Starting phenix.real_space_refine
on Tue Aug  4 20:25:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w0i_65505/08_2026/9w0i_65505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w0i_65505/08_2026/9w0i_65505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w0i_65505/08_2026/9w0i_65505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w0i_65505/08_2026/9w0i_65505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w0i_65505/08_2026/9w0i_65505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w0i_65505/08_2026/9w0i_65505.cif"
  }
  resolution = 2.19
  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=   0.010 sd=   0.052
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      41      5.16       5
     C    4127      2.51       5
     N    1101      2.21       5
     O    1231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6500
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2299
          Classifications: {'peptide': 296}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278}
    Chain: "B"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1880
          Classifications: {'peptide': 238}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221}
    Chain: "C"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1901
          Classifications: {'peptide': 247}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 231}
    Chain: "D"
      Number of atoms: 297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 297
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 3, 'TRANS': 35}
    Chain: "E"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 71
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "G"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {'GAL': 1, 'SIA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'SPH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.41, per 1000 atoms: 0.22
  Number of scatterers: 6500
  At special positions: 0
  Unit cell: (87.514, 102.41, 83.79, 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      41     16.00
     O    1231      8.00
     N    1101      7.00
     C    4127      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
  Links applied
    BETA2-3
      " GAL G   1 " - " SIA G   2 "
       ~> Even though SIA is an alpha isomer, a beta linkage is required...
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 457.0 milliseconds
  

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1550

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 12 sheets defined
      15.0% alpha, 35.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 57
      removed outlier: 3.536A  pdb=" N   THR A  57 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 54 through 57'
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 100 through 108
      removed outlier: 3.793A  pdb=" N   LYS A 106 " --> pdb=" O   GLN A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.812A  pdb=" N   GLN A 164 " --> pdb=" O   PHE A 161 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SER A 165 " --> pdb=" O   HIS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'B' and resid 83 through 87
    Processing helix  chain 'B' and resid 89 through 98
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 157 through 161
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'C' and resid 42 through 48
      removed outlier: 4.174A  pdb=" N   MET C  46 " --> pdb=" O   ASN C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 66
    Processing helix  chain 'C' and resid 97 through 104
    Processing helix  chain 'C' and resid 143 through 148
    Processing helix  chain 'C' and resid 242 through 247
    Processing helix  chain 'D' and resid 35 through 39
    Processing helix  chain 'D' and resid 50 through 55
    Processing helix  chain 'E' and resid 201 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76
      removed outlier: 5.513A  pdb=" N   LEU A  68 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   MET A 241 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ILE A 246 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ARG A 114 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ALA A 248 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TYR A 112 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   PHE A 110 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA C  22 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 194
      removed outlier: 4.894A  pdb=" N   PHE A 110 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TYR A 112 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ALA A 248 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ARG A 114 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ILE A 246 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ALA A 248 " --> pdb=" O   ILE C  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94
    Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18
    Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33
      removed outlier: 6.928A  pdb=" N   CYS B  32 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   HIS B  99 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLY B 241 " --> pdb=" O   HIS B  99 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU B 101 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   PHE B 239 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ARG B 103 " --> pdb=" O   CYS B 237 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   CYS B 237 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33
      removed outlier: 6.928A  pdb=" N   CYS B  32 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   HIS B  99 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLY B 241 " --> pdb=" O   HIS B  99 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU B 101 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   PHE B 239 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ARG B 103 " --> pdb=" O   CYS B 237 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   CYS B 237 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154
      removed outlier: 6.491A  pdb=" N   ALA B 121 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   GLN B 119 " --> pdb=" O   PRO B 216 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85
      removed outlier: 6.702A  pdb=" N   LEU C  80 " --> pdb=" O   MET C 196 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   MET C 196 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE C  82 " --> pdb=" O   CYS C 194 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LYS C 128 " --> pdb=" O   GLN C 197 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ASN C 199 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR C 126 " --> pdb=" O   ASN C 199 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177
      removed outlier: 6.211A  pdb=" N   TYR C 106 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   MET C 227 " --> pdb=" O   TYR C 106 " (cutoff:3.500A)

    217 hydrogen bonds defined for protein.
