Starting phenix.real_space_refine
on Wed Mar 12 09:55:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjh_33227/03_2025/7xjh_33227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjh_33227/03_2025/7xjh_33227.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjh_33227/03_2025/7xjh_33227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjh_33227/03_2025/7xjh_33227.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjh_33227/03_2025/7xjh_33227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjh_33227/03_2025/7xjh_33227.cif"
  }
  resolution = 3.3
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4962      2.51       5
     N    1378      2.21       5
     O    1446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7832
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1884
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2543
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 58
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 63
    Chain: "G"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 393
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 950
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 2047
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2047
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 16, 'TRANS': 259}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'5FW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.81, per 1000 atoms: 0.61
  Number of scatterers: 7832
  At special positions: 0
  Unit cell: (96.3829, 120.479, 86.5255, 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      46     16.00
     O    1446      8.00
     N    1378      7.00
     C    4962      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 189 " - pdb=" SG  CYS R 195 " 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: 2.01
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      43.7% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 3.699A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 302 through 308
      removed outlier: 3.662A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG A 307 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 341
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 3.888A  pdb=" N   ARG A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE A 365 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.644A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 11 through 23
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.674A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 37 through 64
      removed outlier: 3.513A  pdb=" N   ALA R  42 " --> pdb=" O   ALA R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 69
    Processing helix  chain 'R' and resid 70 through 90
      removed outlier: 3.528A  pdb=" N   VAL R  74 " --> pdb=" O   THR R  70 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   PHE R  75 " --> pdb=" O   MET R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 90 through 100
    Processing helix  chain 'R' and resid 106 through 141
      removed outlier: 3.784A  pdb=" N   SER R 124 " --> pdb=" O   CYS R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 144 through 149
    Processing helix  chain 'R' and resid 150 through 170
    Processing helix  chain 'R' and resid 170 through 175
      removed outlier: 3.549A  pdb=" N   MET R 174 " --> pdb=" O   PHE R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 188 through 192
    Processing helix  chain 'R' and resid 201 through 213
    Processing helix  chain 'R' and resid 213 through 243
    Processing helix  chain 'R' and resid 288 through 318
      removed outlier: 3.900A  pdb=" N   ARG R 292 " --> pdb=" O   HIS R 288 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TRP R 305 " --> pdb=" O   PHE R 301 " (cutoff:3.500A)
      Proline residue:  R 307  - end of helix
    Processing helix  chain 'R' and resid 324 through 342
    Processing helix  chain 'R' and resid 343 through 345
      No H-bonds generated for 'chain 'R' and resid 343 through 345'
    Processing helix  chain 'R' and resid 349 through 360
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.319A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   HIS A 352 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU A 279 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.631A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.674A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.043A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150
