R 601 "
       pdb=" O3  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.428 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C8  5XI R 601 "
       pdb=" N1  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.480 -0.041 2.00e-02 2.50e+03 4.22e+00
  bond pdb=" C9  5XI R 601 "
       pdb=" N2  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.452  1.493 -0.041 2.00e-02 2.50e+03 4.12e+00
  bond pdb=" CA  THR B 181 "
       pdb=" CB  THR B 181 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.35e-02 5.49e+03 3.35e+00
  ... (remaining 8765 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11425
        1.54 -     3.08: 407
        3.08 -     4.62: 70
        4.62 -     6.16: 16
        6.16 -     7.70: 5
  Bond angle restraints: 11923
  Sorted by residual:
  angle pdb=" N   VAL R 418 "
        pdb=" CA  VAL R 418 "
        pdb=" C   VAL R 418 "
      ideal   model   delta    sigma   weight residual
     112.96  108.07    4.89 1.00e+00 1.00e+00 2.39e+01
  angle pdb=" CA  TRP R 435 "
        pdb=" CB  TRP R 435 "
        pdb=" CG  TRP R 435 "
      ideal   model   delta    sigma   weight residual
     113.60  119.04   -5.44 1.90e+00 2.77e-01 8.20e+00
  angle pdb=" N   TRP R 435 "
        pdb=" CA  TRP R 435 "
        pdb=" C   TRP R 435 "
      ideal   model   delta    sigma   weight residual
     111.33  107.91    3.42 1.21e+00 6.83e-01 8.00e+00
  angle pdb=" N   ASP B 246 "
        pdb=" CA  ASP B 246 "
        pdb=" C   ASP B 246 "
      ideal   model   delta    sigma   weight residual
     113.38  110.13    3.25 1.23e+00 6.61e-01 6.96e+00
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     122.19  118.54    3.65 1.41e+00 5.03e-01 6.71e+00
  ... (remaining 11918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4695
       17.90 -    35.80: 373
       35.80 -    53.70: 78
       53.70 -    71.60: 11
       71.60 -    89.49: 10
  Dihedral angle restraints: 5167
    sinusoidal: 1908
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CB  CYS R 426 "
           pdb=" SG  CYS R 426 "
           pdb=" SG  CYS R 429 "
           pdb=" CB  CYS R 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.93  -43.93     1      1.00e+01 1.00e-02 2.69e+01
  dihedral pdb=" CA  VAL R 434 "
           pdb=" C   VAL R 434 "
           pdb=" N   TRP R 435 "
           pdb=" CA  TRP R 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  MET S  93 "
           pdb=" C   MET S  93 "
           pdb=" N   TYR S  94 "
           pdb=" CA  TYR S  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1222
       0.069 -    0.137: 156
       0.137 -    0.206: 7
       0.206 -    0.274: 0
       0.274 -    0.343: 2
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" C9  5XI R 601 "
            pdb=" C10 5XI R 601 "
            pdb=" C13 5XI R 601 "
            pdb=" N2  5XI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.65    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" C14 5XI R 601 "
            pdb=" C15 5XI R 601 "
            pdb=" C18 5XI R 601 "
            pdb=" N3  5XI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.62    0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  ILE R  93 "
            pdb=" CA  ILE R  93 "
            pdb=" CG1 ILE R  93 "
            pdb=" CG2 ILE R  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.34e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 414 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO R 415 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO R 415 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 415 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO S  41 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 201 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" C   ILE R 201 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE R 201 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA R 202 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 182
        2.67 -     3.23: 8623
        3.23 -     3.79: 13522
        3.79 -     4.34: 17889
        4.34 -     4.90: 29286
  Nonbonded interactions: 69502
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OH  TYR R 439 "
            pdb=" OH  TYR R 443 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   SER B 160 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.210 3.040
  ... (remaining 69497 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.410
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
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   0.128   8772  Z= 0.196
  Angle     :  0.707   7.697  11927  Z= 0.397
  Chirality :  0.045   0.343   1387
  Planarity :  0.004   0.056   1488
  Dihedral  : 14.081  89.494   3057
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.88 (0.25), residues: 1104
  helix:  0.44 (0.27), residues: 398