    537 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: 0.97

  Time building geometry restraints manager: 0.66 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: 2109
        1.34 -     1.46: 1155
        1.46 -     1.57: 3329
        1.57 -     1.69: 1
        1.69 -     1.81: 68
  Bond restraints: 6662
  Sorted by residual:
  bond pdb=" C4  SPH A 301 "
       pdb=" C5  SPH A 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.472 -0.138 2.00e-02 2.50e+03 4.73e+01
  bond pdb=" N   LYS A 242 "
       pdb=" CA  LYS A 242 "
    ideal  model  delta    sigma   weight residual
    1.462  1.442  0.020 1.00e-02 1.00e+04 3.95e+00
  bond pdb=" CA  ILE A 294 "
       pdb=" C   ILE A 294 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 1.14e-02 7.69e+03 3.34e+00
  bond pdb=" CA  GLN C 235 "
       pdb=" C   GLN C 235 "
    ideal  model  delta    sigma   weight residual
    1.522  1.502  0.020 1.22e-02 6.72e+03 2.70e+00
  bond pdb=" C3  SPH A 301 "
       pdb=" O3  SPH A 301 "
    ideal  model  delta    sigma   weight residual
    1.438  1.409  0.029 2.00e-02 2.50e+03 2.13e+00
  ... (remaining 6657 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 8939
        2.04 -     4.07: 122
        4.07 -     6.11: 11
        6.11 -     8.14: 1
        8.14 -    10.18: 1
  Bond angle restraints: 9074
  Sorted by residual:
  angle pdb=" CB  GLU A 204 "
        pdb=" CG  GLU A 204 "
        pdb=" CD  GLU A 204 "
      ideal   model   delta    sigma   weight residual
     112.60  118.60   -6.00 1.70e+00 3.46e-01 1.25e+01
  angle pdb=" CB  GLU A  19 "
        pdb=" CG  GLU A  19 "
        pdb=" CD  GLU A  19 "
      ideal   model   delta    sigma   weight residual
     112.60  118.39   -5.79 1.70e+00 3.46e-01 1.16e+01
  angle pdb=" C4  SPH A 301 "
        pdb=" C5  SPH A 301 "
        pdb=" C6  SPH A 301 "
      ideal   model   delta    sigma   weight residual
     128.38  118.20   10.18 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" CA  GLU A 204 "
        pdb=" CB  GLU A 204 "
        pdb=" CG  GLU A 204 "
      ideal   model   delta    sigma   weight residual
     114.10  120.34   -6.24 2.00e+00 2.50e-01 9.73e+00
  angle pdb=" N   SER C 236 "
        pdb=" CA  SER C 236 "
        pdb=" C   SER C 236 "
      ideal   model   delta    sigma   weight residual
     113.38  110.17    3.21 1.23e+00 6.61e-01 6.81e+00
  ... (remaining 9069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3537
       17.79 -    35.57: 344
       35.57 -    53.36: 78
       53.36 -    71.14: 25
       71.14 -    88.93: 11
  Dihedral angle restraints: 3995
    sinusoidal: 1595
      harmonic: 2400
  Sorted by residual:
  dihedral pdb=" CG  ARG B  12 "
           pdb=" CD  ARG B  12 "
           pdb=" NE  ARG B  12 "
           pdb=" CZ  ARG B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.01   48.99     2      1.50e+01 4.44e-03 1.21e+01
  dihedral pdb=" CA  THR A  94 "
           pdb=" C   THR A  94 "
           pdb=" N   ILE A  95 "
           pdb=" CA  ILE A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.69  -16.31     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  GLU A 118 "
           pdb=" CG  GLU A 118 "
           pdb=" CD  GLU A 118 "
           pdb=" OE1 GLU A 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.93  -88.93     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 3992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 668
       0.035 -    0.069: 242
       0.069 -    0.104: 81
       0.104 -    0.139: 34
       0.139 -    0.173: 3
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" C2  SIA G   2 "
            pdb=" O3  GAL G   1 "
            pdb=" C1  SIA G   2 "
            pdb=" O6  SIA G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.43   -0.07 2.00e-02 2.50e+03 1.21e+01
  chirality pdb=" C3  SPH A 301 "
            pdb=" C2  SPH A 301 "
            pdb=" C4  SPH A 301 "
            pdb=" O3  SPH A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.25    0.17 2.00e-01 2.50e+01 7.50e-01
  chirality pdb=" CB  ILE A 217 "
            pdb=" CA  ILE A 217 "
            pdb=" CG1 ILE A 217 "
            pdb=" CG2 ILE A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.41e-01
  ... (remaining 1025 not shown)

  Planarity restraints: 1169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 293 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.68e+00