      removed outlier: 4.053A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.684A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.036A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.259A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.244A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    425 hydrogen bonds defined for protein.
    1200 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: 2.22

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2581
        1.34 -     1.46: 1625
        1.46 -     1.58: 3719
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7986
  Sorted by residual:
  bond pdb=" CA  SER N  21 "
       pdb=" CB  SER N  21 "
    ideal  model  delta    sigma   weight residual
    1.532  1.486  0.046 1.74e-02 3.30e+03 6.99e+00
  bond pdb=" CAO 5FW R 401 "
       pdb=" OAC 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.400 -0.049 2.00e-02 2.50e+03 6.06e+00
  bond pdb=" CAM 5FW R 401 "
       pdb=" OAB 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.353  1.401 -0.048 2.00e-02 2.50e+03 5.66e+00
  bond pdb=" C   LEU R 306 "
       pdb=" N   PRO R 307 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.018 1.30e-02 5.92e+03 2.00e+00
  bond pdb=" N   SER N  21 "
       pdb=" CA  SER N  21 "
    ideal  model  delta    sigma   weight residual
    1.454  1.470 -0.016 1.19e-02 7.06e+03 1.79e+00
  ... (remaining 7981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 10580
        1.53 -     3.07: 224
        3.07 -     4.60: 38
        4.60 -     6.13: 13
        6.13 -     7.67: 3
  Bond angle restraints: 10858
  Sorted by residual:
  angle pdb=" N   PHE A 222 "
        pdb=" CA  PHE A 222 "
        pdb=" C   PHE A 222 "
      ideal   model   delta    sigma   weight residual
     108.55  113.15   -4.60 1.62e+00 3.81e-01 8.07e+00
  angle pdb=" N   GLU A  16 "
        pdb=" CA  GLU A  16 "
        pdb=" CB  GLU A  16 "
      ideal   model   delta    sigma   weight residual
     110.28  114.64   -4.36 1.55e+00 4.16e-01 7.90e+00
  angle pdb=" CA  SER N  21 "
        pdb=" C   SER N  21 "
        pdb=" O   SER N  21 "
      ideal   model   delta    sigma   weight residual
     121.16  118.03    3.13 1.13e+00 7.83e-01 7.66e+00
  angle pdb=" C   LEU N  20 "
        pdb=" N   SER N  21 "
        pdb=" CA  SER N  21 "
      ideal   model   delta    sigma   weight residual
     122.87  118.94    3.93 1.61e+00 3.86e-01 5.95e+00
  angle pdb=" C   LEU R  89 "
        pdb=" N   VAL R  90 "
        pdb=" CA  VAL R  90 "
      ideal   model   delta    sigma   weight residual
     122.63  119.81    2.82 1.19e+00 7.06e-01 5.60e+00
  ... (remaining 10853 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4301
       17.97 -    35.93: 382
       35.93 -    53.90: 58
       53.90 -    71.87: 9
       71.87 -    89.83: 8
  Dihedral angle restraints: 4758
    sinusoidal: 1782
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" CB  CYS R 189 "
           pdb=" SG  CYS R 189 "
           pdb=" SG  CYS R 195 "
           pdb=" CB  CYS R 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.54   47.54     1      1.00e+01 1.00e-02 3.12e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.21  -41.21     1      1.00e+01 1.00e-02 2.38e+01
  dihedral pdb=" CA  CYS N 107 "
           pdb=" C   CYS N 107 "
           pdb=" N   PHE N 108 "
           pdb=" CA  PHE N 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.03  -22.97     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 4755 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 967
       0.045 -    0.090: 220
       0.090 -    0.134: 67
       0.134 -    0.179: 2
       0.179 -    0.224: 2
  Chirality restraints: 1258
  Sorted by residual:
  chirality pdb=" CAE 5FW R 401 "
            pdb=" CAF 5FW R 401 "
            pdb=" CAH 5FW R 401 "
            pdb=" OAA 5FW R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.52    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  THR A 315 "
            pdb=" CA  THR A 315 "
            pdb=" OG1 THR A 315 "
            pdb=" CG2 THR A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.94e-01
  chirality pdb=" CA  ILE N  58 "
            pdb=" N   ILE N  58 "
            pdb=" C   ILE N  58 "
            pdb=" CB  ILE N  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.37e-01