  sheet: -2.68 (0.30), residues: 230
  loop : -1.90 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.029   0.002   PHE B 235 
 TYR   0.020   0.002   TYR S 103 
 ARG   0.008   0.001   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17222 (  368)
  hydrogen bonds       : angle       7.27066 ( 1050)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.81040 (    4)
  covalent geometry    : bond        0.00393 ( 8770)
  covalent geometry    : angle       0.70647 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6878 (tm-30)
REVERT: A  210 LYS cc_start: 0.7389 (tptt) cc_final: 0.6844 (mmtm)
REVERT: A  252 SER cc_start: 0.7474 (p) cc_final: 0.7193 (p)
REVERT: A  255 ASN cc_start: 0.6919 (m-40) cc_final: 0.6498 (m-40)
REVERT: A  337 ASP cc_start: 0.6790 (t70) cc_final: 0.6584 (t70)
REVERT: A  345 LYS cc_start: 0.8149 (tptt) cc_final: 0.7755 (tptt)
REVERT: A  353 LEU cc_start: 0.8697 (tp) cc_final: 0.8402 (tp)
REVERT: B  110 ASN cc_start: 0.8503 (m110) cc_final: 0.8224 (m110)
REVERT: B  125 ASN cc_start: 0.8332 (t0) cc_final: 0.8092 (t0)
REVERT: B  161 SER cc_start: 0.8108 (p) cc_final: 0.7846 (p)
REVERT: B  228 ASP cc_start: 0.6713 (p0) cc_final: 0.6192 (p0)
REVERT: B  239 ASN cc_start: 0.7808 (m110) cc_final: 0.7451 (m-40)
REVERT: B  279 SER cc_start: 0.7990 (t) cc_final: 0.7480 (p)
REVERT: B  294 CYS cc_start: 0.7277 (t) cc_final: 0.7024 (t)
REVERT: B  297 TRP cc_start: 0.8425 (m100) cc_final: 0.8143 (m100)
REVERT: C   15 LEU cc_start: 0.8064 (tt) cc_final: 0.7775 (tt)
REVERT: S   45 LEU cc_start: 0.7481 (mp) cc_final: 0.7278 (mt)
REVERT: S  128 MET cc_start: 0.7325 (mtp) cc_final: 0.6859 (mtp)
REVERT: S  179 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7326 (tpp-160)
REVERT: S  214 VAL cc_start: 0.8351 (t) cc_final: 0.8150 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2280
  time to fit residues: 81.1195
Evaluate side-chains
  240 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 82 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 331 ASN
B  88 ASN
B 110 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.149663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.132041 restraints weight = 13465.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.135496 restraints weight = 6272.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.137673 restraints weight = 3545.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8772  Z= 0.165
  Angle     :  0.618  10.715  11927  Z= 0.325
  Chirality :  0.043   0.196   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.179  58.417   1242
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.36 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.69 (0.25), residues: 1104
  helix:  0.58 (0.27), residues: 392
  sheet: -2.25 (0.32), residues: 218
  loop : -1.96 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 339 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.013   0.002   PHE B 234 
 TYR   0.012   0.002   TYR S 223 
 ARG   0.005   0.001   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04022 (  368)
  hydrogen bonds       : angle       5.23476 ( 1050)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       1.12648 (    4)
  covalent geometry    : bond        0.00360 ( 8770)
  covalent geometry    : angle       0.61768 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 243
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6915 (tm-30)
REVERT: A  210 LYS cc_start: 0.7733 (tptt) cc_final: 0.7493 (tptt)
REVERT: A  211 TRP cc_start: 0.7730 (p-90) cc_final: 0.7167 (p-90)
REVERT: A  252 SER cc_start: 0.7410 (p) cc_final: 0.7074 (p)
REVERT: A  255 ASN cc_start: 0.7147 (m-40) cc_final: 0.6735 (m110)
REVERT: A  337 ASP cc_start: 0.6995 (t70) cc_final: 0.6760 (t70)
REVERT: A  351 CYS cc_start: 0.7253 (m) cc_final: 0.6741 (m)
REVERT: B  105 TYR cc_start: 0.8129 (t80) cc_final: 0.7867 (t80)
REVERT: B  110 ASN cc_start: 0.8372 (m-40) cc_final: 0.8167 (m110)
REVERT: B  125 ASN cc_start: 0.8484 (t0) cc_final: 0.8109 (t0)
REVERT: B  228 ASP cc_start: 0.6885 (p0) cc_final: 0.6364 (p0)
REVERT: B  249 THR cc_start: 0.7635 (m) cc_final: 0.7350 (p)
REVERT: B  297 TRP cc_start: 0.8480 (m100) cc_final: 0.8108 (m100)
REVERT: B  301 LYS cc_start: 0.7370 (mttp) cc_final: 0.7161 (mtpp)
REVERT: B  339 TRP cc_start: 0.8175 (m100) cc_final: 0.7917 (m100)
REVERT: S   18 ARG cc_start: 0.5901 (mmt90) cc_final: 0.5695 (mmt90)
REVERT: S  110 PHE cc_start: 0.7846 (t80) cc_final: 0.7522 (t80)
REVERT: S  128 MET cc_start: 0.7573 (mtp) cc_final: 0.6925 (mtp)
REVERT: S  190 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7320 (mtm110)
REVERT: S  202 LEU cc_start: 0.8227 (tp) cc_final: 0.7994 (tt)
REVERT: R  152 MET cc_start: 0.5974 (tpt) cc_final: 0.5673 (tpt)
REVERT: R  190 LEU cc_start: 0.6898 (mm) cc_final: 0.6655 (mp)
