Starting phenix.real_space_refine
on Mon Apr 28 07:51:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6gdg_4390/04_2025/6gdg_4390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6gdg_4390/04_2025/6gdg_4390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6gdg_4390/04_2025/6gdg_4390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6gdg_4390/04_2025/6gdg_4390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6gdg_4390/04_2025/6gdg_4390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6gdg_4390/04_2025/6gdg_4390.cif"
  }
  resolution = 4.11
  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=   0.012
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      49      5.16       5
     C    4611      2.51       5
     N    1246      2.21       5
     O    1317      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7223
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1913
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 9, 'TRANS': 254}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 161
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 98
    Chain: "B"
      Number of atoms: 2377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2377
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 206
          Unresolved non-hydrogen angles: 252
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 157
    Chain: "C"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 262
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 41}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "D"
      Number of atoms: 1721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1721
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 155
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 98
    Chain: "E"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 928
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'NEC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.64, per 1000 atoms: 0.64
  Number of scatterers: 7223
  At special positions: 0
  Unit cell: (92.02, 125.19, 78.11, 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      49     16.00
     O    1317      8.00
     N    1246      7.00
     C    4611      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " 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: 1.91
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1874

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      42.8% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 34
      removed outlier: 3.853A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 59
      removed outlier: 3.510A  pdb=" N   PHE A  44 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 69
      removed outlier: 3.791A  pdb=" N   ILE A  66 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLY A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 108
      removed outlier: 3.612A  pdb=" N   ILE A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 117 through 137
    Processing helix  chain 'A' and resid 167 through 172
      removed outlier: 3.635A  pdb=" N   VAL A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
    Processing helix  chain 'A' and resid 180 through 186
    Processing helix  chain 'A' and resid 186 through 209
      removed outlier: 3.673A  pdb=" N   LYS A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 259
      removed outlier: 3.782A  pdb=" N   PHE A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      Proline residue:  A 248  - end of helix
    Processing helix  chain 'A' and resid 266 through 288
      removed outlier: 3.858A  pdb=" N   ASN A 280 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   SER A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A 282 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 292 through 299
      removed outlier: 3.719A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 12 through 24
      removed outlier: 3.865A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
    Processing helix  chain 'D' and resid 13 through 40
      removed outlier: 3.803A  pdb=" N   LYS D  17 " --> pdb=" O   ARG D  13 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS D  25 " --> pdb=" O   GLU D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 57
      removed outlier: 4.071A  pdb=" N   ILE D  56 " --> pdb=" O   GLY D  52 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL D  57 " --> pdb=" O   LYS D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 52 through 57'
    Processing helix  chain 'D' and resid 234 through 238
    Processing helix  chain 'D' and resid 252 through 269
      removed outlier: 3.813A  pdb=" N   GLN D 257 " --> pdb=" O   TYR D 253 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLU D 258 " --> pdb=" O   ASN D 254 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 283 through 294