  ... (remaining 1255 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 215 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO R 216 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO R 216 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 216 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 323 "    0.027 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO R 324 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO R 324 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 324 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 192 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO R 193 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO R 193 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 193 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1016
        2.75 -     3.29: 7524
        3.29 -     3.83: 13177
        3.83 -     4.36: 15228
        4.36 -     4.90: 27153
  Nonbonded interactions: 64098
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLU B 226 "
            pdb=" NH2 ARG N  98 "
     model   vdw
     2.252 3.120
  ... (remaining 64093 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.200
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
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      :  0.003   0.049   7986  Z= 0.194
  Angle     :  0.584   7.667  10858  Z= 0.315
  Chirality :  0.042   0.224   1258
  Planarity :  0.004   0.045   1390
  Dihedral  : 14.021  89.834   2820
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.27), residues: 1011
  helix:  2.43 (0.26), residues: 377
  sheet: -0.72 (0.33), residues: 212
  loop : -1.14 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.023   0.002   PHE A 222 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.007   0.000   ARG N  19 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6774 (mtmt)
REVERT: A   32 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7353 (mtpt)
REVERT: A   34 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7769 (tttt)
REVERT: A  213 GLN cc_start: 0.7742 (tt0) cc_final: 0.7514 (tt0)
REVERT: A  252 ASP cc_start: 0.7055 (t70) cc_final: 0.6826 (t70)
REVERT: A  304 GLU cc_start: 0.7674 (pm20) cc_final: 0.7462 (pm20)
REVERT: B   42 ARG cc_start: 0.7577 (tmt170) cc_final: 0.6922 (tpt170)
REVERT: B  175 GLN cc_start: 0.7772 (mt0) cc_final: 0.7544 (mt0)
REVERT: B  226 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8450 (mt-10)
REVERT: N   20 LEU cc_start: 0.8027 (mt) cc_final: 0.7764 (mt)
REVERT: N   21 SER cc_start: 0.8305 (m) cc_final: 0.7963 (p)
REVERT: N   77 ASN cc_start: 0.6830 (m-40) cc_final: 0.6525 (m-40)
REVERT: R  236 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6406 (mtm110)
REVERT: R  240 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.7003 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2325
  time to fit residues: 49.4051
Evaluate side-chains
  129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    0.2980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
B 220 GLN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.154758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.121536 restraints weight = 8969.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.78
r_work: 0.3181 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7986  Z= 0.194
  Angle     :  0.542   7.762  10858  Z= 0.283
  Chirality :  0.041   0.152   1258
  Planarity :  0.004   0.047   1390
  Dihedral  :  4.263  28.484   1122
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.50 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 1011
  helix:  2.44 (0.26), residues: 379
  sheet: -0.49 (0.34), residues: 213
  loop : -1.05 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.005   0.000   ARG N  19 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 1.466 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7722 (mtpt)
REVERT: A   34 LYS cc_start: 0.8341 (ttpp) cc_final: 0.8105 (tttt)
REVERT: A  252 ASP cc_start: 0.7539 (t70) cc_final: 0.7259 (t70)
REVERT: A  304 GLU cc_start: 0.8085 (pm20) cc_final: 0.7854 (pm20)
REVERT: A  308 TYR cc_start: 0.7871 (t80) cc_final: 0.7127 (t80)
REVERT: B   42 ARG cc_start: 0.7599 (tmt170) cc_final: 0.6871 (tpt170)
REVERT: B  175 GLN cc_start: 0.8102 (mt0) cc_final: 0.7895 (mt0)
REVERT: B  230 ASN cc_start: 0.8611 (m-40) cc_final: 0.8370 (m110)
REVERT: N   20 LEU cc_start: 0.8141 (mt) cc_final: 0.7873 (mt)
REVERT: N   77 ASN cc_start: 0.6872 (m-40) cc_final: 0.6526 (m-40)
REVERT: R  236 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6761 (mtm110)
  outliers start: 6
  outliers final: 3
  residues processed: 138
  average time/residue: 0.3331
  time to fit residues: 60.6056
Evaluate side-chains
  129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 126
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue  288 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 28 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 3 optimal weight:    0.3980