REVERT: R  459 THR cc_start: 0.6490 (t) cc_final: 0.6242 (m)
  outliers start: 14
  outliers final: 13
  residues processed: 247
  average time/residue: 0.2798
  time to fit residues: 91.8344
Evaluate side-chains
  253 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 240
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  398 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    0.3980
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN
R 417 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.130159 restraints weight = 13617.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.133609 restraints weight = 6267.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.135781 restraints weight = 3497.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8772  Z= 0.214
  Angle     :  0.647  10.897  11927  Z= 0.341
  Chirality :  0.044   0.177   1387
  Planarity :  0.004   0.059   1488
  Dihedral  :  6.380  58.361   1242
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.93 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.79 (0.25), residues: 1104
  helix:  0.50 (0.27), residues: 395
  sheet: -2.29 (0.30), residues: 251
  loop : -1.97 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 435 
 HIS   0.007   0.001   HIS S  35 
 PHE   0.015   0.002   PHE R 409 
 TYR   0.015   0.002   TYR S 102 
 ARG   0.005   0.001   ARG S 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  368)
  hydrogen bonds       : angle       5.12952 ( 1050)
  SS BOND              : bond        0.00169 (    2)
  SS BOND              : angle       1.13804 (    4)
  covalent geometry    : bond        0.00460 ( 8770)
  covalent geometry    : angle       0.64679 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 238
  time to evaluate  : 1.068 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7037 (mt-10)
REVERT: A   14 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6995 (tm-30)
REVERT: A   53 MET cc_start: 0.5447 (mpp) cc_final: 0.4798 (mpp)
REVERT: A  210 LYS cc_start: 0.7860 (tptt) cc_final: 0.7633 (tptt)
REVERT: A  252 SER cc_start: 0.7378 (p) cc_final: 0.7011 (p)
REVERT: A  255 ASN cc_start: 0.7290 (m-40) cc_final: 0.6839 (m110)
REVERT: A  270 LYS cc_start: 0.7330 (mmmt) cc_final: 0.6949 (mmtp)
REVERT: A  337 ASP cc_start: 0.7143 (t70) cc_final: 0.6912 (t70)
REVERT: A  351 CYS cc_start: 0.7250 (m) cc_final: 0.6825 (m)
REVERT: B  105 TYR cc_start: 0.8275 (t80) cc_final: 0.8075 (t80)
REVERT: B  125 ASN cc_start: 0.8525 (t0) cc_final: 0.8156 (t0)
REVERT: B  228 ASP cc_start: 0.7085 (p0) cc_final: 0.6330 (p0)
REVERT: B  239 ASN cc_start: 0.8015 (m110) cc_final: 0.7772 (m-40)
REVERT: B  249 THR cc_start: 0.7592 (m) cc_final: 0.7303 (p)
REVERT: B  339 TRP cc_start: 0.8188 (m100) cc_final: 0.7739 (m100)
REVERT: C   62 ARG cc_start: 0.5916 (mtm-85) cc_final: 0.5609 (mtt180)
REVERT: S   18 ARG cc_start: 0.5978 (mmt90) cc_final: 0.5775 (mmt90)
REVERT: S  128 MET cc_start: 0.7586 (mtp) cc_final: 0.7009 (mtp)
REVERT: S  190 ARG cc_start: 0.7529 (mtm110) cc_final: 0.7287 (mtm110)
REVERT: S  202 LEU cc_start: 0.8219 (tp) cc_final: 0.7986 (tt)
REVERT: R   53 VAL cc_start: 0.7192 (m) cc_final: 0.6953 (p)
REVERT: R  409 PHE cc_start: 0.6546 (t80) cc_final: 0.6341 (t80)
REVERT: R  459 THR cc_start: 0.6540 (t) cc_final: 0.6104 (m)
  outliers start: 27
  outliers final: 21
  residues processed: 247
  average time/residue: 0.2701
  time to fit residues: 88.5931
Evaluate side-chains
  251 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 230
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 90 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0970
   chunk 97 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 423 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.149462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.132192 restraints weight = 13499.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.135647 restraints weight = 6249.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137844 restraints weight = 3496.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8772  Z= 0.139
  Angle     :  0.590  11.493  11927  Z= 0.307
  Chirality :  0.042   0.182   1387
  Planarity :  0.004   0.056   1488
  Dihedral  :  6.116  57.411   1242
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.15 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.57 (0.25), residues: 1104
  helix:  0.69 (0.27), residues: 392
  sheet: -2.24 (0.29), residues: 263
  loop : -1.76 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 435 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.002   PHE B 235 
 TYR   0.012   0.001   TYR S 102 
 ARG   0.004   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  368)
  hydrogen bonds       : angle       4.78472 ( 1050)
  SS BOND              : bond        0.00267 (    2)
  SS BOND              : angle       0.91841 (    4)
