Starting phenix.real_space_refine
on Sun Jul 27 06:28:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ykd_33891/07_2025/7ykd_33891.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ykd_33891/07_2025/7ykd_33891.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2025/7ykd_33891.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2025/7ykd_33891.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2025/7ykd_33891.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2025/7ykd_33891.cif"
  }
  resolution = 2.81
  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=   0.021
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      68      5.16       5
     C    5778      2.51       5
     N    1496      2.21       5
     O    1623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8965
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "L"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 76
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "A"
      Number of atoms: 2250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2250
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 10, 'TRANS': 271}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1716
          Classifications: {'peptide': 216}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 2580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2580
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 431
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 6.01, per 1000 atoms: 0.67
  Number of scatterers: 8965
  At special positions: 0
  Unit cell: (87.98, 121.18, 121.18, 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      68     16.00
     O    1623      8.00
     N    1496      7.00
     C    5778      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      38.2% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 68
    Processing helix  chain 'A' and resid 72 through 101
      removed outlier: 3.675A  pdb=" N   TRP A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      Proline residue:  A  93  - end of helix
    Processing helix  chain 'A' and resid 108 through 143
      removed outlier: 3.987A  pdb=" N   LEU A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 141 " --> pdb=" O   ARG A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 151
    Processing helix  chain 'A' and resid 152 through 172
    Processing helix  chain 'A' and resid 172 through 177
      removed outlier: 3.680A  pdb=" N   VAL A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 177'
    Processing helix  chain 'A' and resid 211 through 250
      removed outlier: 6.143A  pdb=" N   VAL A 231 " --> pdb=" O   CYS A 227 " (cutoff:3.500A)
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 256 through 283
      Proline residue:  A 275  - end of helix
    Processing helix  chain 'A' and resid 285 through 289
    Processing helix  chain 'A' and resid 290 through 317
      removed outlier: 4.018A  pdb=" N   PHE A 294 " --> pdb=" O   PRO A 290 " (cutoff:3.500A)
      Proline residue:  A 299  - end of helix
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'A' and resid 319 through 328
      removed outlier: 3.975A  pdb=" N   PHE A 323 " --> pdb=" O   MET A 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 31
    Processing helix  chain 'C' and resid 45 through 53
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 4.568A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 255
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 4.200A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 286
      removed outlier: 3.610A  pdb=" N   ILE C 285 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 309
      removed outlier: 4.193A  pdb=" N   ALA C 301 " --> pdb=" O   GLU C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 352
      removed outlier: 3.651A  pdb=" N   GLN C 333 " --> pdb=" O   THR C 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.656A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 183
      removed outlier: 3.721A  pdb=" N   LEU A 183 " --> pdb=" O   LYS A 186 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 191
      removed outlier: 3.639A  pdb=" N   PHE C 189 " --> pdb=" O   PHE C 196 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA C 220 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.141A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.511A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.968A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.752A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.651A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.635A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.010A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.654A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.340A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.577A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.661A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1308 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: 2.74

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1438
        1.32 -     1.44: 2502