      removed outlier: 3.520A  pdb=" N   LYS D 290 " --> pdb=" O   LEU D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 302
      removed outlier: 4.118A  pdb=" N   TYR D 301 " --> pdb=" O   LYS D 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 308
      removed outlier: 3.529A  pdb=" N   ALA D 306 " --> pdb=" O   PRO D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 341
      removed outlier: 3.546A  pdb=" N   ILE D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE D 335 " --> pdb=" O   ILE D 331 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE D 338 " --> pdb=" O   GLU D 334 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 381
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.581A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.616A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.657A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.920A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.649A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 4.021A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.066A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 233 through 234
      removed outlier: 3.706A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.657A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 44
      removed outlier: 6.719A  pdb=" N   HIS D  41 " --> pdb=" O   HIS D 220 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   PHE D 222 " --> pdb=" O   HIS D  41 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU D  43 " --> pdb=" O   PHE D 222 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE D 212 " --> pdb=" O   PHE D 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 243 through 244
    Processing sheet with id=AB1, first strand: chain 'D' and resid 247 through 249
    Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.626A  pdb=" N   SER E  71 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.549A  pdb=" N   THR E 122 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1083 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: 2.03

  Time building geometry restraints manager: 2.05 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: 2335
        1.34 -     1.46: 906
        1.46 -     1.58: 4070
        1.58 -     1.70: 0
        1.70 -     1.81: 65
  Bond restraints: 7376
  Sorted by residual:
  bond pdb=" C4  NEC A 400 "
       pdb=" C5  NEC A 400 "
    ideal  model  delta    sigma   weight residual
    1.385  1.474 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C5  NEC A 400 "
       pdb=" C6  NEC A 400 "
    ideal  model  delta    sigma   weight residual
    1.407  1.488 -0.081 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" CA  VAL A 188 "
       pdb=" CB  VAL A 188 "
    ideal  model  delta    sigma   weight residual
    1.539  1.560 -0.021 5.40e-03 3.43e+04 1.47e+01
  bond pdb=" C8  NEC A 400 "
       pdb=" N7  NEC A 400 "
    ideal  model  delta    sigma   weight residual
    1.302  1.359 -0.057 2.00e-02 2.50e+03 8.12e+00
  bond pdb=" CA  ILE A  64 "
       pdb=" CB  ILE A  64 "
    ideal  model  delta    sigma   weight residual
    1.540  1.571 -0.031 1.25e-02 6.40e+03 6.01e+00
  ... (remaining 7371 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 9227
        1.97 -     3.94: 807
        3.94 -     5.92: 41
        5.92 -     7.89: 4
        7.89 -     9.86: 3
  Bond angle restraints: 10082
  Sorted by residual:
  angle pdb=" N   ASP D 229 "
        pdb=" CA  ASP D 229 "
        pdb=" C   ASP D 229 "
      ideal   model   delta    sigma   weight residual
     112.38  118.19   -5.81 1.22e+00 6.72e-01 2.26e+01
  angle pdb=" CA  VAL A 188 "
        pdb=" C   VAL A 188 "
        pdb=" N   PRO A 189 "
      ideal   model   delta    sigma   weight residual
     120.83  118.29    2.54 6.10e-01 2.69e+00 1.73e+01
  angle pdb=" N   SER B 161 "
        pdb=" CA  SER B 161 "
        pdb=" C   SER B 161 "
      ideal   model   delta    sigma   weight residual
     108.38  113.47   -5.09 1.35e+00 5.49e-01 1.42e+01
  angle pdb=" C   PHE D 302 "
        pdb=" N   PRO D 303 "
        pdb=" CA  PRO D 303 "
      ideal   model   delta    sigma   weight residual
     119.47  123.82   -4.35 1.16e+00 7.43e-01 1.40e+01
  angle pdb=" N   THR E 104 "
        pdb=" CA  THR E 104 "
        pdb=" C   THR E 104 "
      ideal   model   delta    sigma   weight residual
     108.38  113.31   -4.93 1.35e+00 5.49e-01 1.34e+01
  ... (remaining 10077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 3959
       16.99 -    33.99: 266
       33.99 -    50.98: 66
       50.98 -    67.97: 12
       67.97 -    84.96: 4
  Dihedral angle restraints: 4307
    sinusoidal: 1411
      harmonic: 2896
  Sorted by residual:
  dihedral pdb=" CB  CYS A  74 "
           pdb=" SG  CYS A  74 "
           pdb=" SG  CYS A 146 "