   chunk 74 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 268 ASN
B 220 GLN
G  59 ASN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.152795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.119162 restraints weight = 9061.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.79
r_work: 0.3136 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7986  Z= 0.211
  Angle     :  0.541   8.182  10858  Z= 0.281
  Chirality :  0.041   0.151   1258
  Planarity :  0.004   0.048   1390
  Dihedral  :  4.292  29.386   1122
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.55 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 1011
  helix:  2.38 (0.26), residues: 384
  sheet: -0.57 (0.34), residues: 206
  loop : -0.97 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.004   0.000   ARG G  27 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7694 (mtpt)
REVERT: A   34 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8130 (tttt)
REVERT: A  230 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7670 (mt-10)
REVERT: A  252 ASP cc_start: 0.7520 (t70) cc_final: 0.7193 (t70)
REVERT: A  304 GLU cc_start: 0.8098 (pm20) cc_final: 0.7890 (pm20)
REVERT: A  329 TYR cc_start: 0.8692 (m-80) cc_final: 0.8335 (m-80)
REVERT: A  338 ILE cc_start: 0.8510 (mm) cc_final: 0.8241 (mm)
REVERT: B   42 ARG cc_start: 0.7642 (tmt170) cc_final: 0.6840 (tpt170)
REVERT: B  175 GLN cc_start: 0.8116 (mt0) cc_final: 0.7905 (mt0)
REVERT: B  256 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7127 (mtm110)
REVERT: B  259 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7927 (mm-40)
REVERT: N   20 LEU cc_start: 0.8130 (mt) cc_final: 0.7859 (mt)
REVERT: N   65 LYS cc_start: 0.6639 (ttmm) cc_final: 0.6375 (tptp)
REVERT: R   68 LEU cc_start: 0.7690 (mt) cc_final: 0.7472 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 130
  average time/residue: 0.2818
  time to fit residues: 48.0967
Evaluate side-chains
  126 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue  288 HIS
Chi-restraints excluded: chain R residue  323 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 40 optimal weight:    0.5980
   chunk 52 optimal weight:   10.0000
   chunk 23 optimal weight:   50.0000
   chunk 46 optimal weight:    0.0070
   chunk 37 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.155555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.122297 restraints weight = 8912.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.79
r_work: 0.3181 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7986  Z= 0.140
  Angle     :  0.501   8.626  10858  Z= 0.261
  Chirality :  0.041   0.293   1258
  Planarity :  0.004   0.043   1390
  Dihedral  :  4.071  27.927   1122
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.64 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1011
  helix:  2.65 (0.26), residues: 379
  sheet: -0.47 (0.33), residues: 216
  loop : -0.99 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.003   0.000   ARG R 226 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 1.368 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7684 (mtpt)
REVERT: A   34 LYS cc_start: 0.8341 (ttpp) cc_final: 0.8133 (tttt)
REVERT: A  252 ASP cc_start: 0.7483 (t70) cc_final: 0.7159 (t70)
REVERT: A  304 GLU cc_start: 0.8066 (pm20) cc_final: 0.7841 (pm20)
REVERT: A  308 TYR cc_start: 0.7827 (t80) cc_final: 0.7308 (t80)
REVERT: A  329 TYR cc_start: 0.8613 (m-80) cc_final: 0.8298 (m-80)
REVERT: B   42 ARG cc_start: 0.7627 (tmt170) cc_final: 0.6779 (tpt170)
REVERT: B  256 ARG cc_start: 0.7890 (mtm110) cc_final: 0.6994 (mtm110)
REVERT: B  259 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7975 (mm-40)
REVERT: B  329 THR cc_start: 0.9165 (m) cc_final: 0.8801 (p)
REVERT: N   20 LEU cc_start: 0.8146 (mt) cc_final: 0.7862 (mt)
REVERT: N   46 GLU cc_start: 0.8495 (pt0) cc_final: 0.8185 (pt0)
REVERT: N   65 LYS cc_start: 0.6623 (ttmm) cc_final: 0.6341 (tptp)
REVERT: R  135 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8239 (mtt180)
  outliers start: 9
  outliers final: 5
  residues processed: 138
  average time/residue: 0.3001
  time to fit residues: 54.2948
Evaluate side-chains
  127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 122
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0970
   chunk 87 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0040
   chunk 75 optimal weight:    0.9990
   chunk 0 optimal weight:   50.0000
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN
** R  73 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 = 0.3740 r_free = 0.3740 target = 0.156540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123511 restraints weight = 8930.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.76
r_work: 0.3193 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7986  Z= 0.135
  Angle     :  0.495   8.612  10858  Z= 0.256
  Chirality :  0.041   0.320   1258
  Planarity :  0.004   0.042   1390
  Dihedral  :  3.956  28.123   1122
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.25 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 1011
  helix:  2.75 (0.26), residues: 379
  sheet: -0.39 (0.33), residues: 216
  loop : -0.96 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.003   0.000   ARG R 226 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 1.382 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7689 (mtpt)
REVERT: A   34 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8163 (tttt)
REVERT: A  213 GLN cc_start: 0.8261 (tt0) cc_final: 0.7882 (tt0)
REVERT: A  252 ASP cc_start: 0.7425 (t70) cc_final: 0.7052 (t70)
REVERT: A  304 GLU cc_start: 0.8034 (pm20) cc_final: 0.7820 (pm20)
REVERT: A  308 TYR cc_start: 0.7798 (t80) cc_final: 0.7281 (t80)
REVERT: B   42 ARG cc_start: 0.7614 (tmt170) cc_final: 0.6763 (tpt170)
REVERT: B  256 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7162 (mtm110)
REVERT: B  259 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8018 (mm-40)
REVERT: B  329 THR cc_start: 0.9145 (m) cc_final: 0.8864 (p)
REVERT: N   20 LEU cc_start: 0.8181 (mt) cc_final: 0.7882 (mt)
REVERT: N   46 GLU cc_start: 0.8493 (pt0) cc_final: 0.8163 (pt0)
REVERT: N   65 LYS cc_start: 0.6607 (ttmm) cc_final: 0.6390 (tptp)
  outliers start: 12
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2953
  time to fit residues: 55.8834
Evaluate side-chains
  132 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  288 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 25 optimal weight:   40.0000
   chunk 74 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 86 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN
N  82 GLN
N  84 ASN
** R  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.151447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.117754 restraints weight = 8950.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.76
r_work: 0.3118 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7986  Z= 0.235
  Angle     :  0.547   8.223  10858  Z= 0.285
  Chirality :  0.042   0.326   1258
  Planarity :  0.004   0.044   1390
  Dihedral  :  4.230  29.521   1122
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.37 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 1011
  helix:  2.37 (0.26), residues: 390
  sheet: -0.37 (0.33), residues: 215
  loop : -1.00 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.016   0.002   PHE R 309 
 TYR   0.012   0.002   TYR A  37 
 ARG   0.004   0.000   ARG N  98 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7711 (mtpt)
REVERT: A   34 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8163 (ttmt)
REVERT: A  213 GLN cc_start: 0.8449 (tt0) cc_final: 0.8086 (tt0)
REVERT: A  252 ASP cc_start: 0.7519 (t70) cc_final: 0.7176 (t70)
REVERT: A  304 GLU cc_start: 0.8026 (pm20) cc_final: 0.7794 (pm20)
REVERT: A  329 TYR cc_start: 0.8698 (m-80) cc_final: 0.8386 (m-80)
REVERT: B   42 ARG cc_start: 0.7631 (tmt170) cc_final: 0.6823 (tpt170)
REVERT: B  256 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7218 (mtm110)
REVERT: B  259 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7993 (mm-40)
REVERT: N   20 LEU cc_start: 0.8108 (mt) cc_final: 0.7775 (mt)
REVERT: N   46 GLU cc_start: 0.8483 (pt0) cc_final: 0.8196 (pt0)
REVERT: N   65 LYS cc_start: 0.6675 (ttmm) cc_final: 0.6391 (tptp)
REVERT: N  108 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8028 (t80)
REVERT: R  353 ARG cc_start: 0.6142 (mtt90) cc_final: 0.5902 (tpp80)
  outliers start: 17
  outliers final: 14
  residues processed: 128
  average time/residue: 0.2503
  time to fit residues: 42.3686
Evaluate side-chains
  128 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  288 HIS
Chi-restraints excluded: chain R residue  323 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 68 optimal weight:    0.1980
   chunk 35 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0040
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN
N  82 GLN
** R  73 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 = 0.3719 r_free = 0.3719 target = 0.154640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120993 restraints weight = 8833.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.71
r_work: 0.3156 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7986  Z= 0.144