        pdb=" C   ASN A 293 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ASN A 293 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE A 294 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  19 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" CD  GLU A  19 "    0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  19 "   -0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  19 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  SPH A 301 "   -0.013 2.00e-02 2.50e+03   1.32e-02 1.74e+00
        pdb=" C4  SPH A 301 "    0.014 2.00e-02 2.50e+03
        pdb=" C5  SPH A 301 "    0.012 2.00e-02 2.50e+03
        pdb=" C6  SPH A 301 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1166 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 3235
        2.98 -     3.46: 6129
        3.46 -     3.94: 11254
        3.94 -     4.42: 13418
        4.42 -     4.90: 21022
  Nonbonded interactions: 55058
  Sorted by model distance:
  nonbonded pdb=" N2  SPH A 301 "
            pdb=" O1  SPH A 301 "
     model   vdw
     2.498 2.496
  nonbonded pdb=" N   GLU A 204 "
            pdb=" OE1 GLU A 204 "
     model   vdw
     2.508 3.120
  nonbonded pdb=" O   VAL A 295 "
            pdb=" C   THR A 296 "
     model   vdw
     2.522 3.270
  nonbonded pdb=" C3  GAL G   1 "
            pdb=" O6  SIA G   2 "
     model   vdw
     2.538 2.776
  nonbonded pdb=" N   ASP C 220 "
            pdb=" OD1 ASP C 220 "
     model   vdw
     2.540 3.120
  ... (remaining 55053 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:             0.660
  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:             0.020
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
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      :  0.004   0.138   6663  Z= 0.182
  Angle     :  0.581  10.176   9077  Z= 0.312
  Chirality :  0.043   0.173   1028
  Planarity :  0.004   0.038   1169
  Dihedral  : 15.996  88.931   2445
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 19.47 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.34 (0.28), residues: 819
  helix: -1.67 (0.64), residues: 60
  sheet:  0.42 (0.37), residues: 189
  loop : -0.25 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  12 
 TYR   0.008   0.001   TYR D  37 
 PHE   0.009   0.001   PHE A 100 
 TRP   0.011   0.001   TRP C 155 
 HIS   0.002   0.000   HIS B  45 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.18 ( 6662)
  covalent geometry    : angle       0.58073 /  0.31 ( 9074)
  hydrogen bonds       : bond        0.18939 / 13.06 (  177)
  hydrogen bonds       : angle       8.91957 /  6.13 (  537)
  link_BETA2-3         : bond        0.00178 /  0.09 (    1)
  link_BETA2-3         : angle       0.93202 /  0.50 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  136 MET cc_start: 0.5031 (ttt) cc_final: 0.4562 (ttt)
REVERT: B   51 ASP cc_start: 0.9055 (p0) cc_final: 0.8822 (p0)
REVERT: B  111 GLN cc_start: 0.9078 (mp10) cc_final: 0.8693 (mp-120)
REVERT: B  243 ARG cc_start: 0.8603 (pmt-80) cc_final: 0.5271 (mtt180)
REVERT: C   90 LEU cc_start: 0.8725 (tp) cc_final: 0.8474 (mt)
  outliers start: 15
  outliers final: 5
  residues processed: 150
  average time/residue: 0.5466
  time to fit residues: 86.0723
Evaluate side-chains
  117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
A 164 GLN
A 219 ASN
A 229 GLN
A 278 ASN
B  15 GLN
B  45 HIS
B  55 GLN
B 111 GLN
B 131 GLN
B 240 ASN
C  39 GLN
C  74 GLN
D  31 ASN
E 200 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.110935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.087671 restraints weight = 8767.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.19
r_work: 0.3002 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6663  Z= 0.128
  Angle     :  0.510   4.188   9077  Z= 0.267
  Chirality :  0.043   0.147   1028
  Planarity :  0.004   0.039   1169
  Dihedral  :  7.861  84.254    961
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.19 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.34 (0.27), residues: 819
  helix: -1.53 (0.62), residues: 60
  sheet:  0.44 (0.36), residues: 190
  loop : -0.28 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  12 
 TYR   0.026   0.001   TYR B  31 
 PHE   0.012   0.001   PHE C 215 