           pdb=" CB  CYS A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.96  -84.96     1      1.00e+01 1.00e-02 8.76e+01
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.29   77.29     1      1.00e+01 1.00e-02 7.49e+01
  dihedral pdb=" CA  THR B 159 "
           pdb=" C   THR B 159 "
           pdb=" N   SER B 160 "
           pdb=" CA  SER B 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.75   18.25     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 4304 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 703
       0.044 -    0.087: 338
       0.087 -    0.131: 105
       0.131 -    0.174: 37
       0.174 -    0.218: 15
  Chirality restraints: 1198
  Sorted by residual:
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  TRP D 234 "
            pdb=" N   TRP D 234 "
            pdb=" C   TRP D 234 "
            pdb=" CB  TRP D 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1195 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 188 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.25e+00
        pdb=" N   PRO A 189 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 284 "   -0.033 5.00e-02 4.00e+02   5.04e-02 4.07e+00
        pdb=" N   PRO A 285 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 138 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO A 139 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 139 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 139 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 2865
        2.94 -     3.43: 7370
        3.43 -     3.92: 11934
        3.92 -     4.41: 13287
        4.41 -     4.90: 22747
  Nonbonded interactions: 58203
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.449 3.040
  nonbonded pdb=" OG1 THR E 104 "
            pdb=" OD1 ASP E 106 "
     model   vdw
     2.471 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" OH  TYR E  32 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" O   TYR B 145 "
            pdb=" N   GLY B 162 "
     model   vdw
     2.509 3.120
  nonbonded pdb=" O   GLN D 380 "
            pdb=" OE1 GLU D 382 "
     model   vdw
     2.537 3.040
  ... (remaining 58198 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:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.600
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
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      :  0.008   0.089   7381  Z= 0.546
  Angle     :  1.102   9.859  10092  Z= 0.739
  Chirality :  0.061   0.218   1198
  Planarity :  0.004   0.052   1283
  Dihedral  : 13.001  79.978   2418
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 0.87
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.89 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  6.80 %
    Favored  : 91.12 %
  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: -3.15 (0.21), residues: 981
  helix: -1.30 (0.21), residues: 357
  sheet: -2.83 (0.35), residues: 135
  loop : -2.46 (0.23), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 234 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.014   0.002   PHE D 208 
 TYR   0.009   0.001   TYR B 124 
 ARG   0.003   0.001   ARG A 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25478 (  378)
  hydrogen bonds       : angle       9.54611 ( 1083)
  SS BOND              : bond        0.00417 (    5)
  SS BOND              : angle       0.42834 (   10)
  covalent geometry    : bond        0.00778 ( 7376)
  covalent geometry    : angle       1.10276 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 306
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 VAL cc_start: 0.8227 (t) cc_final: 0.7849 (p)
REVERT: A   34 ASN cc_start: 0.7194 (t0) cc_final: 0.6900 (t0)
REVERT: A   38 GLN cc_start: 0.8132 (pt0) cc_final: 0.7557 (pt0)
REVERT: A   82 CYS cc_start: 0.8532 (m) cc_final: 0.8010 (t)
REVERT: A  129 TRP cc_start: 0.6886 (m100) cc_final: 0.6671 (m-10)
REVERT: A  135 ILE cc_start: 0.8309 (mt) cc_final: 0.8091 (tt)
REVERT: A  145 ASN cc_start: 0.7660 (t0) cc_final: 0.6839 (p0)
REVERT: A  193 MET cc_start: 0.7549 (mtp) cc_final: 0.7347 (mtm)
REVERT: A  199 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7934 (ttp-110)
REVERT: A  290 TYR cc_start: 0.8656 (t80) cc_final: 0.8406 (t80)
REVERT: B  111 TYR cc_start: 0.8582 (m-80) cc_final: 0.8201 (m-80)
REVERT: B  125 ASN cc_start: 0.7963 (t0) cc_final: 0.7606 (p0)
REVERT: B  187 VAL cc_start: 0.8688 (t) cc_final: 0.8405 (t)
REVERT: B  218 CYS cc_start: 0.8586 (t) cc_final: 0.8335 (t)
REVERT: B  290 ASP cc_start: 0.7257 (m-30) cc_final: 0.7033 (m-30)
REVERT: B  325 MET cc_start: 0.8631 (ttm) cc_final: 0.8105 (tpt)
REVERT: C   21 MET cc_start: 0.6129 (ttm) cc_final: 0.5835 (mmm)
REVERT: D   17 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8709 (tppt)
REVERT: D  252 ASP cc_start: 0.8738 (m-30) cc_final: 0.8306 (t0)