  Angle     :  0.504   8.688  10858  Z= 0.263
  Chirality :  0.041   0.415   1258
  Planarity :  0.004   0.043   1390
  Dihedral  :  4.020  28.101   1122
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.50 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 1011
  helix:  2.71 (0.26), residues: 379
  sheet: -0.33 (0.33), residues: 216
  loop : -0.97 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.003   0.000   ARG R 240 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7703 (mtpt)
REVERT: A   34 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8183 (ttmt)
REVERT: A  213 GLN cc_start: 0.8399 (tt0) cc_final: 0.8066 (tt0)
REVERT: A  252 ASP cc_start: 0.7516 (t70) cc_final: 0.7112 (t70)
REVERT: A  304 GLU cc_start: 0.8065 (pm20) cc_final: 0.7816 (pm20)
REVERT: A  308 TYR cc_start: 0.7844 (t80) cc_final: 0.7315 (t80)
REVERT: A  329 TYR cc_start: 0.8643 (m-80) cc_final: 0.8351 (m-80)
REVERT: B   42 ARG cc_start: 0.7713 (tmt170) cc_final: 0.6884 (tpt170)
REVERT: B  256 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7148 (mtm110)
REVERT: B  259 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8043 (mm-40)
REVERT: N   20 LEU cc_start: 0.8164 (mt) cc_final: 0.7871 (mt)
REVERT: N   46 GLU cc_start: 0.8497 (pt0) cc_final: 0.8205 (pt0)
REVERT: N   65 LYS cc_start: 0.6689 (ttmm) cc_final: 0.6411 (tptp)
REVERT: N  108 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7887 (t80)
REVERT: R  353 ARG cc_start: 0.6148 (mtt90) cc_final: 0.5917 (tpp80)
  outliers start: 21
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2368
  time to fit residues: 42.3238
Evaluate side-chains
  136 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  288 HIS
Chi-restraints excluded: chain R residue  303 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 26 optimal weight:   40.0000
   chunk 64 optimal weight:    7.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0470
   chunk 83 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.3684

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN
N  82 GLN
** R  73 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 = 0.3701 r_free = 0.3701 target = 0.153093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.118583 restraints weight = 8952.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.83
r_work: 0.3136 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7986  Z= 0.185
  Angle     :  0.534  10.454  10858  Z= 0.276
  Chirality :  0.042   0.421   1258
  Planarity :  0.004   0.043   1390
  Dihedral  :  4.092  28.706   1122
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.72 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1011
  helix:  2.58 (0.26), residues: 385
  sheet: -0.25 (0.34), residues: 206
  loop : -0.95 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.014   0.001   PHE R 308 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.003   0.000   ARG N  98 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7721 (mtpt)
REVERT: A   34 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8194 (ttmt)
REVERT: A  213 GLN cc_start: 0.8448 (tt0) cc_final: 0.8111 (tt0)
REVERT: A  252 ASP cc_start: 0.7502 (t70) cc_final: 0.7123 (t70)
REVERT: A  304 GLU cc_start: 0.8056 (pm20) cc_final: 0.7807 (pm20)
REVERT: A  329 TYR cc_start: 0.8686 (m-80) cc_final: 0.8375 (m-80)
REVERT: B   42 ARG cc_start: 0.7682 (tmt170) cc_final: 0.6876 (tpt170)
REVERT: B  256 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7170 (mtm110)
REVERT: B  259 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8130 (mm-40)
REVERT: N   20 LEU cc_start: 0.8124 (mt) cc_final: 0.7823 (mt)
REVERT: N   46 GLU cc_start: 0.8456 (pt0) cc_final: 0.8137 (pt0)
REVERT: N   65 LYS cc_start: 0.6691 (ttmm) cc_final: 0.6424 (tptp)
REVERT: R  353 ARG cc_start: 0.6188 (mtt90) cc_final: 0.5944 (tpp80)
  outliers start: 17
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2508
  time to fit residues: 42.8990
Evaluate side-chains
  129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  288 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 220 GLN
N  77 ASN
** R  73 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 = 0.3701 r_free = 0.3701 target = 0.153057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.118444 restraints weight = 9053.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.82
r_work: 0.3131 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7986  Z= 0.187
  Angle     :  0.535  10.392  10858  Z= 0.277
  Chirality :  0.042   0.436   1258
  Planarity :  0.004   0.043   1390
  Dihedral  :  4.125  28.625   1122