        1.44 -     1.56: 5131
        1.56 -     1.69: 0
        1.69 -     1.81: 99
  Bond restraints: 9170
  Sorted by residual:
  bond pdb=" CA  ASP B 291 "
       pdb=" C   ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.523  1.442  0.081 1.34e-02 5.57e+03 3.68e+01
  bond pdb=" CA  LYS B 337 "
       pdb=" C   LYS B 337 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 1.24e-02 6.50e+03 1.61e+01
  bond pdb=" C   LEU A 143 "
       pdb=" N   PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.336  1.381 -0.045 1.23e-02 6.61e+03 1.36e+01
  bond pdb=" CA  PHE B 335 "
       pdb=" C   PHE B 335 "
    ideal  model  delta    sigma   weight residual
    1.522  1.479  0.043 1.20e-02 6.94e+03 1.30e+01
  bond pdb=" C   LYS B 337 "
       pdb=" O   LYS B 337 "
    ideal  model  delta    sigma   weight residual
    1.235  1.196  0.039 1.22e-02 6.72e+03 1.02e+01
  ... (remaining 9165 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 11910
        1.85 -     3.71: 438
        3.71 -     5.56: 75
        5.56 -     7.41: 19
        7.41 -     9.27: 7
  Bond angle restraints: 12449
  Sorted by residual:
  angle pdb=" N   VAL S   2 "
        pdb=" CA  VAL S   2 "
        pdb=" C   VAL S   2 "
      ideal   model   delta    sigma   weight residual
     112.43  104.83    7.60 9.20e-01 1.18e+00 6.82e+01
  angle pdb=" N   LEU B 336 "
        pdb=" CA  LEU B 336 "
        pdb=" C   LEU B 336 "
      ideal   model   delta    sigma   weight residual
     109.40  102.00    7.40 1.63e+00 3.76e-01 2.06e+01
  angle pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
        pdb=" O   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     120.51  114.44    6.07 1.43e+00 4.89e-01 1.80e+01
  angle pdb=" N   VAL A 141 "
        pdb=" CA  VAL A 141 "
        pdb=" C   VAL A 141 "
      ideal   model   delta    sigma   weight residual
     111.90  108.60    3.30 8.10e-01 1.52e+00 1.66e+01
  angle pdb=" CA  LEU A 143 "
        pdb=" C   LEU A 143 "
        pdb=" N   PRO A 144 "
      ideal   model   delta    sigma   weight residual
     117.73  121.77   -4.04 1.04e+00 9.25e-01 1.51e+01
  ... (remaining 12444 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.97: 5384
       23.97 -    47.94: 217
       47.94 -    71.91: 31
       71.91 -    95.88: 19
       95.88 -   119.85: 1
  Dihedral angle restraints: 5652
    sinusoidal: 2373
      harmonic: 3279
  Sorted by residual:
  dihedral pdb=" CB  CYS A 112 "
           pdb=" SG  CYS A 112 "
           pdb=" SG  CYS A 189 "
           pdb=" CB  CYS A 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.98  -68.98     1      1.00e+01 1.00e-02 6.16e+01
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.46   27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  PHE A  67 "
           pdb=" C   PHE A  67 "
           pdb=" N   LYS A  68 "
           pdb=" CA  LYS A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.32  -21.68     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 5649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1218
       0.075 -    0.150: 204
       0.150 -    0.226: 5
       0.226 -    0.301: 3
       0.301 -    0.376: 3
  Chirality restraints: 1433
  Sorted by residual:
  chirality pdb=" CA  ASP B 312 "
            pdb=" N   ASP B 312 "
            pdb=" C   ASP B 312 "
            pdb=" CB  ASP B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" C20 CLR A 403 "
            pdb=" C17 CLR A 403 "
            pdb=" C21 CLR A 403 "
            pdb=" C22 CLR A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.23    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" C20 CLR A 405 "
            pdb=" C17 CLR A 405 "
            pdb=" C21 CLR A 405 "
            pdb=" C22 CLR A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.24    0.35 2.00e-01 2.50e+01 3.09e+00
  ... (remaining 1430 not shown)

  Planarity restraints: 1535
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE L  23 "    0.033 2.00e-02 2.50e+03   2.02e-02 7.16e+00
        pdb=" CG  PHE L  23 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE L  23 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE L  23 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE L  23 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE L  23 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE L  23 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.037 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO S  75 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 226 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   LEU A 226 "    0.032 2.00e-02 2.50e+03
        pdb=" O   LEU A 226 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 227 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1532 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 202
        2.67 -     3.23: 8639
        3.23 -     3.79: 14242
        3.79 -     4.34: 19809
        4.34 -     4.90: 33702
  Nonbonded interactions: 76594
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" C25 CLR A 402 "
            pdb=" C21 CLR A 403 "
     model   vdw
     2.146 3.890