REVERT: D  268 ASN cc_start: 0.9355 (m-40) cc_final: 0.9154 (m-40)
REVERT: D  270 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8146 (ttt90)
REVERT: D  272 LEU cc_start: 0.9230 (mt) cc_final: 0.9007 (mp)
REVERT: D  334 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: D  346 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8735 (mtp85)
REVERT: D  361 ASN cc_start: 0.8566 (m-40) cc_final: 0.8265 (m110)
REVERT: D  383 LEU cc_start: 0.7660 (tp) cc_final: 0.7437 (mt)
REVERT: E   20 LEU cc_start: 0.7879 (mt) cc_final: 0.7590 (mt)
REVERT: E   60 TYR cc_start: 0.9074 (m-80) cc_final: 0.8525 (m-80)
REVERT: E   68 PHE cc_start: 0.8183 (m-10) cc_final: 0.6736 (m-10)
REVERT: E   69 THR cc_start: 0.8530 (m) cc_final: 0.8164 (p)
REVERT: E   72 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7621 (ttm110)
REVERT: E   74 ASN cc_start: 0.6871 (m-40) cc_final: 0.6050 (t0)
REVERT: E   80 TYR cc_start: 0.7377 (m-80) cc_final: 0.6911 (m-80)
  outliers start: 14
  outliers final: 4
  residues processed: 315
  average time/residue: 0.1965
  time to fit residues: 81.2165
Evaluate side-chains
  189 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 185
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  19 GLN
D 257 GLN
D 347 HIS
E  35 ASN
E  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.138943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.123781 restraints weight = 14403.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.125598 restraints weight = 9632.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.127069 restraints weight = 7156.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7381  Z= 0.141
  Angle     :  0.623  10.120  10092  Z= 0.332
  Chirality :  0.044   0.152   1198
  Planarity :  0.005   0.064   1283
  Dihedral  :  5.424  33.719   1084
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.25 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.38 (0.25), residues: 981
  helix:  0.65 (0.25), residues: 371
  sheet: -2.08 (0.32), residues: 195
  loop : -1.71 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 339 
 HIS   0.016   0.002   HIS D 347 
 PHE   0.015   0.002   PHE B 234 
 TYR   0.027   0.002   TYR B  59 
 ARG   0.004   0.001   ARG A 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04695 (  378)
  hydrogen bonds       : angle       5.83782 ( 1083)
  SS BOND              : bond        0.01016 (    5)
  SS BOND              : angle       1.52058 (   10)
  covalent geometry    : bond        0.00303 ( 7376)
  covalent geometry    : angle       0.62168 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 226
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7788 (t0) cc_final: 0.7085 (p0)
REVERT: A  182 PHE cc_start: 0.8404 (t80) cc_final: 0.7900 (t80)
REVERT: B  166 CYS cc_start: 0.7877 (m) cc_final: 0.7642 (m)
REVERT: B  188 MET cc_start: 0.7729 (mmm) cc_final: 0.6880 (mmm)
REVERT: B  230 ASN cc_start: 0.7800 (m-40) cc_final: 0.7553 (m110)
REVERT: C   36 ASP cc_start: 0.7420 (t0) cc_final: 0.7181 (t70)
REVERT: D   17 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8523 (tppt)
REVERT: D  233 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8094 (mmmt)
REVERT: D  239 ASN cc_start: 0.8334 (p0) cc_final: 0.7876 (p0)
REVERT: D  274 THR cc_start: 0.8146 (p) cc_final: 0.7783 (p)
REVERT: D  298 ILE cc_start: 0.7962 (mp) cc_final: 0.7727 (mp)
REVERT: E   60 TYR cc_start: 0.8699 (m-80) cc_final: 0.7827 (m-80)
REVERT: E   69 THR cc_start: 0.7464 (m) cc_final: 0.7249 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 228
  average time/residue: 0.1657
  time to fit residues: 51.8696
Evaluate side-chains
  158 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:   50.0000
   chunk 65 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
B 156 GLN
E  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.116410 restraints weight = 14732.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.118459 restraints weight = 9506.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.120051 restraints weight = 6948.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7381  Z= 0.192
  Angle     :  0.646  11.490  10092  Z= 0.341
  Chirality :  0.044   0.161   1198
  Planarity :  0.005   0.052   1283
  Dihedral  :  5.197  35.779   1084
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -0.78 (0.26), residues: 981
  helix:  1.17 (0.26), residues: 366
  sheet: -1.82 (0.32), residues: 203
  loop : -1.32 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 332 
 HIS   0.008   0.002   HIS D 347 
 PHE   0.020   0.002   PHE A 257 
 TYR   0.028   0.002   TYR B  59 
 ARG   0.009   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04491 (  378)
  hydrogen bonds       : angle       5.55001 ( 1083)
  SS BOND              : bond        0.00293 (    5)
  SS BOND              : angle       2.79150 (   10)