 TRP   0.009   0.001   TRP C 155 
 HIS   0.002   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 6662)
  covalent geometry    : angle       0.50964 /  0.27 ( 9074)
  hydrogen bonds       : bond        0.03624 /  2.40 (  177)
  hydrogen bonds       : angle       6.30450 /  4.35 (  537)
  link_BETA2-3         : bond        0.00262 /  0.14 (    1)
  link_BETA2-3         : angle       1.00686 /  0.52 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8592 (mm110) cc_final: 0.7340 (mp10)
REVERT: A  136 MET cc_start: 0.5120 (ttt) cc_final: 0.4643 (ttt)
REVERT: B  111 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8626 (mp-120)
REVERT: B  243 ARG cc_start: 0.8606 (pmt-80) cc_final: 0.5297 (mtt180)
  outliers start: 18
  outliers final: 11
  residues processed: 127
  average time/residue: 0.5305
  time to fit residues: 70.8531
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain E residue  200 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  44 GLN
A 164 GLN
A 229 GLN
B  88 ASN
B 206 GLN
C  74 GLN
E 200 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.109685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.086385 restraints weight = 8694.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 2.18
r_work: 0.2977 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6663  Z= 0.161
  Angle     :  0.512   6.762   9077  Z= 0.266
  Chirality :  0.043   0.141   1028
  Planarity :  0.004   0.037   1169
  Dihedral  :  7.535  82.693    958
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.75 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.28 (0.27), residues: 819
  helix: -1.45 (0.62), residues: 60
  sheet:  0.50 (0.37), residues: 190
  loop : -0.25 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  12 
 TYR   0.010   0.001   TYR D  37 
 PHE   0.011   0.001   PHE A 100 
 TRP   0.006   0.001   TRP C 155 
 HIS   0.004   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 6662)
  covalent geometry    : angle       0.51159 /  0.27 ( 9074)
  hydrogen bonds       : bond        0.03783 /  2.53 (  177)
  hydrogen bonds       : angle       6.04185 /  4.18 (  537)
  link_BETA2-3         : bond        0.00156 /  0.08 (    1)
  link_BETA2-3         : angle       0.99629 /  0.52 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8671 (mm110) cc_final: 0.7420 (mp10)
REVERT: A  136 MET cc_start: 0.5210 (ttt) cc_final: 0.2945 (mtp)
REVERT: A  257 MET cc_start: 0.9286 (mmp) cc_final: 0.8919 (mmp)
REVERT: B  243 ARG cc_start: 0.8645 (pmt-80) cc_final: 0.5309 (mtt180)
REVERT: C  186 ASN cc_start: 0.7788 (p0) cc_final: 0.7554 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 132
  average time/residue: 0.5758
  time to fit residues: 79.6930
Evaluate side-chains
  118 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0060
   chunk 13 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    2.8002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
A 164 GLN
A 229 GLN
B 111 GLN
B 206 GLN
C  74 GLN
C 186 ASN
D  31 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.109922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.086554 restraints weight = 8793.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.18
r_work: 0.2979 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6663  Z= 0.150
  Angle     :  0.507   4.561   9077  Z= 0.264
  Chirality :  0.043   0.141   1028
  Planarity :  0.004   0.040   1169
  Dihedral  :  7.365  81.719    958
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.93 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.23 (0.27), residues: 819
  helix: -1.20 (0.64), residues: 60
  sheet:  0.55 (0.37), residues: 190
  loop : -0.25 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  12 
 TYR   0.009   0.001   TYR A 193 
 PHE   0.010   0.001   PHE A 100 
 TRP   0.005   0.001   TRP C 155 
 HIS   0.002   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 6662)
  covalent geometry    : angle       0.50665 /  0.26 ( 9074)
  hydrogen bonds       : bond        0.03483 /  2.34 (  177)
  hydrogen bonds       : angle       5.80499 /  4.02 (  537)
  link_BETA2-3         : bond        0.00298 /  0.16 (    1)
  link_BETA2-3         : angle       0.94199 /  0.49 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8634 (mm110) cc_final: 0.7373 (mp10)
REVERT: A  136 MET cc_start: 0.5232 (ttt) cc_final: 0.3220 (mtp)