  nonbonded pdb=" NZ  LYS S 244 "
            pdb=" OE2 GLU S 246 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.175 3.120
  ... (remaining 76589 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.030
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.530
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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      :  0.012   0.753   9174  Z= 0.877
  Angle     :  0.863   9.265  12455  Z= 0.462
  Chirality :  0.055   0.376   1433
  Planarity :  0.004   0.057   1535
  Dihedral  : 14.190 119.850   3525
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.83 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.18 (0.25), residues: 1111
  helix:  0.91 (0.26), residues: 382
  sheet: -0.04 (0.32), residues: 288
  loop : -1.01 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP S  47 
 HIS   0.006   0.002   HIS A 217 
 PHE   0.033   0.003   PHE L  23 
 TYR   0.019   0.002   TYR B 105 
 ARG   0.009   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16320 (  465)
  hydrogen bonds       : angle       6.98139 ( 1308)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       3.50994 (    6)
  covalent geometry    : bond        0.00870 ( 9170)
  covalent geometry    : angle       0.85964 (12449)
  Misc. bond           : bond        0.75319 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.964 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   33 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7468 (mm-30)
REVERT: B  291 ASP cc_start: 0.7436 (m-30) cc_final: 0.7077 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 1.6106
  time to fit residues: 253.0083
Evaluate side-chains
  118 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 87 optimal weight:    0.0070
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 100 optimal weight:    0.4980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.148088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.103649 restraints weight = 11461.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.39
r_work: 0.3151 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9174  Z= 0.138
  Angle     :  0.660   8.102  12455  Z= 0.330
  Chirality :  0.046   0.300   1433
  Planarity :  0.004   0.049   1535
  Dihedral  :  7.084  57.368   1539
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.27 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.32 (0.25), residues: 1111
  helix:  1.61 (0.26), residues: 385
  sheet:  0.07 (0.32), residues: 263
  loop : -0.87 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.009   0.001   HIS A 184 
 PHE   0.017   0.001   PHE A 190 
 TYR   0.016   0.001   TYR A 103 
 ARG   0.011   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  465)
  hydrogen bonds       : angle       5.04238 ( 1308)
  SS BOND              : bond        0.00418 (    3)
  SS BOND              : angle       1.33120 (    6)
  covalent geometry    : bond        0.00301 ( 9170)
  covalent geometry    : angle       0.65981 (12449)
  Misc. bond           : bond        0.00118 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 1.003 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   33 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: C  248 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7542 (mmtt)
REVERT: B   13 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8465 (pp30)
REVERT: B   19 ARG cc_start: 0.7593 (tmm160) cc_final: 0.7346 (ttp-110)
REVERT: B  198 LEU cc_start: 0.8244 (pp) cc_final: 0.8023 (pt)
REVERT: S   18 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8340 (tpp80)
REVERT: S  202 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7731 (ptt-90)
  outliers start: 15
  outliers final: 4
  residues processed: 134
  average time/residue: 1.5760
  time to fit residues: 223.9497
Evaluate side-chains
  120 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.100226 restraints weight = 11714.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.62
r_work: 0.3117 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9174  Z= 0.146
  Angle     :  0.633  13.049  12455  Z= 0.314
  Chirality :  0.045   0.256   1433
  Planarity :  0.004   0.046   1535
  Dihedral  :  7.488  74.468   1539
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.98 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.47 (0.26), residues: 1111
  helix:  1.87 (0.26), residues: 385
  sheet: -0.09 (0.30), residues: 282
  loop : -0.76 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.011   0.001   PHE A 124 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  465)
  hydrogen bonds       : angle       4.80360 ( 1308)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.89239 (    6)
  covalent geometry    : bond        0.00333 ( 9170)
  covalent geometry    : angle       0.63256 (12449)
  Misc. bond           : bond        0.00531 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6544 (tt0)
REVERT: C  248 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7367 (mmtt)
REVERT: B   19 ARG cc_start: 0.7479 (tmm160) cc_final: 0.7118 (ttp-110)