  covalent geometry    : bond        0.00431 ( 7376)
  covalent geometry    : angle       0.64004 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  145 ASN cc_start: 0.7784 (t0) cc_final: 0.6952 (p0)
REVERT: A  182 PHE cc_start: 0.8589 (t80) cc_final: 0.8317 (t80)
REVERT: A  237 ILE cc_start: 0.7986 (tt) cc_final: 0.7712 (tp)
REVERT: B  166 CYS cc_start: 0.8037 (m) cc_final: 0.7747 (m)
REVERT: B  188 MET cc_start: 0.7776 (mmm) cc_final: 0.7241 (mmm)
REVERT: B  227 SER cc_start: 0.8652 (t) cc_final: 0.8272 (p)
REVERT: B  230 ASN cc_start: 0.7645 (m-40) cc_final: 0.7423 (m110)
REVERT: C   36 ASP cc_start: 0.7405 (t0) cc_final: 0.7189 (t70)
REVERT: D   17 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8554 (tppt)
REVERT: D  222 PHE cc_start: 0.5933 (t80) cc_final: 0.4321 (t80)
REVERT: D  233 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8566 (mmtt)
REVERT: D  239 ASN cc_start: 0.8474 (p0) cc_final: 0.8101 (p0)
REVERT: D  369 CYS cc_start: 0.8360 (m) cc_final: 0.8026 (m)
REVERT: E   60 TYR cc_start: 0.8734 (m-80) cc_final: 0.8511 (m-10)
REVERT: E   72 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7494 (ptm160)
REVERT: E   79 LEU cc_start: 0.8499 (tp) cc_final: 0.8251 (tp)
REVERT: E  125 THR cc_start: 0.7836 (p) cc_final: 0.7620 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1800
  time to fit residues: 45.6793
Evaluate side-chains
  149 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:    0.3980
   chunk 79 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.133649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.118413 restraints weight = 14871.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120224 restraints weight = 9866.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.121617 restraints weight = 7369.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7381  Z= 0.141
  Angle     :  0.584   7.505  10092  Z= 0.310
  Chirality :  0.043   0.200   1198
  Planarity :  0.004   0.058   1283
  Dihedral  :  4.924  28.374   1084
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.85 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.26), residues: 981
  helix:  1.49 (0.27), residues: 367
  sheet: -1.64 (0.32), residues: 220
  loop : -1.08 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.004   0.001   HIS D 347 
 PHE   0.024   0.002   PHE E  68 
 TYR   0.023   0.001   TYR B  59 
 ARG   0.004   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  378)
  hydrogen bonds       : angle       5.30494 ( 1083)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       1.42975 (   10)
  covalent geometry    : bond        0.00322 ( 7376)
  covalent geometry    : angle       0.58223 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7735 (t0) cc_final: 0.6943 (p0)
REVERT: A  182 PHE cc_start: 0.8533 (t80) cc_final: 0.8284 (t80)
REVERT: A  237 ILE cc_start: 0.7739 (tt) cc_final: 0.7398 (tp)
REVERT: A  276 LEU cc_start: 0.9334 (tp) cc_final: 0.8824 (tp)
REVERT: B  227 SER cc_start: 0.8526 (t) cc_final: 0.8173 (p)
REVERT: B  291 ASP cc_start: 0.7384 (p0) cc_final: 0.6944 (m-30)
REVERT: C   36 ASP cc_start: 0.7422 (t0) cc_final: 0.7213 (t70)
REVERT: D   17 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8524 (tppt)
REVERT: D  222 PHE cc_start: 0.5664 (t80) cc_final: 0.4156 (t80)
REVERT: D  265 SER cc_start: 0.8696 (m) cc_final: 0.8495 (t)
REVERT: D  269 ASN cc_start: 0.8611 (t0) cc_final: 0.8239 (t0)
REVERT: D  274 THR cc_start: 0.8209 (p) cc_final: 0.8005 (p)
REVERT: D  282 ASN cc_start: 0.8152 (t0) cc_final: 0.7938 (t0)
REVERT: E  125 THR cc_start: 0.7820 (p) cc_final: 0.7558 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1687
  time to fit residues: 42.5558
Evaluate side-chains
  145 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0870
   chunk 81 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    3.0164

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
A 253 ASN
B 230 ASN
** D  19 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.129992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114997 restraints weight = 14846.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.116757 restraints weight = 9961.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.118058 restraints weight = 7514.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   7381  Z= 0.221
  Angle     :  0.660   7.703  10092  Z= 0.349
  Chirality :  0.045   0.220   1198
  Planarity :  0.005   0.053   1283
  Dihedral  :  5.222  36.343   1084
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -0.32 (0.27), residues: 981
  helix:  1.50 (0.27), residues: 363
  sheet: -1.48 (0.33), residues: 218
  loop : -0.99 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 339 
 HIS   0.007   0.002   HIS B 311 
 PHE   0.031   0.002   PHE E  68 
 TYR   0.028   0.002   TYR B  59 
