Starting phenix.real_space_refine
on Sat May  2 15:03:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w0t_65515/05_2026/9w0t_65515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w0t_65515/05_2026/9w0t_65515.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w0t_65515/05_2026/9w0t_65515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w0t_65515/05_2026/9w0t_65515.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w0t_65515/05_2026/9w0t_65515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w0t_65515/05_2026/9w0t_65515.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.074
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      42      5.16       5
     C    4208      2.51       5
     N    1112      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6548
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1687
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 35
    Chain: "B"
      Number of atoms: 2439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2439
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 145
          Unresolved non-hydrogen angles: 175
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 103
    Chain: "C"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 364
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "R"
      Number of atoms: 2034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2034
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 7, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 248
          Unresolved non-hydrogen dihedrals: 165
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 5, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 123
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'WK3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.85, per 1000 atoms: 0.28
  Number of scatterers: 6548
  At special positions: 0
  Unit cell: (84.609, 97.461, 122.094, 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      42     16.00
     O    1186      8.00
     N    1112      7.00
     C    4208      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.57
  Conformation dependent library (CDL) restraints added in 383.4 milliseconds
  

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1672

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      48.6% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.504A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.180A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.982A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 4.435A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 3.587A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 46
      removed outlier: 4.553A  pdb=" N   LYS C  46 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 9 through 39
    Processing helix  chain 'R' and resid 42 through 70
      removed outlier: 3.849A  pdb=" N   GLN R  46 " --> pdb=" O   SER R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 111
      removed outlier: 3.670A  pdb=" N   TRP R  97 " --> pdb=" O   HIS R  93 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 124
      removed outlier: 3.910A  pdb=" N   ARG R 124 " --> pdb=" O   HIS R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 135
      removed outlier: 3.553A  pdb=" N   VAL R 129 " --> pdb=" O   VAL R 125 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LEU R 130 " --> pdb=" O   LYS R 126 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 151
    Processing helix  chain 'R' and resid 176 through 212
      Proline residue:  R 187  - end of helix
      removed outlier: 3.506A  pdb=" N   LEU R 192 " --> pdb=" O   PHE R 188 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU R 211 " --> pdb=" O   LYS R 207 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   HIS R 212 " --> pdb=" O   LYS R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 251
    Processing helix  chain 'R' and resid 257 through 284
      Proline residue:  R 272  - end of helix
      Proline residue:  R 276  - end of helix
      removed outlier: 3.961A  pdb=" N   LYS R 284 " --> pdb=" O   ILE R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 285 through 302
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.922A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.256A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 4.461A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.905A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.812A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191
      removed outlier: 6.884A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 3.831A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.512A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1158 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: 1.08

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1048
        1.31 -     1.44: 1828
        1.44 -     1.56: 3749
        1.56 -     1.69: 0
        1.69 -     1.82: 58
  Bond restraints: 6683
  Sorted by residual:
  bond pdb=" C5  WK3 R 401 "
       pdb=" N6  WK3 R 401 "
    ideal  model  delta    sigma   weight residual
    1.348  1.457 -0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C18 WK3 R 401 "
       pdb=" N3  WK3 R 401 "
    ideal  model  delta    sigma   weight residual
    1.542  1.472  0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C16 WK3 R 401 "
       pdb=" N3  WK3 R 401 "
    ideal  model  delta    sigma   weight residual
    1.526  1.461  0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" C2  WK3 R 401 "
       pdb=" N3  WK3 R 401 "
    ideal  model  delta    sigma   weight residual