REVERT: B  160 SER cc_start: 0.8527 (t) cc_final: 0.7740 (p)
REVERT: B  198 LEU cc_start: 0.8014 (pp) cc_final: 0.7734 (pt)
REVERT: S    6 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6948 (mt-10)
REVERT: S   18 ARG cc_start: 0.8320 (tpp80) cc_final: 0.8079 (tpp80)
REVERT: S  202 ARG cc_start: 0.7767 (ptt-90) cc_final: 0.7501 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8019 (mp0)
  outliers start: 18
  outliers final: 8
  residues processed: 141
  average time/residue: 1.9635
  time to fit residues: 294.2275
Evaluate side-chains
  133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ASN
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0070
   chunk 52 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 65 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 107 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 256 ASN
B  75 GLN
S 142 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.147371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.101805 restraints weight = 11558.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.61
r_work: 0.3143 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9174  Z= 0.123
  Angle     :  0.613  13.919  12455  Z= 0.303
  Chirality :  0.044   0.263   1433
  Planarity :  0.004   0.044   1535
  Dihedral  :  6.903  57.395   1539
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.06 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.59 (0.26), residues: 1111
  helix:  2.05 (0.26), residues: 385
  sheet: -0.02 (0.30), residues: 273
  loop : -0.77 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.014   0.001   PHE A  52 
 TYR   0.011   0.001   TYR B 264 
 ARG   0.004   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03496 (  465)
  hydrogen bonds       : angle       4.66057 ( 1308)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       0.87197 (    6)
  covalent geometry    : bond        0.00274 ( 9170)
  covalent geometry    : angle       0.61300 (12449)
  Misc. bond           : bond        0.00348 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6471 (tt0)
REVERT: C   33 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7205 (mt-10)
REVERT: C  248 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7383 (mmtt)
REVERT: C  263 SER cc_start: 0.9022 (m) cc_final: 0.8734 (p)
REVERT: B   19 ARG cc_start: 0.7567 (tmm160) cc_final: 0.7281 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7998 (mm-40)
REVERT: B  160 SER cc_start: 0.8479 (t) cc_final: 0.7883 (p)
REVERT: S    6 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6985 (mt-10)
REVERT: S   18 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8000 (tpp80)
REVERT: S  186 GLN cc_start: 0.8228 (tt0) cc_final: 0.8004 (pt0)
REVERT: S  202 ARG cc_start: 0.7731 (ptt-90) cc_final: 0.7401 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8036 (mt-10)
  outliers start: 19
  outliers final: 8
  residues processed: 146
  average time/residue: 1.2420
  time to fit residues: 193.3089
Evaluate side-chains
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0370
   overall best weight:    1.6064

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 256 ASN

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 = 0.143749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.097645 restraints weight = 11598.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.61
r_work: 0.3065 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9174  Z= 0.228
  Angle     :  0.680  14.956  12455  Z= 0.340
  Chirality :  0.047   0.269   1433
  Planarity :  0.004   0.046   1535
  Dihedral  :  7.068  58.830   1539
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.38 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.48 (0.25), residues: 1111
  helix:  2.02 (0.26), residues: 385
  sheet: -0.19 (0.29), residues: 279
  loop : -0.82 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  77 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.017   0.002   PHE A 124 
 TYR   0.015   0.002   TYR B 264 
 ARG   0.008   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  465)
  hydrogen bonds       : angle       4.79894 ( 1308)
  SS BOND              : bond        0.00427 (    3)
  SS BOND              : angle       1.11135 (    6)
  covalent geometry    : bond        0.00544 ( 9170)
  covalent geometry    : angle       0.67946 (12449)
  Misc. bond           : bond        0.00393 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 1.012 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6561 (tt0)
REVERT: C   33 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7289 (mt-10)
REVERT: C   53 MET cc_start: 0.6495 (mpp) cc_final: 0.6275 (mtt)
REVERT: C  248 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7428 (mmtt)
REVERT: B   19 ARG cc_start: 0.7520 (tmm160) cc_final: 0.7072 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8015 (mm-40)
REVERT: B  198 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (pt)
REVERT: B  217 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7091 (pmm)
REVERT: G   42 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6638 (mp0)