 ARG   0.006   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 (  378)
  hydrogen bonds       : angle       5.42901 ( 1083)
  SS BOND              : bond        0.00260 (    5)
  SS BOND              : angle       2.26599 (   10)
  covalent geometry    : bond        0.00502 ( 7376)
  covalent geometry    : angle       0.65634 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7806 (t0) cc_final: 0.7002 (p0)
REVERT: A  174 MET cc_start: 0.8305 (tpp) cc_final: 0.7778 (mmt)
REVERT: A  276 LEU cc_start: 0.9357 (tp) cc_final: 0.8880 (tp)
REVERT: B   32 GLN cc_start: 0.7429 (mp10) cc_final: 0.7224 (mp10)
REVERT: B  188 MET cc_start: 0.7841 (mmm) cc_final: 0.7317 (mmm)
REVERT: B  227 SER cc_start: 0.8638 (t) cc_final: 0.8295 (p)
REVERT: B  230 ASN cc_start: 0.7862 (m-40) cc_final: 0.7536 (m110)
REVERT: C   21 MET cc_start: 0.5921 (ttt) cc_final: 0.5602 (mmm)
REVERT: C   36 ASP cc_start: 0.7507 (t0) cc_final: 0.7302 (t70)
REVERT: D   17 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8575 (tppt)
REVERT: D  222 PHE cc_start: 0.5704 (t80) cc_final: 0.4183 (t80)
REVERT: D  233 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8547 (mmtt)
REVERT: D  360 GLU cc_start: 0.7506 (tp30) cc_final: 0.7270 (mm-30)
REVERT: E   32 TYR cc_start: 0.7819 (m-80) cc_final: 0.7608 (m-80)
REVERT: E   34 MET cc_start: 0.8244 (mmm) cc_final: 0.7641 (mmm)
REVERT: E   53 GLN cc_start: 0.8593 (mp10) cc_final: 0.8203 (mp10)
REVERT: E  125 THR cc_start: 0.8053 (p) cc_final: 0.7770 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1684
  time to fit residues: 42.4532
Evaluate side-chains
  149 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 14 optimal weight:   20.0000
   chunk 22 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 250 HIS
A 253 ASN
D 220 HIS
E  31 ASN
E 123 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.135000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.119854 restraints weight = 14653.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.121659 restraints weight = 9769.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.123073 restraints weight = 7310.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7381  Z= 0.129
  Angle     :  0.588   8.880  10092  Z= 0.310
  Chirality :  0.044   0.262   1198
  Planarity :  0.004   0.052   1283
  Dihedral  :  4.901  37.294   1084
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -0.11 (0.27), residues: 981
  helix:  1.68 (0.27), residues: 369
  sheet: -1.42 (0.33), residues: 211
  loop : -0.91 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.006   0.001   HIS D 220 
 PHE   0.038   0.002   PHE E  68 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.006   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  378)
  hydrogen bonds       : angle       5.19529 ( 1083)
  SS BOND              : bond        0.00224 (    5)
  SS BOND              : angle       2.20912 (   10)
  covalent geometry    : bond        0.00295 ( 7376)
  covalent geometry    : angle       0.58383 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 GLN cc_start: 0.8380 (tp40) cc_final: 0.8147 (tp40)
REVERT: A  145 ASN cc_start: 0.7728 (t0) cc_final: 0.6950 (p0)
REVERT: B   46 ARG cc_start: 0.6886 (mmp-170) cc_final: 0.6319 (mtt180)
REVERT: B   51 LEU cc_start: 0.7208 (mp) cc_final: 0.6875 (mp)
REVERT: B  188 MET cc_start: 0.7798 (mmm) cc_final: 0.7115 (mmm)
REVERT: B  227 SER cc_start: 0.8455 (t) cc_final: 0.8095 (p)
REVERT: B  230 ASN cc_start: 0.7935 (m-40) cc_final: 0.7351 (m110)
REVERT: D   17 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8517 (tppt)
REVERT: D  233 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8356 (mmtt)
REVERT: E  125 THR cc_start: 0.7866 (p) cc_final: 0.7606 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1779
  time to fit residues: 44.9401
Evaluate side-chains
  150 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 86 optimal weight:    0.1980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS
E   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118394 restraints weight = 14744.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120181 restraints weight = 9819.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.121593 restraints weight = 7359.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7381  Z= 0.151
  Angle     :  0.586   6.917  10092  Z= 0.314
  Chirality :  0.044   0.170   1198
  Planarity :  0.005   0.086   1283
  Dihedral  :  4.910  38.264   1084
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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: -0.01 (0.27), residues: 981
  helix:  1.70 (0.28), residues: 369
  sheet: -1.35 (0.34), residues: 213
  loop : -0.78 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 250 
 PHE   0.024   0.002   PHE B 292 
 TYR   0.022   0.001   TYR B  59 