  covalent geometry    : bond        0.00305 ( 8770)
  covalent geometry    : angle       0.59012 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 244
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6954 (mt-10)
REVERT: A   14 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6974 (tm-30)
REVERT: A  210 LYS cc_start: 0.7799 (tptt) cc_final: 0.7585 (tptt)
REVERT: A  249 LEU cc_start: 0.8249 (tt) cc_final: 0.7979 (tp)
REVERT: A  252 SER cc_start: 0.7230 (p) cc_final: 0.6877 (p)
REVERT: A  255 ASN cc_start: 0.7240 (m-40) cc_final: 0.6911 (m110)
REVERT: A  270 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6962 (mmtp)
REVERT: A  337 ASP cc_start: 0.7073 (t70) cc_final: 0.6825 (t70)
REVERT: A  351 CYS cc_start: 0.7228 (m) cc_final: 0.6767 (m)
REVERT: B   13 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5786 (tp40)
REVERT: B  105 TYR cc_start: 0.8285 (t80) cc_final: 0.8056 (t80)
REVERT: B  125 ASN cc_start: 0.8521 (t0) cc_final: 0.8102 (t0)
REVERT: B  137 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7382 (tpp-160)
REVERT: B  228 ASP cc_start: 0.7040 (p0) cc_final: 0.6359 (p0)
REVERT: B  239 ASN cc_start: 0.7887 (m110) cc_final: 0.7626 (m-40)
REVERT: B  249 THR cc_start: 0.7531 (m) cc_final: 0.7268 (p)
REVERT: B  279 SER cc_start: 0.7952 (t) cc_final: 0.7557 (p)
REVERT: B  297 TRP cc_start: 0.8452 (m100) cc_final: 0.8203 (m100)
REVERT: B  308 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6843 (mp)
REVERT: B  339 TRP cc_start: 0.8168 (m100) cc_final: 0.7832 (m100)
REVERT: S  128 MET cc_start: 0.7561 (mtp) cc_final: 0.6991 (mtp)
REVERT: S  190 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7244 (mtm110)
REVERT: S  202 LEU cc_start: 0.8223 (tp) cc_final: 0.8000 (tt)
REVERT: R  459 THR cc_start: 0.6280 (t) cc_final: 0.5793 (m)
  outliers start: 36
  outliers final: 25
  residues processed: 259
  average time/residue: 0.2242
  time to fit residues: 77.0538
Evaluate side-chains
  259 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 232
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 423 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.150470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.133042 restraints weight = 13515.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136463 restraints weight = 6240.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138643 restraints weight = 3506.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8772  Z= 0.134
  Angle     :  0.598  11.519  11927  Z= 0.307
  Chirality :  0.042   0.189   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.011  56.359   1242
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 19.04 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.31 (0.26), residues: 1104
  helix:  0.75 (0.27), residues: 399
  sheet: -2.02 (0.30), residues: 266
  loop : -1.53 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.014   0.001   PHE S  29 
 TYR   0.012   0.001   TYR R 113 
 ARG   0.004   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03487 (  368)
  hydrogen bonds       : angle       4.65474 ( 1050)
  SS BOND              : bond        0.00244 (    2)
  SS BOND              : angle       0.89726 (    4)
  covalent geometry    : bond        0.00298 ( 8770)
  covalent geometry    : angle       0.59792 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 246
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6927 (mt-10)
REVERT: A   14 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6945 (tm-30)
REVERT: A  249 LEU cc_start: 0.8267 (tt) cc_final: 0.7979 (tp)
REVERT: A  252 SER cc_start: 0.6601 (p) cc_final: 0.6398 (p)
REVERT: A  270 LYS cc_start: 0.7300 (mmmt) cc_final: 0.7031 (mmtp)
REVERT: A  337 ASP cc_start: 0.7068 (t70) cc_final: 0.6827 (t70)
REVERT: A  351 CYS cc_start: 0.7241 (m) cc_final: 0.6773 (m)
REVERT: B   13 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5874 (tp40)
REVERT: B  105 TYR cc_start: 0.8297 (t80) cc_final: 0.8047 (t80)
REVERT: B  125 ASN cc_start: 0.8484 (t0) cc_final: 0.8072 (t0)
REVERT: B  137 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7405 (tpp-160)
REVERT: B  228 ASP cc_start: 0.7008 (p0) cc_final: 0.6539 (p0)
REVERT: B  249 THR cc_start: 0.7385 (m) cc_final: 0.7133 (p)
REVERT: B  297 TRP cc_start: 0.8512 (m100) cc_final: 0.8199 (m100)
REVERT: B  308 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6817 (mp)
REVERT: B  339 TRP cc_start: 0.8136 (m100) cc_final: 0.7848 (m100)
REVERT: C   11 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7698 (tp-100)
REVERT: S   67 ARG cc_start: 0.5334 (mtp180) cc_final: 0.4815 (mtp180)
REVERT: S  128 MET cc_start: 0.7540 (mtp) cc_final: 0.7038 (mtp)
REVERT: S  162 LEU cc_start: 0.8102 (tt) cc_final: 0.7772 (tt)