    1.523  1.469  0.054 2.00e-02 2.50e+03 7.25e+00
  bond pdb=" C4  WK3 R 401 "
       pdb=" N3  WK3 R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.462  0.040 2.00e-02 2.50e+03 3.97e+00
  ... (remaining 6678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 8936
        1.72 -     3.44: 139
        3.44 -     5.16: 20
        5.16 -     6.88: 5
        6.88 -     8.60: 4
  Bond angle restraints: 9104
  Sorted by residual:
  angle pdb=" C   GLN R  39 "
        pdb=" CA  GLN R  39 "
        pdb=" CB  GLN R  39 "
      ideal   model   delta    sigma   weight residual
     116.54  110.21    6.33 1.15e+00 7.56e-01 3.03e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.71  109.07    4.64 9.50e-01 1.11e+00 2.39e+01
  angle pdb=" CA  MET A  53 "
        pdb=" CB  MET A  53 "
        pdb=" CG  MET A  53 "
      ideal   model   delta    sigma   weight residual
     114.10  121.29   -7.19 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" CA  GLN R  39 "
        pdb=" C   GLN R  39 "
        pdb=" N   LYS R  40 "
      ideal   model   delta    sigma   weight residual
     119.52  116.91    2.61 7.90e-01 1.60e+00 1.09e+01
  angle pdb=" C   LEU R 185 "
        pdb=" N   VAL R 186 "
        pdb=" CA  VAL R 186 "
      ideal   model   delta    sigma   weight residual
     120.24  122.11   -1.87 6.30e-01 2.52e+00 8.78e+00
  ... (remaining 9099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 3528
       17.23 -    34.45: 317
       34.45 -    51.68: 46
       51.68 -    68.90: 11
       68.90 -    86.13: 9
  Dihedral angle restraints: 3911
    sinusoidal: 1347
      harmonic: 2564
  Sorted by residual:
  dihedral pdb=" CA  LYS B 301 "
           pdb=" C   LYS B 301 "
           pdb=" N   ALA B 302 "
           pdb=" CA  ALA B 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.79  -16.21     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CG  ARG B  68 "
           pdb=" CD  ARG B  68 "
           pdb=" NE  ARG B  68 "
           pdb=" CZ  ARG B  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.72   44.28     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  ASP B 322 "
           pdb=" CB  ASP B 322 "
           pdb=" CG  ASP B 322 "
           pdb=" OD1 ASP B 322 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.29   55.29     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 3908 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 718
       0.029 -    0.059: 242
       0.059 -    0.088: 85
       0.088 -    0.118: 38
       0.118 -    0.147: 6
  Chirality restraints: 1089
  Sorted by residual:
  chirality pdb=" CA  MET A  53 "
            pdb=" N   MET A  53 "
            pdb=" C   MET A  53 "
            pdb=" CB  MET A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  chirality pdb=" CA  PRO R 219 "
            pdb=" N   PRO R 219 "
            pdb=" C   PRO R 219 "
            pdb=" CB  PRO R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.57e-01
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 1086 not shown)

  Planarity restraints: 1134
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 186 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO R 187 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO R 187 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 187 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 218 "    0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO R 219 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO R 219 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 219 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R  84 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" C   ALA R  84 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ALA R  84 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR R  85 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1131 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1054
        2.77 -     3.30: 6356
        3.30 -     3.83: 11024
        3.83 -     4.37: 11962
        4.37 -     4.90: 21712
  Nonbonded interactions: 52108
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" ND2 ASN B 119 "
            pdb=" O   GLY B 144 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER B 275 "
            pdb=" O   SER B 316 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.322 3.040
  ... (remaining 52103 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:             1.390
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.250
  Find NCS groups from input model:        0.020
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   6683  Z= 0.152
  Angle     :  0.551   8.605   9104  Z= 0.313
  Chirality :  0.038   0.147   1089
  Planarity :  0.003   0.055   1134
  Dihedral  : 14.022  86.127   2239
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.30), residues: 865
  helix:  2.66 (0.26), residues: 401
  sheet:  1.01 (0.43), residues: 162
  loop : -1.55 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  21 
 TYR   0.004   0.001   TYR C  40 
 PHE   0.014   0.001   PHE R 290 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6683)
  covalent geometry    : angle       0.55123 ( 9104)
  hydrogen bonds       : bond        0.17640 (  396)
  hydrogen bonds       : angle       6.38452 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7374 (mtm110) cc_final: 0.6989 (mtt180)
REVERT: B   43 ILE cc_start: 0.6572 (mp) cc_final: 0.6272 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0795
  time to fit residues: 12.3965
Evaluate side-chains
  91 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:   50.0000