 ARG   0.007   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  378)
  hydrogen bonds       : angle       5.17101 ( 1083)
  SS BOND              : bond        0.00286 (    5)
  SS BOND              : angle       1.92659 (   10)
  covalent geometry    : bond        0.00347 ( 7376)
  covalent geometry    : angle       0.58318 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7264 (t0) cc_final: 0.6854 (t0)
REVERT: A  145 ASN cc_start: 0.7731 (t0) cc_final: 0.6941 (p0)
REVERT: A  193 MET cc_start: 0.7289 (mtp) cc_final: 0.6988 (mtm)
REVERT: A  245 CYS cc_start: 0.8080 (m) cc_final: 0.7553 (m)
REVERT: A  274 ILE cc_start: 0.7787 (mt) cc_final: 0.7517 (pt)
REVERT: B   46 ARG cc_start: 0.6893 (mmp-170) cc_final: 0.5944 (ttm-80)
REVERT: B  188 MET cc_start: 0.7790 (mmm) cc_final: 0.6782 (mmm)
REVERT: B  227 SER cc_start: 0.8503 (t) cc_final: 0.7997 (p)
REVERT: B  230 ASN cc_start: 0.7940 (m-40) cc_final: 0.7510 (m110)
REVERT: D   17 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8502 (tppt)
REVERT: D  233 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8272 (mmmt)
REVERT: D  275 ILE cc_start: 0.8606 (mm) cc_final: 0.8392 (tp)
REVERT: E   65 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7830 (mtpp)
REVERT: E  125 THR cc_start: 0.8015 (p) cc_final: 0.7696 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1687
  time to fit residues: 41.8613
Evaluate side-chains
  144 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0060
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 253 ASN
** D  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.137184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.122140 restraints weight = 14521.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.123836 restraints weight = 9807.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.125094 restraints weight = 7441.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7381  Z= 0.126
  Angle     :  0.584   8.504  10092  Z= 0.305
  Chirality :  0.043   0.175   1198
  Planarity :  0.005   0.059   1283
  Dihedral  :  4.699  32.670   1084
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.12 (0.27), residues: 981
  helix:  1.76 (0.27), residues: 366
  sheet: -1.14 (0.33), residues: 225
  loop : -0.70 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  82 
 HIS   0.005   0.001   HIS D 347 
 PHE   0.031   0.002   PHE A 182 
 TYR   0.021   0.001   TYR A 290 
 ARG   0.007   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (  378)
  hydrogen bonds       : angle       5.04262 ( 1083)
  SS BOND              : bond        0.00325 (    5)
  SS BOND              : angle       1.69972 (   10)
  covalent geometry    : bond        0.00285 ( 7376)
  covalent geometry    : angle       0.58168 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7299 (t0) cc_final: 0.6965 (t0)
REVERT: A  145 ASN cc_start: 0.7638 (t0) cc_final: 0.6891 (p0)
REVERT: A  193 MET cc_start: 0.7255 (mtp) cc_final: 0.6913 (mtm)
REVERT: A  245 CYS cc_start: 0.8078 (m) cc_final: 0.7469 (m)
REVERT: B   46 ARG cc_start: 0.6718 (mmp-170) cc_final: 0.6009 (ttm-80)
REVERT: B  188 MET cc_start: 0.7740 (mmm) cc_final: 0.7000 (mmm)
REVERT: B  227 SER cc_start: 0.8434 (t) cc_final: 0.7959 (p)
REVERT: B  230 ASN cc_start: 0.7880 (m-40) cc_final: 0.7413 (m110)
REVERT: D  233 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8418 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1691
  time to fit residues: 42.0039
Evaluate side-chains
  139 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.133027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.117800 restraints weight = 14727.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119594 restraints weight = 9797.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.121024 restraints weight = 7315.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7381  Z= 0.195
  Angle     :  0.650   9.273  10092  Z= 0.342
  Chirality :  0.045   0.225   1198
  Planarity :  0.004   0.052   1283
  Dihedral  :  4.837  33.046   1084
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.04 (0.27), residues: 981
  helix:  1.72 (0.27), residues: 365
  sheet: -1.05 (0.34), residues: 210
  loop : -0.88 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP D 271 
 HIS   0.006   0.002   HIS B  91 
 PHE   0.026   0.002   PHE A 182 
 TYR   0.024   0.002   TYR B  59 
 ARG   0.004   0.001   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  378)
  hydrogen bonds       : angle       5.19956 ( 1083)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       1.86596 (   10)
  covalent geometry    : bond        0.00447 ( 7376)
  covalent geometry    : angle       0.64785 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7496 (t0) cc_final: 0.7149 (t0)
REVERT: A  145 ASN cc_start: 0.7736 (t0) cc_final: 0.6954 (p0)
