Starting phenix.real_space_refine
on Wed Feb 12 02:54:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvx_32861/02_2025/7wvx_32861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvx_32861/02_2025/7wvx_32861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvx_32861/02_2025/7wvx_32861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvx_32861/02_2025/7wvx_32861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvx_32861/02_2025/7wvx_32861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvx_32861/02_2025/7wvx_32861.cif"
  }
  resolution = 2.8
  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=   0.000 sd=   0.005
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      52      5.16       5
     C    4554      2.51       5
     N    1197      2.21       5
     O    1267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7070
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 114
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2331
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1680
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2557
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 388
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 4.36, per 1000 atoms: 0.62
  Number of scatterers: 7070
  At special positions: 0
  Unit cell: (114.95, 119.13, 85.69, 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      52     16.00
     O    1267      8.00
     N    1197      7.00
     C    4554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1726

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      48.6% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.752A  pdb=" N   MET R  55 " --> pdb=" O   ALA R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 86
      removed outlier: 3.699A  pdb=" N   THR R  77 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 3.784A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 180 through 185
      removed outlier: 3.922A  pdb=" N   GLY R 185 " --> pdb=" O   ALA R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 186 through 209
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 274
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.835A  pdb=" N   ILE R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.799A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.118A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.958A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.818A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.234A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.647A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 25
      removed outlier: 4.332A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.564A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.234A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 8.841A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.057A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.775A  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: 3.518A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.670A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.512A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.711A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.400A  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: 6.498A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.388A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1119 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: 1.98

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2252
        1.34 -     1.46: 1339
        1.46 -     1.58: 3553
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 7218
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.751  0.054 2.00e-02 2.50e+03 7.27e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.770  0.047 2.00e-02 2.50e+03 5.54e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.377 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C   LEU R 212 "
       pdb=" N   PRO R 213 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.34e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.436  0.022 1.90e-02 2.77e+03 1.31e+00
  ... (remaining 7213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 9645
        1.56 -     3.13: 118
        3.13 -     4.69: 29
        4.69 -     6.25: 6
        6.25 -     7.81: 1
  Bond angle restraints: 9799
  Sorted by residual:
  angle pdb=" C   ASP A 329 "
        pdb=" N   THR A 330 "
        pdb=" CA  THR A 330 "
      ideal   model   delta    sigma   weight residual
     122.46  125.84   -3.38 1.41e+00 5.03e-01 5.76e+00
  angle pdb=" C   PHE R 161 "
        pdb=" N   LEU R 162 "
        pdb=" CA  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     122.53  118.15    4.38 1.92e+00 2.71e-01 5.20e+00
  angle pdb=" CA  LEU R 162 "
        pdb=" CB  LEU R 162 "
        pdb=" CG  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.11   -7.81 3.50e+00 8.16e-02 4.98e+00
  angle pdb=" CA  TRP R  95 "
        pdb=" CB  TRP R  95 "
        pdb=" CG  TRP R  95 "