REVERT: B   67 ARG cc_start: 0.8468 (ptp-170) cc_final: 0.8265 (ptp-170)
REVERT: B   72 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7984 (mm-30)
REVERT: B  111 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8815 (mp-120)
REVERT: B  243 ARG cc_start: 0.8680 (pmt-80) cc_final: 0.5377 (mtt180)
  outliers start: 28
  outliers final: 14
  residues processed: 123
  average time/residue: 0.4917
  time to fit residues: 63.7586
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 27 optimal weight:    0.4980
   chunk 58 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   overall best weight:    4.0386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B  88 ASN
B 111 GLN
B 206 GLN
C  74 GLN
D  31 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.108538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.084871 restraints weight = 8871.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.22
r_work: 0.2954 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6663  Z= 0.196
  Angle     :  0.532   4.863   9077  Z= 0.277
  Chirality :  0.044   0.137   1028
  Planarity :  0.004   0.035   1169
  Dihedral  :  7.414  81.038    958
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.07 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.27 (0.28), residues: 819
  helix: -1.36 (0.60), residues: 66
  sheet:  0.51 (0.37), residues: 190
  loop : -0.24 (0.24), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  12 
 TYR   0.011   0.001   TYR D  37 
 PHE   0.011   0.001   PHE A 100 
 TRP   0.006   0.001   TRP B  79 
 HIS   0.006   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.20 ( 6662)
  covalent geometry    : angle       0.53191 /  0.28 ( 9074)
  hydrogen bonds       : bond        0.03678 /  2.48 (  177)
  hydrogen bonds       : angle       5.80198 /  4.01 (  537)
  link_BETA2-3         : bond        0.00246 /  0.13 (    1)
  link_BETA2-3         : angle       1.06153 /  0.55 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8652 (mm110) cc_final: 0.7402 (mp10)
REVERT: A  136 MET cc_start: 0.5238 (ttt) cc_final: 0.3687 (mtp)
REVERT: B   72 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7991 (mm-30)
REVERT: B  111 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8843 (mp-120)
  outliers start: 24
  outliers final: 17
  residues processed: 126
  average time/residue: 0.4853
  time to fit residues: 64.2253
Evaluate side-chains
  123 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 78 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B  88 ASN
B 111 GLN
B 206 GLN
D  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.083688 restraints weight = 8850.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 2.21
r_work: 0.2933 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   6663  Z= 0.242
  Angle     :  0.565   5.165   9077  Z= 0.295
  Chirality :  0.045   0.136   1028
  Planarity :  0.004   0.034   1169
  Dihedral  :  7.546  80.690    958
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.77 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.32 (0.27), residues: 819
  helix: -1.36 (0.61), residues: 67
  sheet:  0.45 (0.37), residues: 190
  loop : -0.27 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  12 
 TYR   0.012   0.001   TYR D  37 
 PHE   0.012   0.002   PHE A 100 
 TRP   0.007   0.001   TRP C 109 
 HIS   0.005   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00569 /  0.24 ( 6662)
  covalent geometry    : angle       0.56494 /  0.29 ( 9074)
  hydrogen bonds       : bond        0.03889 /  2.63 (  177)
  hydrogen bonds       : angle       5.86007 /  4.04 (  537)
  link_BETA2-3         : bond        0.00168 /  0.09 (    1)
  link_BETA2-3         : angle       1.09510 /  0.57 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8644 (mm110) cc_final: 0.7416 (mp10)
REVERT: A  136 MET cc_start: 0.5190 (ttt) cc_final: 0.3719 (mtp)
REVERT: B   72 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8081 (mm-30)
REVERT: B  111 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8834 (mp-120)
  outliers start: 23
  outliers final: 16
  residues processed: 117
  average time/residue: 0.4999
  time to fit residues: 61.5720
Evaluate side-chains
  126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0570
   chunk 30 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    2.5904