REVERT: A  193 MET cc_start: 0.7268 (mtp) cc_final: 0.7016 (mtm)
REVERT: A  241 LEU cc_start: 0.8361 (mp) cc_final: 0.7629 (mp)
REVERT: A  245 CYS cc_start: 0.7808 (m) cc_final: 0.7121 (m)
REVERT: B   46 ARG cc_start: 0.6905 (mmp-170) cc_final: 0.5992 (ttm170)
REVERT: B  188 MET cc_start: 0.7727 (mmm) cc_final: 0.6660 (mmm)
REVERT: B  227 SER cc_start: 0.8482 (t) cc_final: 0.8012 (p)
REVERT: B  230 ASN cc_start: 0.7974 (m-40) cc_final: 0.7626 (m110)
REVERT: B  293 ASN cc_start: 0.8102 (m-40) cc_final: 0.7388 (p0)
REVERT: B  323 ASP cc_start: 0.8024 (p0) cc_final: 0.7778 (p0)
REVERT: D  233 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8316 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1604
  time to fit residues: 38.8485
Evaluate side-chains
  138 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 27 optimal weight:   30.0000
   chunk 3 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0670
   overall best weight:    1.3322

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119967 restraints weight = 14743.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121926 restraints weight = 9702.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.123458 restraints weight = 7139.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.5743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7381  Z= 0.144
  Angle     :  0.609   7.496  10092  Z= 0.319
  Chirality :  0.043   0.153   1198
  Planarity :  0.004   0.051   1283
  Dihedral  :  4.899  36.499   1084
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.06 (0.27), residues: 981
  helix:  1.72 (0.27), residues: 370
  sheet: -1.08 (0.34), residues: 215
  loop : -0.85 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  82 
 HIS   0.008   0.001   HIS D 220 
 PHE   0.028   0.002   PHE A 182 
 TYR   0.019   0.002   TYR A 290 
 ARG   0.011   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  378)
  hydrogen bonds       : angle       5.12042 ( 1083)
  SS BOND              : bond        0.00310 (    5)
  SS BOND              : angle       1.75922 (   10)
  covalent geometry    : bond        0.00335 ( 7376)
  covalent geometry    : angle       0.60703 (10082)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASN cc_start: 0.7433 (t0) cc_final: 0.7110 (t0)
REVERT: A   89 GLN cc_start: 0.8813 (tp40) cc_final: 0.8291 (tp40)
REVERT: A   90 SER cc_start: 0.8537 (t) cc_final: 0.8267 (t)
REVERT: A  145 ASN cc_start: 0.7738 (t0) cc_final: 0.6965 (p0)
REVERT: A  193 MET cc_start: 0.7357 (mtp) cc_final: 0.7081 (mtm)
REVERT: A  241 LEU cc_start: 0.8290 (mp) cc_final: 0.7503 (mp)
REVERT: A  245 CYS cc_start: 0.7840 (m) cc_final: 0.7366 (m)
REVERT: A  246 TRP cc_start: 0.8357 (m100) cc_final: 0.7787 (m100)
REVERT: B  188 MET cc_start: 0.7774 (mmm) cc_final: 0.7133 (mmm)
REVERT: B  227 SER cc_start: 0.8490 (t) cc_final: 0.7911 (p)
REVERT: B  230 ASN cc_start: 0.7912 (m-40) cc_final: 0.7507 (m110)
REVERT: B  293 ASN cc_start: 0.8000 (m-40) cc_final: 0.7362 (p0)
REVERT: B  323 ASP cc_start: 0.7998 (p0) cc_final: 0.7698 (p0)
REVERT: D  233 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8445 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1678
  time to fit residues: 41.2564
Evaluate side-chains
  142 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 59 optimal weight:    0.0020
   chunk 85 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0770
   chunk 18 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   overall best weight:    1.8152

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.133876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.119253 restraints weight = 14645.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.120722 restraints weight = 10004.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.122241 restraints weight = 7680.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7381  Z= 0.163
  Angle     :  0.623   8.951  10092  Z= 0.328
  Chirality :  0.044   0.231   1198
  Planarity :  0.004   0.051   1283
  Dihedral  :  4.976  43.207   1084
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.01 (0.27), residues: 981
  helix:  1.72 (0.27), residues: 369
  sheet: -1.04 (0.34), residues: 218
  loop : -0.98 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 271 
 HIS   0.005   0.001   HIS D 347 
 PHE   0.025   0.002   PHE A 182 
 TYR   0.020   0.002   TYR A 290 
 ARG   0.011   0.001   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  378)
  hydrogen bonds       : angle       5.06317 ( 1083)
  SS BOND              : bond        0.00298 (    5)
  SS BOND              : angle       1.77295 (   10)
  covalent geometry    : bond        0.00379 ( 7376)
  covalent geometry    : angle       0.62117 (10082)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2508.29 seconds
wall clock time: 44 minutes 11.03 seconds (2651.03 seconds total)