      ideal   model   delta    sigma   weight residual
     113.60  117.82   -4.22 1.90e+00 2.77e-01 4.94e+00
  angle pdb=" C   PHE C  61 "
        pdb=" N   ARG C  62 "
        pdb=" CA  ARG C  62 "
      ideal   model   delta    sigma   weight residual
     121.70  125.20   -3.50 1.80e+00 3.09e-01 3.78e+00
  ... (remaining 9794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 3894
       17.28 -    34.56: 282
       34.56 -    51.83: 61
       51.83 -    69.11: 2
       69.11 -    86.39: 2
  Dihedral angle restraints: 4241
    sinusoidal: 1582
      harmonic: 2659
  Sorted by residual:
  dihedral pdb=" CG  ARG R 137 "
           pdb=" CD  ARG R 137 "
           pdb=" NE  ARG R 137 "
           pdb=" CZ  ARG R 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.63  -44.63     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG B  22 "
           pdb=" CD  ARG B  22 "
           pdb=" NE  ARG B  22 "
           pdb=" CZ  ARG B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.47  -42.53     2      1.50e+01 4.44e-03 9.75e+00
  dihedral pdb=" CA  LYS C  14 "
           pdb=" CB  LYS C  14 "
           pdb=" CG  LYS C  14 "
           pdb=" CD  LYS C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.00   56.00     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 4238 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 719
       0.029 -    0.058: 263
       0.058 -    0.087: 112
       0.087 -    0.115: 53
       0.115 -    0.144: 7
  Chirality restraints: 1154
  Sorted by residual:
  chirality pdb=" CB  ILE R 101 "
            pdb=" CA  ILE R 101 "
            pdb=" CG1 ILE R 101 "
            pdb=" CG2 ILE R 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  PRO R 187 "
            pdb=" N   PRO R 187 "
            pdb=" C   PRO R 187 "
            pdb=" CB  PRO R 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1151 not shown)

  Planarity restraints: 1223
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.033 5.00e-02 4.00e+02   5.05e-02 4.08e+00
        pdb=" N   PRO R 149 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 186 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO R 187 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R 187 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 187 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B 236 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1220 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1451
        2.78 -     3.31: 6959
        3.31 -     3.84: 12150
        3.84 -     4.37: 14439
        4.37 -     4.90: 24954
  Nonbonded interactions: 59953
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" NH1 ARG B 314 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.324 3.120
  ... (remaining 59948 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.850
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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      :  0.002   0.054   7218  Z= 0.134
  Angle     :  0.492   7.814   9799  Z= 0.267
  Chirality :  0.040   0.144   1154
  Planarity :  0.004   0.051   1223
  Dihedral  : 12.148  86.390   2512
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 903
  helix:  1.86 (0.25), residues: 407
  sheet:  0.42 (0.42), residues: 158
  loop : -0.95 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R  95 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.005   0.001   TYR A 231 
 ARG   0.004   0.000   ARG R 190 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.764 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8050 (tt) cc_final: 0.7831 (tm)
REVERT: A  194 ASP cc_start: 0.7448 (m-30) cc_final: 0.7237 (m-30)
  outliers start: 0
  outliers final: 1
  residues processed: 132
  average time/residue: 1.1071
  time to fit residues: 154.7084
Evaluate side-chains
  114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  129 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.153128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117976 restraints weight = 7987.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.90
r_work: 0.3252 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7218  Z= 0.250
  Angle     :  0.565   7.714   9799  Z= 0.297
  Chirality :  0.043   0.143   1154
  Planarity :  0.005   0.098   1223
  Dihedral  :  4.262  45.405    977
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.46 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.28), residues: 903
  helix:  1.75 (0.25), residues: 422
  sheet: -0.03 (0.37), residues: 189
  loop : -0.73 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.014   0.002   PHE A 197 
 TYR   0.011   0.001   TYR R 221 
 ARG   0.005   0.001   ARG R 123 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.742 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8364 (tt) cc_final: 0.8122 (tm)
REVERT: R  224 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7804 (mt)
REVERT: R  238 ARG cc_start: 0.8290 (tmt90) cc_final: 0.7895 (tpt-90)
REVERT: R  304 PHE cc_start: 0.8186 (m-10) cc_final: 0.7932 (m-10)