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.85 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.27), residues: 1011
  helix:  2.58 (0.26), residues: 385
  sheet: -0.24 (0.34), residues: 214
  loop : -0.97 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.004   0.000   ARG N  98 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7733 (mtpt)
REVERT: A   34 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8210 (ttmt)
REVERT: A  213 GLN cc_start: 0.8494 (tt0) cc_final: 0.8193 (tt0)
REVERT: A  252 ASP cc_start: 0.7525 (t70) cc_final: 0.7136 (t70)
REVERT: A  329 TYR cc_start: 0.8687 (m-80) cc_final: 0.8382 (m-80)
REVERT: B   42 ARG cc_start: 0.7693 (tmt170) cc_final: 0.6863 (tpt170)
REVERT: B  256 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7166 (mtm110)
REVERT: B  259 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8140 (mm-40)
REVERT: N   20 LEU cc_start: 0.8124 (mt) cc_final: 0.7831 (mt)
REVERT: N   46 GLU cc_start: 0.8534 (pt0) cc_final: 0.8271 (pt0)
REVERT: N   60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8567 (m-80)
REVERT: N   89 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6931 (mp0)
REVERT: R  353 ARG cc_start: 0.6118 (mtt90) cc_final: 0.5868 (tpp80)
  outliers start: 16
  outliers final: 14
  residues processed: 127
  average time/residue: 0.2291
  time to fit residues: 38.2323
Evaluate side-chains
  131 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  288 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
N  77 ASN
** R  73 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 = 0.3693 r_free = 0.3693 target = 0.152405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.117489 restraints weight = 8987.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.83
r_work: 0.3120 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7986  Z= 0.200
  Angle     :  0.548  10.241  10858  Z= 0.282
  Chirality :  0.043   0.443   1258
  Planarity :  0.004   0.043   1390
  Dihedral  :  4.165  28.503   1122
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.72 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.27), residues: 1011
  helix:  2.44 (0.26), residues: 389
  sheet: -0.22 (0.34), residues: 215
  loop : -1.02 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.015   0.001   TYR A 348 
 ARG   0.004   0.000   ARG N  98 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7695 (mtpt)
REVERT: A   34 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8178 (ttmt)
REVERT: A  213 GLN cc_start: 0.8472 (tt0) cc_final: 0.8068 (tt0)
REVERT: A  252 ASP cc_start: 0.7498 (t70) cc_final: 0.7091 (t70)
REVERT: A  329 TYR cc_start: 0.8653 (m-80) cc_final: 0.8333 (m-80)
REVERT: B   42 ARG cc_start: 0.7676 (tmt170) cc_final: 0.6863 (tpt170)
REVERT: B  256 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7114 (mtm110)
REVERT: B  259 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8111 (mm-40)
REVERT: N   20 LEU cc_start: 0.8087 (mt) cc_final: 0.7800 (mt)
REVERT: N   46 GLU cc_start: 0.8550 (pt0) cc_final: 0.8275 (pt0)
REVERT: N   60 TYR cc_start: 0.8802 (m-80) cc_final: 0.8575 (m-80)
REVERT: N   65 LYS cc_start: 0.6724 (ttmm) cc_final: 0.6394 (tptp)
REVERT: N   89 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7049 (mp0)
REVERT: R  353 ARG cc_start: 0.6111 (mtt90) cc_final: 0.5854 (tpp80)
  outliers start: 19
  outliers final: 16
  residues processed: 127
  average time/residue: 0.2480
  time to fit residues: 41.6034
Evaluate side-chains
  133 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  288 HIS
Chi-restraints excluded: chain R residue  303 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 96 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
N 123 GLN
** R  73 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 = 0.3714 r_free = 0.3714 target = 0.154383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.119988 restraints weight = 8962.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.83
r_work: 0.3148 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7986  Z= 0.152
  Angle     :  0.528   9.845  10858  Z= 0.272
  Chirality :  0.042   0.437   1258
  Planarity :  0.004   0.043   1390
  Dihedral  :  4.020  28.139   1122
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.72 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1011
  helix:  2.66 (0.26), residues: 385
  sheet: -0.22 (0.34), residues: 214
  loop : -0.97 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.003   0.000   ARG R 240 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4749.66 seconds
wall clock time: 85 minutes 51.36 seconds (5151.36 seconds total)