   chunk 62 optimal weight:    0.0970
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
R 120 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.219732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.190736 restraints weight = 7617.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.4249 rms_B_bonded: 1.93
r_work: 0.3833 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6683  Z= 0.134
  Angle     :  0.544   8.260   9104  Z= 0.282
  Chirality :  0.041   0.266   1089
  Planarity :  0.004   0.039   1134
  Dihedral  :  6.046  87.367    934
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  7.50 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.29), residues: 865
  helix:  2.79 (0.25), residues: 404
  sheet:  0.75 (0.41), residues: 155
  loop : -1.51 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.006   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 290 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.008   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6683)
  covalent geometry    : angle       0.54373 ( 9104)
  hydrogen bonds       : bond        0.03768 (  396)
  hydrogen bonds       : angle       4.46211 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7487 (mtm110) cc_final: 0.6824 (mtt180)
REVERT: B   43 ILE cc_start: 0.7028 (mp) cc_final: 0.6788 (mp)
REVERT: R  195 PHE cc_start: 0.6708 (m-10) cc_final: 0.6299 (m-10)
REVERT: R  277 PHE cc_start: 0.8025 (m-10) cc_final: 0.7733 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 98
  average time/residue: 0.0762
  time to fit residues: 10.3958
Evaluate side-chains
  95 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  140 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 73 optimal weight:    9.9990
   chunk 85 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.221573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.192283 restraints weight = 7589.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 1.76
r_work: 0.3911 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6683  Z= 0.126
  Angle     :  0.521   7.778   9104  Z= 0.269
  Chirality :  0.041   0.307   1089
  Planarity :  0.004   0.043   1134
  Dihedral  :  5.485  86.534    934
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.33 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.29), residues: 865
  helix:  2.79 (0.25), residues: 403
  sheet:  0.28 (0.40), residues: 165
  loop : -1.45 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  49 
 TYR   0.006   0.001   TYR B  59 
 PHE   0.015   0.001   PHE R 290 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6683)
  covalent geometry    : angle       0.52066 ( 9104)
  hydrogen bonds       : bond        0.03257 (  396)
  hydrogen bonds       : angle       4.17731 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7538 (mtm110) cc_final: 0.6885 (mtt180)
REVERT: A  194 LEU cc_start: 0.8366 (tp) cc_final: 0.8095 (tp)
REVERT: A  323 PHE cc_start: 0.6052 (m-10) cc_final: 0.5790 (m-10)
REVERT: B  234 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7177 (m-80)
REVERT: R  195 PHE cc_start: 0.7021 (m-10) cc_final: 0.6278 (m-10)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.0802
  time to fit residues: 11.4743
Evaluate side-chains
  99 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  140 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0570
   chunk 25 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 65 optimal weight:   40.0000
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
R 120 HIS
** R 224 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 = 0.4528 r_free = 0.4528 target = 0.218379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.188324 restraints weight = 7606.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.4239 rms_B_bonded: 1.82
r_work: 0.3825 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6683  Z= 0.140
  Angle     :  0.539   8.415   9104  Z= 0.276
  Chirality :  0.041   0.208   1089
  Planarity :  0.004   0.045   1134
  Dihedral  :  5.595  85.038    934
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 13.17 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.29), residues: 865
  helix:  2.79 (0.25), residues: 402
  sheet: -0.14 (0.39), residues: 170
  loop : -1.46 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.014   0.002   PHE R 290 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.007   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6683)
  covalent geometry    : angle       0.53933 ( 9104)
  hydrogen bonds       : bond        0.03104 (  396)
  hydrogen bonds       : angle       4.09614 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7536 (mtm110) cc_final: 0.6839 (mtt180)
REVERT: A  194 LEU cc_start: 0.8425 (tp) cc_final: 0.8149 (tp)
REVERT: A  323 PHE cc_start: 0.6197 (m-10) cc_final: 0.5962 (m-10)
REVERT: B  234 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7595 (m-80)
  outliers start: 19
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0877
  time to fit residues: 11.9143
Evaluate side-chains
  101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  151 GLN
Chi-restraints excluded: chain R residue  206 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 120 HIS
** R 224 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 = 0.4518 r_free = 0.4518 target = 0.217125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.185681 restraints weight = 7605.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.4235 rms_B_bonded: 1.85
r_work: 0.3744 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6683  Z= 0.140
  Angle     :  0.534   8.249   9104  Z= 0.273