REVERT: S  166 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: S  190 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7229 (mtm110)
REVERT: S  202 LEU cc_start: 0.8213 (tp) cc_final: 0.7964 (tt)
REVERT: R  190 LEU cc_start: 0.7102 (mp) cc_final: 0.6740 (mp)
REVERT: R  419 MET cc_start: 0.5122 (ppp) cc_final: 0.4622 (ppp)
  outliers start: 38
  outliers final: 31
  residues processed: 260
  average time/residue: 0.2536
  time to fit residues: 89.7944
Evaluate side-chains
  273 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 239
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  208 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 85 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0470
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.151877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.134783 restraints weight = 13488.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138222 restraints weight = 6205.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140391 restraints weight = 3463.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8772  Z= 0.117
  Angle     :  0.598  11.724  11927  Z= 0.302
  Chirality :  0.042   0.193   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  5.890  55.418   1242
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 20.49 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 (0.26), residues: 1104
  helix:  0.89 (0.27), residues: 400
  sheet: -1.87 (0.30), residues: 271
  loop : -1.48 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.018   0.001   PHE S  29 
 TYR   0.010   0.001   TYR S 102 
 ARG   0.005   0.000   ARG S 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03346 (  368)
  hydrogen bonds       : angle       4.52167 ( 1050)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.88954 (    4)
  covalent geometry    : bond        0.00259 ( 8770)
  covalent geometry    : angle       0.59793 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 252
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6868 (mt-10)
REVERT: A   14 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6921 (tm-30)
REVERT: A  249 LEU cc_start: 0.8246 (tt) cc_final: 0.7968 (tp)
REVERT: A  252 SER cc_start: 0.6578 (p) cc_final: 0.6344 (p)
REVERT: A  270 LYS cc_start: 0.7270 (mmmt) cc_final: 0.7015 (mmtp)
REVERT: A  337 ASP cc_start: 0.7070 (t70) cc_final: 0.6819 (t70)
REVERT: A  351 CYS cc_start: 0.7237 (m) cc_final: 0.6744 (m)
REVERT: B   13 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.5798 (tp40)
REVERT: B   70 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8139 (mp)
REVERT: B  105 TYR cc_start: 0.8303 (t80) cc_final: 0.8047 (t80)
REVERT: B  125 ASN cc_start: 0.8482 (t0) cc_final: 0.8057 (t0)
REVERT: B  137 ARG cc_start: 0.7719 (tpp-160) cc_final: 0.7423 (tpp-160)
REVERT: B  169 TRP cc_start: 0.8154 (m100) cc_final: 0.7727 (m100)
REVERT: B  228 ASP cc_start: 0.7010 (p0) cc_final: 0.6526 (p0)
REVERT: B  249 THR cc_start: 0.7370 (m) cc_final: 0.7132 (p)
REVERT: B  255 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7289 (mm)
REVERT: B  297 TRP cc_start: 0.8512 (m100) cc_final: 0.8179 (m100)
REVERT: B  308 LEU cc_start: 0.7314 (tp) cc_final: 0.6776 (mp)
REVERT: B  339 TRP cc_start: 0.8108 (m100) cc_final: 0.7833 (m100)
REVERT: S   29 PHE cc_start: 0.7929 (t80) cc_final: 0.7428 (t80)
REVERT: S   38 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7894 (ptp90)
REVERT: S   67 ARG cc_start: 0.5034 (mtp180) cc_final: 0.4595 (mtp180)
REVERT: S   87 ARG cc_start: 0.7595 (mpt-90) cc_final: 0.7314 (mpt-90)
REVERT: S  128 MET cc_start: 0.7532 (mtp) cc_final: 0.7304 (mtt)
REVERT: S  166 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7321 (tt)
REVERT: S  190 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7330 (mtm110)
REVERT: S  202 LEU cc_start: 0.8193 (tp) cc_final: 0.7969 (tt)
REVERT: R   86 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5930 (mpt)
REVERT: R  152 MET cc_start: 0.5843 (tpt) cc_final: 0.5615 (tpt)
REVERT: R  419 MET cc_start: 0.5049 (ppp) cc_final: 0.4495 (ppp)
  outliers start: 47
  outliers final: 36
  residues processed: 273
  average time/residue: 0.2420
  time to fit residues: 88.8521
Evaluate side-chains
  289 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 248
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
C  11 GLN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.149786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132476 restraints weight = 13650.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.135944 restraints weight = 6290.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138113 restraints weight = 3521.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8772  Z= 0.169
  Angle     :  0.640  11.536  11927  Z= 0.328
  Chirality :  0.043   0.255   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.026  52.347   1242