REVERT: S    6 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6947 (mt-10)
REVERT: S   18 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7942 (tpp80)
REVERT: S  202 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7388 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (mt-10)
  outliers start: 27
  outliers final: 9
  residues processed: 138
  average time/residue: 1.2682
  time to fit residues: 186.8151
Evaluate side-chains
  135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 88 optimal weight:    0.6980
   chunk 50 optimal weight:    8.9990
   chunk 38 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 HIS ** 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 = 0.3795 r_free = 0.3795 target = 0.146502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.100577 restraints weight = 11524.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.63
r_work: 0.3100 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9174  Z= 0.152
  Angle     :  0.622  15.674  12455  Z= 0.312
  Chirality :  0.044   0.271   1433
  Planarity :  0.004   0.045   1535
  Dihedral  :  6.387  59.661   1539
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.21 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.55 (0.26), residues: 1111
  helix:  2.07 (0.26), residues: 385
  sheet: -0.17 (0.30), residues: 274
  loop : -0.75 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  77 
 HIS   0.009   0.001   HIS A 184 
 PHE   0.017   0.001   PHE A  52 
 TYR   0.013   0.001   TYR B 264 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  465)
  hydrogen bonds       : angle       4.66109 ( 1308)
  SS BOND              : bond        0.00363 (    3)
  SS BOND              : angle       0.95692 (    6)
  covalent geometry    : bond        0.00353 ( 9170)
  covalent geometry    : angle       0.62212 (12449)
  Misc. bond           : bond        0.00372 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.965 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6617 (tt0)
REVERT: C   33 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7337 (mt-10)
REVERT: C  248 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7464 (mmtt)
REVERT: B   19 ARG cc_start: 0.7656 (tmm160) cc_final: 0.7210 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8071 (mm-40)
REVERT: B  198 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7776 (pt)
REVERT: B  217 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7167 (pmm)
REVERT: B  301 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7909 (mtpp)
REVERT: G   21 MET cc_start: 0.8324 (tpp) cc_final: 0.8037 (tpp)
REVERT: G   42 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6723 (mp0)
REVERT: S    6 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6984 (mt-10)
REVERT: S   18 ARG cc_start: 0.8307 (tpp80) cc_final: 0.8045 (tpp80)
REVERT: S  186 GLN cc_start: 0.8261 (tt0) cc_final: 0.7942 (pt0)
REVERT: S  202 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7362 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8136 (mt-10)
  outliers start: 27
  outliers final: 9
  residues processed: 138
  average time/residue: 1.3974
  time to fit residues: 204.5472
Evaluate side-chains
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0060
   chunk 19 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.147915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.102268 restraints weight = 11661.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.62
r_work: 0.3135 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9174  Z= 0.128
  Angle     :  0.609  16.696  12455  Z= 0.304
  Chirality :  0.044   0.268   1433
  Planarity :  0.004   0.044   1535
  Dihedral  :  6.116  57.864   1539
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.88 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.72 (0.26), residues: 1111
  helix:  2.18 (0.26), residues: 385
  sheet: -0.03 (0.29), residues: 287
  loop : -0.68 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.015   0.001   PHE A 190 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  465)
  hydrogen bonds       : angle       4.53483 ( 1308)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       0.92037 (    6)
  covalent geometry    : bond        0.00290 ( 9170)
  covalent geometry    : angle       0.60841 (12449)
  Misc. bond           : bond        0.00170 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 1.051 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6526 (tt0)
REVERT: C   33 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7325 (mt-10)
REVERT: C  248 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7436 (mmtt)
REVERT: C  263 SER cc_start: 0.9029 (m) cc_final: 0.8751 (p)
REVERT: B   19 ARG cc_start: 0.7658 (tmm160) cc_final: 0.7196 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8049 (mm-40)
REVERT: B  135 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8724 (p)
REVERT: B  198 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7596 (pp)
REVERT: B  217 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7202 (pmm)
REVERT: B  262 MET cc_start: 0.8500 (ttm) cc_final: 0.8006 (mtm)