  Chirality :  0.041   0.190   1089
  Planarity :  0.003   0.041   1134
  Dihedral  :  5.527  83.577    934
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 13.48 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.29), residues: 865
  helix:  2.83 (0.25), residues: 402
  sheet: -0.15 (0.38), residues: 170
  loop : -1.48 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  49 
 TYR   0.012   0.001   TYR B 264 
 PHE   0.016   0.002   PHE R 290 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.010   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6683)
  covalent geometry    : angle       0.53410 ( 9104)
  hydrogen bonds       : bond        0.03084 (  396)
  hydrogen bonds       : angle       4.10239 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7563 (mtm110) cc_final: 0.6795 (mtt180)
REVERT: A  323 PHE cc_start: 0.6587 (m-10) cc_final: 0.6074 (m-10)
REVERT: B  234 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7688 (m-80)
REVERT: B  239 ASN cc_start: 0.7992 (p0) cc_final: 0.7791 (p0)
REVERT: B  263 THR cc_start: 0.8018 (m) cc_final: 0.7500 (p)
REVERT: B  338 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8079 (mp)
REVERT: R   51 LEU cc_start: 0.8077 (tp) cc_final: 0.7801 (tp)
REVERT: R  221 MET cc_start: 0.7734 (mmp) cc_final: 0.7478 (mmp)
  outliers start: 24
  outliers final: 17
  residues processed: 108
  average time/residue: 0.0804
  time to fit residues: 11.7468
Evaluate side-chains
  111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  151 GLN
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  290 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0970
   chunk 8 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
R 120 HIS
R 224 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.214698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.184207 restraints weight = 7606.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 1.89
r_work: 0.3733 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6683  Z= 0.161
  Angle     :  0.554   9.091   9104  Z= 0.283
  Chirality :  0.041   0.150   1089
  Planarity :  0.003   0.044   1134
  Dihedral  :  5.610  83.390    934
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 12.86 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.29), residues: 865
  helix:  2.68 (0.25), residues: 407
  sheet: -0.33 (0.37), residues: 171
  loop : -1.58 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  21 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.015   0.002   PHE R 290 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.011   0.002   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6683)
  covalent geometry    : angle       0.55401 ( 9104)
  hydrogen bonds       : bond        0.03171 (  396)
  hydrogen bonds       : angle       4.16039 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7565 (mtm110) cc_final: 0.6815 (mtt180)
REVERT: B  234 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7814 (m-80)
REVERT: B  263 THR cc_start: 0.8068 (m) cc_final: 0.7618 (p)
REVERT: R   51 LEU cc_start: 0.8019 (tp) cc_final: 0.7746 (tp)
REVERT: R  143 HIS cc_start: 0.5575 (m-70) cc_final: 0.5372 (m170)
REVERT: R  221 MET cc_start: 0.7725 (mmp) cc_final: 0.7444 (mmp)
  outliers start: 29
  outliers final: 19
  residues processed: 112
  average time/residue: 0.0721
  time to fit residues: 11.1323
Evaluate side-chains
  112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  290 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 224 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.215198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.183697 restraints weight = 7520.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 1.84
r_work: 0.3782 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6683  Z= 0.146
  Angle     :  0.557   8.769   9104  Z= 0.285
  Chirality :  0.041   0.243   1089
  Planarity :  0.003   0.045   1134
  Dihedral  :  5.588  82.750    934
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 14.09 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.29), residues: 865
  helix:  2.63 (0.25), residues: 409
  sheet: -0.56 (0.37), residues: 175
  loop : -1.52 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.015   0.002   PHE R 290 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.014   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6683)
  covalent geometry    : angle       0.55680 ( 9104)
  hydrogen bonds       : bond        0.03082 (  396)
  hydrogen bonds       : angle       4.17186 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6892 (mtt180)
REVERT: B  234 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7804 (m-80)
REVERT: B  263 THR cc_start: 0.8059 (m) cc_final: 0.7635 (p)
REVERT: R  221 MET cc_start: 0.7749 (mmp) cc_final: 0.7532 (mmp)
  outliers start: 25
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0773
  time to fit residues: 11.3898
Evaluate side-chains
  112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  290 PHE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 1 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 120 HIS
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.215264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.184104 restraints weight = 7525.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 1.88
r_work: 0.3730 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6683  Z= 0.139
  Angle     :  0.553   7.995   9104  Z= 0.282
  Chirality :  0.041   0.244   1089
  Planarity :  0.003   0.048   1134
  Dihedral  :  5.549  81.993    934