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 21.05 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.26), residues: 1104
  helix:  0.79 (0.27), residues: 400
  sheet: -1.87 (0.30), residues: 274
  loop : -1.52 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.012   0.001   PHE B 234 
 TYR   0.012   0.002   TYR R 113 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03479 (  368)
  hydrogen bonds       : angle       4.63285 ( 1050)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       1.00300 (    4)
  covalent geometry    : bond        0.00371 ( 8770)
  covalent geometry    : angle       0.64002 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 243
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7243 (mt-10) cc_final: 0.7037 (mt-10)
REVERT: A   14 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6933 (tm-30)
REVERT: A  249 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (tp)
REVERT: A  252 SER cc_start: 0.6550 (p) cc_final: 0.6247 (p)
REVERT: A  255 ASN cc_start: 0.7229 (m-40) cc_final: 0.6958 (m110)
REVERT: A  270 LYS cc_start: 0.7295 (mmmt) cc_final: 0.7054 (mmtp)
REVERT: A  337 ASP cc_start: 0.7116 (t70) cc_final: 0.6893 (t70)
REVERT: B   13 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5782 (tp40)
REVERT: B   70 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8223 (mp)
REVERT: B  105 TYR cc_start: 0.8315 (t80) cc_final: 0.8085 (t80)
REVERT: B  125 ASN cc_start: 0.8515 (t0) cc_final: 0.8086 (t0)
REVERT: B  137 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7429 (tpp-160)
REVERT: B  228 ASP cc_start: 0.7006 (p0) cc_final: 0.6541 (p0)
REVERT: B  249 THR cc_start: 0.7401 (m) cc_final: 0.7112 (p)
REVERT: B  255 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7408 (mm)
REVERT: B  308 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6834 (mp)
REVERT: B  339 TRP cc_start: 0.8195 (m100) cc_final: 0.7895 (m100)
REVERT: S  128 MET cc_start: 0.7562 (mtp) cc_final: 0.7323 (mtt)
REVERT: S  190 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7315 (mtm110)
REVERT: S  202 LEU cc_start: 0.8218 (tp) cc_final: 0.7984 (tt)
REVERT: R   86 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6023 (mpt)
REVERT: R  152 MET cc_start: 0.6000 (tpt) cc_final: 0.5749 (tpt)
REVERT: R  419 MET cc_start: 0.5079 (ppp) cc_final: 0.4838 (ppp)
  outliers start: 51
  outliers final: 41
  residues processed: 263
  average time/residue: 0.2245
  time to fit residues: 79.1462
Evaluate side-chains
  286 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 239
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   77 ASN
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0980
   chunk 98 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0670
   overall best weight:    0.3278

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.151439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.134164 restraints weight = 13848.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137658 restraints weight = 6357.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.139944 restraints weight = 3546.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8772  Z= 0.118
  Angle     :  0.628  11.844  11927  Z= 0.313
  Chirality :  0.042   0.186   1387
  Planarity :  0.003   0.055   1488
  Dihedral  :  5.885  52.489   1242
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.27 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.26), residues: 1104
  helix:  0.94 (0.27), residues: 400
  sheet: -1.70 (0.30), residues: 269
  loop : -1.43 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 435 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.020   0.001   PHE S  29 
 TYR   0.010   0.001   TYR R 113 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03288 (  368)
  hydrogen bonds       : angle       4.46140 ( 1050)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.88588 (    4)
  covalent geometry    : bond        0.00264 ( 8770)
  covalent geometry    : angle       0.62766 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 253
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6910 (mt-10)
REVERT: A   14 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6898 (tm-30)
REVERT: A  249 LEU cc_start: 0.8238 (tt) cc_final: 0.7938 (tp)
REVERT: A  252 SER cc_start: 0.6522 (p) cc_final: 0.6275 (p)
REVERT: A  270 LYS cc_start: 0.7227 (mmmt) cc_final: 0.7016 (mmtp)
REVERT: A  317 LYS cc_start: 0.7867 (ptmt) cc_final: 0.7600 (ptmt)
REVERT: A  337 ASP cc_start: 0.7263 (t70) cc_final: 0.7004 (t70)
REVERT: A  351 CYS cc_start: 0.7271 (m) cc_final: 0.6799 (m)
REVERT: B   13 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5788 (tp40)
REVERT: B   70 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8169 (mp)
REVERT: B  105 TYR cc_start: 0.8304 (t80) cc_final: 0.8042 (t80)