REVERT: B  274 THR cc_start: 0.8752 (p) cc_final: 0.8461 (p)
REVERT: B  301 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7927 (mtpp)
REVERT: G   21 MET cc_start: 0.8353 (tpp) cc_final: 0.8070 (tpp)
REVERT: G   42 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6765 (mp0)
REVERT: S   18 ARG cc_start: 0.8343 (tpp80) cc_final: 0.8073 (tpp80)
REVERT: S  186 GLN cc_start: 0.8272 (tt0) cc_final: 0.7822 (pt0)
REVERT: S  202 ARG cc_start: 0.7757 (ptt-90) cc_final: 0.7377 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (mt-10)
  outliers start: 25
  outliers final: 11
  residues processed: 138
  average time/residue: 1.6212
  time to fit residues: 238.1313
Evaluate side-chains
  135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 HIS ** 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 = 0.3785 r_free = 0.3785 target = 0.145643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.099336 restraints weight = 11772.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.64
r_work: 0.3088 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9174  Z= 0.193
  Angle     :  0.656  17.190  12455  Z= 0.328
  Chirality :  0.045   0.267   1433
  Planarity :  0.004   0.044   1535
  Dihedral  :  6.232  58.495   1539
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.08 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.63 (0.26), residues: 1111
  helix:  2.10 (0.26), residues: 385
  sheet: -0.08 (0.30), residues: 277
  loop : -0.71 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  77 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.020   0.002   PHE A  52 
 TYR   0.015   0.001   TYR B 264 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  465)
  hydrogen bonds       : angle       4.63927 ( 1308)
  SS BOND              : bond        0.00413 (    3)
  SS BOND              : angle       1.15369 (    6)
  covalent geometry    : bond        0.00459 ( 9170)
  covalent geometry    : angle       0.65551 (12449)
  Misc. bond           : bond        0.00185 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 1.780 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6637 (tt0)
REVERT: C   33 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7325 (mt-10)
REVERT: C  248 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7416 (mmtt)
REVERT: B   19 ARG cc_start: 0.7649 (tmm160) cc_final: 0.7207 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8001 (mm-40)
REVERT: B  198 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7752 (pt)
REVERT: B  217 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7163 (pmm)
REVERT: B  301 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7924 (mtpp)
REVERT: G   21 MET cc_start: 0.8339 (tpp) cc_final: 0.8052 (tpp)
REVERT: G   42 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6713 (mp0)
REVERT: S   18 ARG cc_start: 0.8346 (tpp80) cc_final: 0.8058 (tpp80)
REVERT: S  186 GLN cc_start: 0.8232 (tt0) cc_final: 0.7886 (pt0)
REVERT: S  202 ARG cc_start: 0.7752 (ptt-90) cc_final: 0.7349 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8134 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 136
  average time/residue: 2.6198
  time to fit residues: 376.5217
Evaluate side-chains
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 104 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.147024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.101165 restraints weight = 11581.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.63
r_work: 0.3124 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9174  Z= 0.145
  Angle     :  0.638  17.717  12455  Z= 0.319
  Chirality :  0.044   0.260   1433
  Planarity :  0.004   0.043   1535
  Dihedral  :  6.069  57.540   1539
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.81 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.73 (0.26), residues: 1111
  helix:  2.17 (0.26), residues: 385
  sheet: -0.09 (0.29), residues: 285
  loop : -0.60 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  77 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.017   0.001   PHE A 190 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  465)
  hydrogen bonds       : angle       4.55718 ( 1308)
  SS BOND              : bond        0.00357 (    3)
  SS BOND              : angle       1.34012 (    6)
  covalent geometry    : bond        0.00337 ( 9170)
  covalent geometry    : angle       0.63700 (12449)
  Misc. bond           : bond        0.00146 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.938 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6543 (tt0)
REVERT: C   33 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7339 (mt-10)
REVERT: C  248 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7425 (mmtt)
REVERT: C  263 SER cc_start: 0.9033 (m) cc_final: 0.8752 (p)
REVERT: B   19 ARG cc_start: 0.7616 (tmm160) cc_final: 0.7171 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8009 (mm-40)
REVERT: B  135 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8731 (p)
REVERT: B  198 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7579 (pp)