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B 111 GLN
C  74 GLN
D  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.108996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.085490 restraints weight = 8757.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.19
r_work: 0.2962 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6663  Z= 0.145
  Angle     :  0.520   5.657   9077  Z= 0.272
  Chirality :  0.043   0.141   1028
  Planarity :  0.004   0.039   1169
  Dihedral  :  7.427  80.440    958
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.05 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.32 (0.27), residues: 819
  helix: -1.26 (0.63), residues: 62
  sheet:  0.45 (0.37), residues: 190
  loop : -0.29 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  12 
 TYR   0.009   0.001   TYR A 193 
 PHE   0.010   0.001   PHE A 100 
 TRP   0.008   0.001   TRP C 155 
 HIS   0.003   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 6662)
  covalent geometry    : angle       0.52032 /  0.27 ( 9074)
  hydrogen bonds       : bond        0.03448 /  2.32 (  177)
  hydrogen bonds       : angle       5.72513 /  3.96 (  537)
  link_BETA2-3         : bond        0.00196 /  0.10 (    1)
  link_BETA2-3         : angle       0.83588 /  0.44 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8661 (mm110) cc_final: 0.7422 (mp10)
REVERT: A  136 MET cc_start: 0.5063 (ttt) cc_final: 0.3617 (mtp)
REVERT: A  257 MET cc_start: 0.9331 (mmp) cc_final: 0.9018 (mmp)
REVERT: B   72 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8110 (mm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 123
  average time/residue: 0.5609
  time to fit residues: 72.3055
Evaluate side-chains
  117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0980
   chunk 57 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   overall best weight:    4.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
B  40 ASN
B  88 ASN
B 111 GLN
D  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.108078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.084440 restraints weight = 8813.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.21
r_work: 0.2945 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6663  Z= 0.197
  Angle     :  0.555   5.688   9077  Z= 0.289
  Chirality :  0.044   0.137   1028
  Planarity :  0.004   0.037   1169
  Dihedral  :  7.433  79.817    958
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.33 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.32 (0.27), residues: 819
  helix: -1.31 (0.62), residues: 67
  sheet:  0.46 (0.37), residues: 190
  loop : -0.28 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  12 
 TYR   0.026   0.002   TYR B  31 
 PHE   0.011   0.001   PHE A 100 
 TRP   0.009   0.001   TRP C 155 
 HIS   0.004   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.20 ( 6662)
  covalent geometry    : angle       0.55475 /  0.29 ( 9074)
  hydrogen bonds       : bond        0.03673 /  2.48 (  177)
  hydrogen bonds       : angle       5.77434 /  3.98 (  537)
  link_BETA2-3         : bond        0.00134 /  0.07 (    1)
  link_BETA2-3         : angle       0.90668 /  0.47 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8667 (mm110) cc_final: 0.7428 (mp10)
REVERT: A  136 MET cc_start: 0.5085 (ttt) cc_final: 0.3575 (mtp)
REVERT: A  257 MET cc_start: 0.9343 (mmp) cc_final: 0.9023 (mmp)
REVERT: B   72 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8132 (mm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 114
  average time/residue: 0.4692
  time to fit residues: 56.0840
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
A  87 HIS
A 229 GLN
B 111 GLN
D  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.109451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.086106 restraints weight = 8850.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.19
r_work: 0.2968 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6663  Z= 0.143
  Angle     :  0.528   5.789   9077  Z= 0.276
  Chirality :  0.043   0.141   1028
  Planarity :  0.004   0.041   1169
  Dihedral  :  7.332  79.115    958
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.61 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.30 (0.27), residues: 819
  helix: -1.24 (0.63), residues: 62