REVERT: B  125 ASN cc_start: 0.8439 (t0) cc_final: 0.8033 (t0)
REVERT: B  126 LEU cc_start: 0.8150 (mp) cc_final: 0.7926 (mt)
REVERT: B  137 ARG cc_start: 0.7692 (tpp-160) cc_final: 0.7337 (tpp-160)
REVERT: B  145 TYR cc_start: 0.7699 (p90) cc_final: 0.7376 (p90)
REVERT: B  228 ASP cc_start: 0.7023 (p0) cc_final: 0.6574 (p0)
REVERT: B  249 THR cc_start: 0.7345 (m) cc_final: 0.7106 (p)
REVERT: B  255 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7270 (mm)
REVERT: B  297 TRP cc_start: 0.8484 (m100) cc_final: 0.8121 (m100)
REVERT: B  308 LEU cc_start: 0.7337 (tp) cc_final: 0.6841 (mp)
REVERT: B  339 TRP cc_start: 0.8097 (m100) cc_final: 0.7863 (m100)
REVERT: S   38 ARG cc_start: 0.8253 (ptt180) cc_final: 0.7937 (ptp90)
REVERT: S  190 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7344 (mtm110)
REVERT: S  202 LEU cc_start: 0.8189 (tp) cc_final: 0.7969 (tt)
REVERT: R   86 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5916 (mpt)
REVERT: R  138 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6333 (mt)
REVERT: R  152 MET cc_start: 0.5909 (tpt) cc_final: 0.5636 (tpt)
REVERT: R  215 TYR cc_start: 0.7661 (m-10) cc_final: 0.7311 (m-80)
REVERT: R  419 MET cc_start: 0.5044 (ppp) cc_final: 0.4742 (ppp)
  outliers start: 45
  outliers final: 37
  residues processed: 272
  average time/residue: 0.2478
  time to fit residues: 90.6165
Evaluate side-chains
  291 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 249
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   77 ASN
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.149990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.132291 restraints weight = 13681.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.135879 restraints weight = 6392.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138166 restraints weight = 3585.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8772  Z= 0.159
  Angle     :  0.657  11.565  11927  Z= 0.331
  Chirality :  0.043   0.245   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  5.963  50.014   1242
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 22.16 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.26), residues: 1104
  helix:  0.90 (0.27), residues: 399
  sheet: -1.74 (0.30), residues: 276
  loop : -1.51 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.020   0.001   PHE S  29 
 TYR   0.012   0.001   TYR R 113 
 ARG   0.004   0.000   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03389 (  368)
  hydrogen bonds       : angle       4.54485 ( 1050)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.93741 (    4)
  covalent geometry    : bond        0.00355 ( 8770)
  covalent geometry    : angle       0.65654 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 248
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7010 (mt-10)
REVERT: A   14 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6945 (tm-30)
REVERT: A  249 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8060 (tp)
REVERT: A  252 SER cc_start: 0.6484 (p) cc_final: 0.6245 (p)
REVERT: A  270 LYS cc_start: 0.7283 (mmmt) cc_final: 0.7035 (mmtp)
REVERT: A  317 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7625 (ptmt)
REVERT: A  351 CYS cc_start: 0.7339 (m) cc_final: 0.6880 (m)
REVERT: B   13 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5832 (tp40)
REVERT: B   70 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8228 (mp)
REVERT: B  105 TYR cc_start: 0.8321 (t80) cc_final: 0.8049 (t80)
REVERT: B  125 ASN cc_start: 0.8479 (t0) cc_final: 0.8066 (t0)
REVERT: B  126 LEU cc_start: 0.8219 (mp) cc_final: 0.7973 (mt)
REVERT: B  228 ASP cc_start: 0.7026 (p0) cc_final: 0.6586 (p0)
REVERT: B  249 THR cc_start: 0.7359 (m) cc_final: 0.7075 (p)
REVERT: B  255 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7499 (mm)
REVERT: B  297 TRP cc_start: 0.8492 (m100) cc_final: 0.8156 (m100)
REVERT: B  308 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6812 (mp)
REVERT: B  339 TRP cc_start: 0.8168 (m100) cc_final: 0.7890 (m100)
REVERT: S   38 ARG cc_start: 0.8265 (ptt180) cc_final: 0.7808 (ptp-170)
REVERT: S  190 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7346 (mtm110)
REVERT: S  202 LEU cc_start: 0.8200 (tp) cc_final: 0.7973 (tt)
REVERT: R   86 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6116 (mpt)
REVERT: R  152 MET cc_start: 0.5999 (tpt) cc_final: 0.5711 (tpt)
  outliers start: 49
  outliers final: 40
  residues processed: 269
  average time/residue: 0.2903
  time to fit residues: 103.0684
Evaluate side-chains
  290 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 244
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   77 ASN
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 105 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0870
   chunk 33 optimal weight:    0.7980