REVERT: A   33 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8279 (mm-30)
REVERT: A  194 ASP cc_start: 0.8410 (m-30) cc_final: 0.8141 (m-30)
REVERT: A  314 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7415 (mmt90)
REVERT: A  350 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7777 (mtpt)
REVERT: B  220 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7593 (mt0)
REVERT: C   21 MET cc_start: 0.3602 (OUTLIER) cc_final: 0.2712 (ppp)
  outliers start: 15
  outliers final: 7
  residues processed: 135
  average time/residue: 1.1341
  time to fit residues: 162.0280
Evaluate side-chains
  127 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 VAL
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain C residue   21 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.151577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.115732 restraints weight = 7947.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.94
r_work: 0.3217 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7218  Z= 0.218
  Angle     :  0.543   9.506   9799  Z= 0.282
  Chirality :  0.042   0.145   1154
  Planarity :  0.004   0.056   1223
  Dihedral  :  4.106  42.138    975
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.55 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.28), residues: 903
  helix:  1.62 (0.25), residues: 424
  sheet: -0.07 (0.38), residues: 178
  loop : -0.70 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.011   0.001   PHE A 197 
 TYR   0.007   0.001   TYR R 221 
 ARG   0.007   0.001   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.792 
Fit side-chains
REVERT: R  238 ARG cc_start: 0.8313 (tmt90) cc_final: 0.8052 (tpt-90)
REVERT: A   33 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8273 (mm-30)
REVERT: A  194 ASP cc_start: 0.8388 (m-30) cc_final: 0.8110 (m-30)
REVERT: A  350 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7910 (mtpt)
REVERT: B   45 MET cc_start: 0.8403 (mtt) cc_final: 0.8090 (mtt)
REVERT: B   52 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8228 (mtp85)
REVERT: B  220 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7668 (mt0)
  outliers start: 17
  outliers final: 4
  residues processed: 138
  average time/residue: 1.2047
  time to fit residues: 175.4728
Evaluate side-chains
  121 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  220 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 31 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
R 294 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113135 restraints weight = 8058.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.94
r_work: 0.3179 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7218  Z= 0.243
  Angle     :  0.548   7.980   9799  Z= 0.286
  Chirality :  0.042   0.147   1154
  Planarity :  0.004   0.048   1223
  Dihedral  :  4.161  42.426    975
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.96 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.28), residues: 903
  helix:  1.66 (0.25), residues: 419
  sheet: -0.35 (0.36), residues: 183
  loop : -0.72 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.018   0.001   PHE R  37 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.008   0.000   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.746 
Fit side-chains
REVERT: R  238 ARG cc_start: 0.8242 (tmt90) cc_final: 0.7922 (tpt-90)
REVERT: A   33 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8244 (mm-30)
REVERT: A  209 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8094 (ttm110)
REVERT: A  314 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7483 (mmt90)
REVERT: A  350 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7943 (mtpt)
REVERT: B   52 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8215 (mtp85)
REVERT: B  220 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7565 (mt0)
REVERT: B  243 THR cc_start: 0.8679 (p) cc_final: 0.8461 (p)
REVERT: C   46 LYS cc_start: 0.8417 (mptt) cc_final: 0.8093 (pmtt)
  outliers start: 20
  outliers final: 10
  residues processed: 134
  average time/residue: 1.1894
  time to fit residues: 168.3286
Evaluate side-chains
  129 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0370
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.111685 restraints weight = 7948.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.90
r_work: 0.3158 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7218  Z= 0.265
  Angle     :  0.557   8.162   9799  Z= 0.291
  Chirality :  0.042   0.148   1154
  Planarity :  0.004   0.048   1223
  Dihedral  :  4.242  42.663    975
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.69 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.27), residues: 903
  helix:  1.66 (0.25), residues: 419
  sheet: -0.54 (0.35), residues: 185
  loop : -0.77 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.013   0.001   PHE A 197 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.005   0.000   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.820 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8357 (mp) cc_final: 0.7665 (tm)