  sheet:  0.49 (0.37), residues: 190
  loop : -0.28 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  12 
 TYR   0.033   0.001   TYR B  31 
 PHE   0.010   0.001   PHE A 100 
 TRP   0.008   0.001   TRP C 155 
 HIS   0.005   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 6662)
  covalent geometry    : angle       0.52823 /  0.28 ( 9074)
  hydrogen bonds       : bond        0.03382 /  2.27 (  177)
  hydrogen bonds       : angle       5.66666 /  3.92 (  537)
  link_BETA2-3         : bond        0.00191 /  0.10 (    1)
  link_BETA2-3         : angle       0.73735 /  0.38 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8684 (mm110) cc_final: 0.7434 (mp10)
REVERT: A  136 MET cc_start: 0.4995 (ttt) cc_final: 0.3510 (mtp)
REVERT: A  257 MET cc_start: 0.9341 (mmp) cc_final: 0.9015 (mmp)
REVERT: B   72 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (mm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 114
  average time/residue: 0.5418
  time to fit residues: 65.0774
Evaluate side-chains
  114 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
A 229 GLN
B  88 ASN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.107707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.084366 restraints weight = 8709.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.16
r_work: 0.2941 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6663  Z= 0.213
  Angle     :  0.559   5.661   9077  Z= 0.292
  Chirality :  0.044   0.137   1028
  Planarity :  0.004   0.037   1169
  Dihedral  :  7.506  78.514    958
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.31 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.31 (0.28), residues: 819
  helix: -1.27 (0.62), residues: 67
  sheet:  0.48 (0.37), residues: 190
  loop : -0.28 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  12 
 TYR   0.011   0.001   TYR D  37 
 PHE   0.011   0.002   PHE A 100 
 TRP   0.007   0.001   TRP C 155 
 HIS   0.005   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.21 ( 6662)
  covalent geometry    : angle       0.55905 /  0.29 ( 9074)
  hydrogen bonds       : bond        0.03721 /  2.51 (  177)
  hydrogen bonds       : angle       5.75696 /  3.97 (  537)
  link_BETA2-3         : bond        0.00172 /  0.09 (    1)
  link_BETA2-3         : angle       0.91295 /  0.47 (    3)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  102 GLN cc_start: 0.8669 (mm110) cc_final: 0.7439 (mp10)
REVERT: A  136 MET cc_start: 0.5111 (ttt) cc_final: 0.3742 (mtp)
REVERT: A  257 MET cc_start: 0.9355 (mmp) cc_final: 0.9031 (mmp)
  outliers start: 16
  outliers final: 14
  residues processed: 122
  average time/residue: 0.5192
  time to fit residues: 66.4689
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain D residue   47 SER
Chi-restraints excluded: chain D residue   51 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    3.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  17 ASN
A 229 GLN
B  40 ASN
C  74 GLN
D  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.108822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.085188 restraints weight = 8770.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.21
r_work: 0.2957 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6663  Z= 0.167
  Angle     :  0.537   5.773   9077  Z= 0.282
  Chirality :  0.043   0.139   1028
  Planarity :  0.004   0.039   1169
  Dihedral  :  7.458  78.151    958
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.17 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.32 (0.27), residues: 819
  helix: -1.24 (0.63), residues: 62
  sheet:  0.49 (0.37), residues: 190
  loop : -0.31 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  12 
 TYR   0.031   0.001   TYR B  31 
 PHE   0.011   0.001   PHE A 100 
 TRP   0.006   0.001   TRP C 155 
 HIS   0.004   0.001   HIS B 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.17 ( 6662)
  covalent geometry    : angle       0.53684 /  0.28 ( 9074)
  hydrogen bonds       : bond        0.03508 /  2.36 (  177)
  hydrogen bonds       : angle       5.67096 /  3.91 (  537)
  link_BETA2-3         : bond        0.00147 /  0.08 (    1)
  link_BETA2-3         : angle       0.75027 /  0.39 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3150.02 seconds
wall clock time: 54 minutes 13.26 seconds (3253.26 seconds total)