   chunk 85 optimal weight:    0.2980
   chunk 100 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.150730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133183 restraints weight = 13739.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136726 restraints weight = 6489.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138987 restraints weight = 3662.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8772  Z= 0.137
  Angle     :  0.670  11.751  11927  Z= 0.335
  Chirality :  0.043   0.232   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.040  52.825   1242
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 23.05 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.03 (0.26), residues: 1104
  helix:  0.86 (0.27), residues: 403
  sheet: -1.57 (0.31), residues: 265
  loop : -1.49 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.041   0.002   PHE R 186 
 TYR   0.012   0.001   TYR R 113 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  368)
  hydrogen bonds       : angle       4.52348 ( 1050)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       0.91674 (    4)
  covalent geometry    : bond        0.00311 ( 8770)
  covalent geometry    : angle       0.66988 (11923)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 251
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6926 (mt-10)
REVERT: A   14 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6913 (tm-30)
REVERT: A  249 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: A  252 SER cc_start: 0.6275 (p) cc_final: 0.6041 (p)
REVERT: A  270 LYS cc_start: 0.7248 (mmmt) cc_final: 0.7024 (mmtp)
REVERT: A  317 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7686 (ptmt)
REVERT: A  351 CYS cc_start: 0.7309 (m) cc_final: 0.6851 (m)
REVERT: B   13 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.5846 (tp-100)
REVERT: B   70 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8222 (mp)
REVERT: B  105 TYR cc_start: 0.8261 (t80) cc_final: 0.7995 (t80)
REVERT: B  125 ASN cc_start: 0.8459 (t0) cc_final: 0.8058 (t0)
REVERT: B  126 LEU cc_start: 0.8166 (mp) cc_final: 0.7944 (mt)
REVERT: B  137 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7267 (tpp80)
REVERT: B  145 TYR cc_start: 0.7683 (p90) cc_final: 0.7145 (p90)
REVERT: B  186 ASP cc_start: 0.7626 (p0) cc_final: 0.6996 (p0)
REVERT: B  228 ASP cc_start: 0.7030 (p0) cc_final: 0.6571 (p0)
REVERT: B  249 THR cc_start: 0.7332 (m) cc_final: 0.7098 (p)
REVERT: B  255 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7450 (mm)
REVERT: B  297 TRP cc_start: 0.8515 (m100) cc_final: 0.8180 (m100)
REVERT: B  308 LEU cc_start: 0.7338 (tp) cc_final: 0.6867 (mp)
REVERT: B  339 TRP cc_start: 0.8130 (m100) cc_final: 0.7881 (m100)
REVERT: S   38 ARG cc_start: 0.8252 (ptt180) cc_final: 0.7916 (ptp-170)
REVERT: S  190 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7300 (mtm110)
REVERT: S  202 LEU cc_start: 0.8195 (tp) cc_final: 0.7980 (tt)
REVERT: R   86 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6087 (mpt)
REVERT: R  215 TYR cc_start: 0.7657 (m-10) cc_final: 0.7328 (m-80)
  outliers start: 46
  outliers final: 39
  residues processed: 272
  average time/residue: 0.3149
  time to fit residues: 113.0362
Evaluate side-chains
  288 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 244
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 70 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:
B 340 ASN
S 130 GLN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.149389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.131586 restraints weight = 13718.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.135125 restraints weight = 6463.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.137424 restraints weight = 3682.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8772  Z= 0.172
  Angle     :  0.687  11.557  11927  Z= 0.346
  Chirality :  0.044   0.248   1387
  Planarity :  0.004   0.056   1488
  Dihedral  :  6.141  51.953   1242
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 23.72 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.08 (0.26), residues: 1104
  helix:  0.84 (0.27), residues: 400
  sheet: -1.56 (0.31), residues: 259
  loop : -1.55 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.021   0.002   PHE S  29 
 TYR   0.013   0.001   TYR R 113 
 ARG   0.004   0.000   ARG S  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  368)
  hydrogen bonds       : angle       4.65925 ( 1050)
  SS BOND              : bond        0.00200 (    2)
  SS BOND              : angle       0.96921 (    4)
  covalent geometry    : bond        0.00383 ( 8770)
  covalent geometry    : angle       0.68699 (11923)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3753.61 seconds
wall clock time: 69 minutes 30.41 seconds (4170.41 seconds total)