REVERT: R  238 ARG cc_start: 0.8277 (tmt90) cc_final: 0.8031 (ttm-80)
REVERT: A   29 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8102 (ttmt)
REVERT: A   33 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8241 (mm-30)
REVERT: A  350 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7950 (mtpt)
REVERT: B  220 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7572 (mt0)
REVERT: C   46 LYS cc_start: 0.8409 (mptt) cc_final: 0.8101 (pmtt)
  outliers start: 24
  outliers final: 10
  residues processed: 131
  average time/residue: 1.0477
  time to fit residues: 145.9949
Evaluate side-chains
  125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.144977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.109305 restraints weight = 7987.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.88
r_work: 0.3126 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7218  Z= 0.343
  Angle     :  0.599   8.284   9799  Z= 0.313
  Chirality :  0.044   0.152   1154
  Planarity :  0.004   0.054   1223
  Dihedral  :  4.461  40.971    975
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.57 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 903
  helix:  1.36 (0.25), residues: 425
  sheet: -0.50 (0.34), residues: 189
  loop : -0.90 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  99 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.016   0.002   PHE A 197 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.007   0.000   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.763 
Fit side-chains
REVERT: R  143 MET cc_start: 0.7832 (mtt) cc_final: 0.7469 (mtt)
REVERT: R  304 PHE cc_start: 0.8477 (m-10) cc_final: 0.8228 (m-10)
REVERT: A   29 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8169 (ttmt)
REVERT: A   33 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8166 (mm-30)
REVERT: A  314 ARG cc_start: 0.7837 (mmt-90) cc_final: 0.7572 (mmt-90)
REVERT: A  350 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8111 (mtpt)
REVERT: B  220 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7631 (mt0)
REVERT: B  226 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8277 (mt-10)
REVERT: B  243 THR cc_start: 0.8718 (p) cc_final: 0.8501 (p)
  outliers start: 23
  outliers final: 14
  residues processed: 134
  average time/residue: 1.0352
  time to fit residues: 147.4210
Evaluate side-chains
  125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  342 ASP
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 20 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.147871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.112682 restraints weight = 7812.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.85
r_work: 0.3171 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7218  Z= 0.241
  Angle     :  0.560   7.638   9799  Z= 0.290
  Chirality :  0.042   0.149   1154
  Planarity :  0.004   0.047   1223
  Dihedral  :  4.318  39.303    975
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.18 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.27), residues: 903
  helix:  1.42 (0.25), residues: 423
  sheet: -0.61 (0.34), residues: 188
  loop : -0.83 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.013   0.001   PHE A 197 
 TYR   0.014   0.001   TYR B 124 
 ARG   0.005   0.000   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.780 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7744 (tm)
REVERT: R  304 PHE cc_start: 0.8391 (m-10) cc_final: 0.8129 (m-10)
REVERT: A   33 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8205 (mm-30)
REVERT: A  314 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7572 (mmt-90)
REVERT: A  350 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8134 (mtpt)
REVERT: B  220 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7589 (mt0)
REVERT: B  226 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8244 (mt-10)
REVERT: B  337 LYS cc_start: 0.8621 (mttp) cc_final: 0.8392 (mttp)
REVERT: C   46 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8172 (pmtt)
  outliers start: 20
  outliers final: 12
  residues processed: 127
  average time/residue: 0.9662
  time to fit residues: 131.6755
Evaluate side-chains
  123 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0980
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.145587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.110840 restraints weight = 7914.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.86
r_work: 0.3107 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074   7218  Z= 0.533
  Angle     :  0.690   7.420   9799  Z= 0.357
  Chirality :  0.048   0.209   1154
  Planarity :  0.005   0.067   1223
  Dihedral  :  4.807  41.445    975
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.45 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 903
  helix:  1.10 (0.25), residues: 425
  sheet: -0.66 (0.34), residues: 187
  loop : -1.02 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 311 