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.47 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.29), residues: 865
  helix:  2.65 (0.25), residues: 408
  sheet: -0.55 (0.37), residues: 170
  loop : -1.58 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.015   0.002   PHE R 290 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.016   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6683)
  covalent geometry    : angle       0.55347 ( 9104)
  hydrogen bonds       : bond        0.03041 (  396)
  hydrogen bonds       : angle       4.17901 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7513 (mtm110) cc_final: 0.6874 (mtt180)
REVERT: B  234 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7862 (m-80)
REVERT: B  263 THR cc_start: 0.8113 (m) cc_final: 0.7712 (p)
REVERT: C   38 MET cc_start: 0.7805 (mmm) cc_final: 0.7500 (tpt)
  outliers start: 22
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0817
  time to fit residues: 11.4651
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  290 PHE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 85 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   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 306 GLN
R 120 HIS
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.215438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.184149 restraints weight = 7577.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 1.85
r_work: 0.3776 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6683  Z= 0.134
  Angle     :  0.552   8.335   9104  Z= 0.281
  Chirality :  0.041   0.309   1089
  Planarity :  0.003   0.048   1134
  Dihedral  :  5.525  81.796    934
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.93 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.29), residues: 865
  helix:  2.68 (0.25), residues: 407
  sheet: -0.58 (0.37), residues: 170
  loop : -1.60 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.010   0.001   TYR R 271 
 PHE   0.015   0.001   PHE R 290 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.012   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6683)
  covalent geometry    : angle       0.55221 ( 9104)
  hydrogen bonds       : bond        0.03013 (  396)
  hydrogen bonds       : angle       4.16190 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7498 (mtm110) cc_final: 0.6878 (mtt180)
REVERT: B  234 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7837 (m-80)
REVERT: B  263 THR cc_start: 0.8060 (m) cc_final: 0.7680 (p)
  outliers start: 20
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0821
  time to fit residues: 11.5833
Evaluate side-chains
  109 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  290 PHE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 55 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
R 120 HIS
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 224 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.213907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.182300 restraints weight = 7523.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 1.75
r_work: 0.3781 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6683  Z= 0.165
  Angle     :  0.580   8.604   9104  Z= 0.294
  Chirality :  0.042   0.319   1089
  Planarity :  0.003   0.047   1134
  Dihedral  :  5.594  82.092    934
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.77 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.29), residues: 865
  helix:  2.55 (0.25), residues: 409
  sheet: -0.67 (0.37), residues: 170
  loop : -1.67 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.011   0.001   TYR R 271 
 PHE   0.015   0.002   PHE R 290 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.008   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6683)
  covalent geometry    : angle       0.58016 ( 9104)
  hydrogen bonds       : bond        0.03136 (  396)
  hydrogen bonds       : angle       4.23273 ( 1158)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7511 (mtm110) cc_final: 0.6886 (mtt180)
REVERT: B  234 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7872 (m-80)
REVERT: B  263 THR cc_start: 0.8057 (m) cc_final: 0.7696 (p)
  outliers start: 21
  outliers final: 20
  residues processed: 104
  average time/residue: 0.0743
  time to fit residues: 10.7724
Evaluate side-chains
  109 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  290 PHE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
R 120 HIS
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 224 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.215283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.184204 restraints weight = 7560.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 1.85
r_work: 0.3778 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6683  Z= 0.130
  Angle     :  0.557   9.527   9104  Z= 0.282
  Chirality :  0.040   0.155   1089
  Planarity :  0.003   0.047   1134
  Dihedral  :  5.523  81.389    934
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.62 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.29), residues: 865
  helix:  2.62 (0.25), residues: 409
  sheet: -0.74 (0.37), residues: 172
  loop : -1.63 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.011   0.001   TYR A 296 
 PHE   0.015   0.001   PHE R 290 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6683)
  covalent geometry    : angle       0.55718 ( 9104)
  hydrogen bonds       : bond        0.03026 (  396)
  hydrogen bonds       : angle       4.13247 ( 1158)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1651.27 seconds
wall clock time: 29 minutes 13.85 seconds (1753.85 seconds total)