REVERT: B  217 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7177 (pmm)
REVERT: B  274 THR cc_start: 0.8783 (p) cc_final: 0.8496 (p)
REVERT: B  301 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7934 (mtpp)
REVERT: G   21 MET cc_start: 0.8345 (tpp) cc_final: 0.8058 (tpp)
REVERT: G   42 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6769 (mp0)
REVERT: G   47 GLU cc_start: 0.7874 (mp0) cc_final: 0.7664 (mp0)
REVERT: S   18 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8054 (tpp80)
REVERT: S  186 GLN cc_start: 0.8276 (tt0) cc_final: 0.7943 (pt0)
REVERT: S  202 ARG cc_start: 0.7751 (ptt-90) cc_final: 0.7348 (ptt-90)
REVERT: S  246 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8097 (mt-10)
  outliers start: 21
  outliers final: 11
  residues processed: 137
  average time/residue: 1.4066
  time to fit residues: 204.1829
Evaluate side-chains
  133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.147394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.101438 restraints weight = 11658.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.64
r_work: 0.3122 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9174  Z= 0.143
  Angle     :  0.634  18.343  12455  Z= 0.317
  Chirality :  0.044   0.249   1433
  Planarity :  0.004   0.043   1535
  Dihedral  :  5.973  56.292   1539
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.92 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.73 (0.26), residues: 1111
  helix:  2.16 (0.26), residues: 386
  sheet: -0.07 (0.29), residues: 285
  loop : -0.60 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  77 
 HIS   0.009   0.001   HIS A 184 
 PHE   0.023   0.001   PHE A  52 
 TYR   0.015   0.001   TYR B 264 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  465)
  hydrogen bonds       : angle       4.52668 ( 1308)
  SS BOND              : bond        0.00369 (    3)
  SS BOND              : angle       1.62713 (    6)
  covalent geometry    : bond        0.00333 ( 9170)
  covalent geometry    : angle       0.63269 (12449)
  Misc. bond           : bond        0.00139 (    1)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 1.024 
Fit side-chains
TARDY: cannot create tardy model for: "GLU G  63 " (corrupted residue). Skipping it.
REVERT: C   25 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6548 (tt0)
REVERT: C  248 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7440 (mmtt)
REVERT: C  263 SER cc_start: 0.9034 (m) cc_final: 0.8754 (p)
REVERT: B   19 ARG cc_start: 0.7619 (tmm160) cc_final: 0.7152 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8027 (mm-40)
REVERT: B  135 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8723 (p)
REVERT: B  198 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7583 (pp)
REVERT: B  217 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7182 (pmm)
REVERT: B  274 THR cc_start: 0.8811 (p) cc_final: 0.8525 (p)
REVERT: B  301 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7943 (mtpp)
REVERT: G   21 MET cc_start: 0.8323 (tpp) cc_final: 0.8030 (tpp)
REVERT: G   42 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6759 (mp0)
REVERT: G   47 GLU cc_start: 0.7899 (mp0) cc_final: 0.7687 (mp0)
REVERT: S   18 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8037 (tpp80)
REVERT: S   46 GLU cc_start: 0.7916 (tt0) cc_final: 0.7279 (pt0)
REVERT: S  186 GLN cc_start: 0.8274 (tt0) cc_final: 0.7933 (pt0)
REVERT: S  246 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8111 (mt-10)
  outliers start: 23
  outliers final: 11
  residues processed: 138
  average time/residue: 1.3990
  time to fit residues: 204.6649
Evaluate side-chains
  134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue  147 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 HIS
C 241 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.146504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.100574 restraints weight = 11556.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.62
r_work: 0.3105 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9174  Z= 0.166
  Angle     :  0.655  18.045  12455  Z= 0.327
  Chirality :  0.044   0.239   1433
  Planarity :  0.004   0.045   1535
  Dihedral  :  5.994  53.759   1539
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.12 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.70 (0.26), residues: 1111
  helix:  2.12 (0.26), residues: 387
  sheet: -0.04 (0.30), residues: 277
  loop : -0.64 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  77 
 HIS   0.009   0.001   HIS A 184 
 PHE   0.017   0.001   PHE A 190 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.013   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  465)
  hydrogen bonds       : angle       4.55793 ( 1308)
  SS BOND              : bond        0.00341 (    3)
  SS BOND              : angle       1.44218 (    6)
  covalent geometry    : bond        0.00392 ( 9170)
  covalent geometry    : angle       0.65402 (12449)
  Misc. bond           : bond        0.00150 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8313.75 seconds
wall clock time: 149 minutes 6.04 seconds (8946.04 seconds total)