 PHE   0.022   0.002   PHE A 197 
 TYR   0.019   0.002   TYR B  59 
 ARG   0.005   0.001   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.811 
Fit side-chains
REVERT: R  175 TYR cc_start: 0.7599 (m-80) cc_final: 0.7332 (m-80)
REVERT: R  304 PHE cc_start: 0.8638 (m-10) cc_final: 0.8254 (m-10)
REVERT: A   33 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8244 (mm-30)
REVERT: A  350 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8126 (mtpt)
REVERT: B  226 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8438 (mt-10)
REVERT: B  243 THR cc_start: 0.8752 (p) cc_final: 0.8551 (p)
REVERT: C   46 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8195 (pmtt)
  outliers start: 25
  outliers final: 15
  residues processed: 130
  average time/residue: 0.9871
  time to fit residues: 137.6277
Evaluate side-chains
  125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  342 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 73 optimal weight:    0.1980
   chunk 65 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 270 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.146663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.111864 restraints weight = 8025.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.85
r_work: 0.3150 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7218  Z= 0.231
  Angle     :  0.580   7.614   9799  Z= 0.297
  Chirality :  0.042   0.148   1154
  Planarity :  0.004   0.048   1223
  Dihedral  :  4.413  35.131    975
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 23.06 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.27), residues: 903
  helix:  1.29 (0.25), residues: 423
  sheet: -0.63 (0.35), residues: 184
  loop : -0.97 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.011   0.001   PHE R  37 
 TYR   0.018   0.001   TYR B 124 
 ARG   0.006   0.000   ARG B 251 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.673 
Fit side-chains
REVERT: R  304 PHE cc_start: 0.8422 (m-10) cc_final: 0.8185 (m-10)
REVERT: A   33 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8158 (mm-30)
REVERT: A  350 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8108 (mtpt)
REVERT: B  337 LYS cc_start: 0.8654 (mttp) cc_final: 0.8414 (mttp)
REVERT: C   46 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8195 (pmtt)
  outliers start: 17
  outliers final: 11
  residues processed: 129
  average time/residue: 0.9329
  time to fit residues: 129.0235
Evaluate side-chains
  121 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110100 restraints weight = 8088.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.91
r_work: 0.3153 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7218  Z= 0.252
  Angle     :  0.587   7.156   9799  Z= 0.302
  Chirality :  0.042   0.148   1154
  Planarity :  0.004   0.050   1223
  Dihedral  :  4.378  32.718    975
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 23.46 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 903
  helix:  1.37 (0.25), residues: 424
  sheet: -0.73 (0.34), residues: 186
  loop : -0.94 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.025   0.002   PHE R  37 
 TYR   0.019   0.001   TYR B 124 
 ARG   0.008   0.000   ARG A 209 

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.788 
Fit side-chains
REVERT: R  243 LEU cc_start: 0.7887 (tt) cc_final: 0.7519 (mp)
REVERT: R  304 PHE cc_start: 0.8430 (m-10) cc_final: 0.8194 (m-10)
REVERT: A   33 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8206 (mm-30)
REVERT: A  350 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8107 (mtpt)
REVERT: B  234 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.6989 (m-80)
REVERT: B  337 LYS cc_start: 0.8678 (mttp) cc_final: 0.8455 (mttp)
REVERT: C   46 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8188 (pmtt)
  outliers start: 13
  outliers final: 10
  residues processed: 124
  average time/residue: 0.9534
  time to fit residues: 126.5270
Evaluate side-chains
  123 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    0.0970
   chunk 68 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0060
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.113745 restraints weight = 7871.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.88
r_work: 0.3188 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7218  Z= 0.205
  Angle     :  0.566   7.085   9799  Z= 0.289
  Chirality :  0.041   0.145   1154
  Planarity :  0.004   0.047   1223
  Dihedral  :  4.202  29.241    975
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 23.46 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.27), residues: 903
  helix:  1.43 (0.25), residues: 427
  sheet: -0.75 (0.34), residues: 188
  loop : -0.91 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.018   0.001   PHE R  37 
 TYR   0.020   0.001   TYR B 124 
 ARG   0.006   0.000   ARG A 209 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5758.16 seconds
wall clock time: 102 minutes 9.79 seconds (6129.79 seconds total)