Starting phenix.real_space_refine
on Sat Aug 23 01:36:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t3s_41010/08_2025/8t3s_41010.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t3s_41010/08_2025/8t3s_41010.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t3s_41010/08_2025/8t3s_41010.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t3s_41010/08_2025/8t3s_41010.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t3s_41010/08_2025/8t3s_41010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t3s_41010/08_2025/8t3s_41010.map"
  }
  resolution = 3.07
  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=  -0.000 sd=   0.043
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      53      5.16       5
     C    5600      2.51       5
     N    1496      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8769
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1797
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 49
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 1781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1781
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2063
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 14, 'TRANS': 243}
          Chain breaks: 3
    Chain: "R"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 70
          Unusual residues: {'BUA': 1, 'CLR': 1, 'PLM': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.95, per 1000 atoms: 0.22
  Number of scatterers: 8769
  At special positions: 0
  Unit cell: (84.252, 123.9, 119.77, 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      53     16.00
     O    1620      8.00
     N    1496      7.00
     C    5600      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 160 " - pdb=" SG  CYS N 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  82 " - pdb=" SG  CYS R 164 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 228.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2092

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      38.5% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 49
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.527A  pdb=" N   GLN A  98 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 3.895A  pdb=" N   ARG A 135 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.522A  pdb=" N   LEU A 149 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.026A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
      removed outlier: 3.512A  pdb=" N   ALA A 168 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 165 through 168'
    Processing helix  chain 'A' and resid 183 through 203
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.613A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 53 through 56
      removed outlier: 3.757A  pdb=" N   GLY N  56 " --> pdb=" O   SER N  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 53 through 56'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.037A  pdb=" N   THR N  91 " --> pdb=" O   SER N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 38
      Proline residue:  R  23  - end of helix
      removed outlier: 3.607A  pdb=" N   GLN R  38 " --> pdb=" O   GLY R  34 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 61
      removed outlier: 3.526A  pdb=" N   LEU R  61 " --> pdb=" O   LEU R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 72
      removed outlier: 3.523A  pdb=" N   LYS R  65 " --> pdb=" O   LEU R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 113
      removed outlier: 3.718A  pdb=" N   TYR R  90 " --> pdb=" O   SER R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 121
    Processing helix  chain 'R' and resid 122 through 149
      removed outlier: 3.908A  pdb=" N   GLY R 126 " --> pdb=" O   ARG R 122 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE R 143 " --> pdb=" O   GLY R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 187
      removed outlier: 3.692A  pdb=" N   VAL R 176 " --> pdb=" O   GLN R 172 " (cutoff:3.500A)
      Proline residue:  R 178  - end of helix
      removed outlier: 3.533A  pdb=" N   CYS R 184 " --> pdb=" O   ARG R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 188 through 209
    Processing helix  chain 'R' and resid 216 through 249
      removed outlier: 3.596A  pdb=" N   VAL R 221 " --> pdb=" O   ARG R 217 " (cutoff:3.500A)
      Proline residue:  R 237  - end of helix
      removed outlier: 3.524A  pdb=" N   SER R 241 " --> pdb=" O   PRO R 237 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   HIS R 242 " --> pdb=" O   TYR R 238 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 254 through 274
      removed outlier: 3.869A  pdb=" N   VAL R 260 " --> pdb=" O   SER R 256 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   PHE R 261 " --> pdb=" O   ILE R 257 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASN R 265 " --> pdb=" O   PHE R 261 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   ALA R 266 " --> pdb=" O   SER R 262 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   SER R 267 " --> pdb=" O   SER R 263 " (cutoff:3.500A)
      Proline residue:  R 270  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.386A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 50
      removed outlier: 6.256A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.713A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.814A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.665A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.932A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.465A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.410A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.741A  pdb=" N   MET N  34 " --> pdb=" O   TYR N  50 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   TYR N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12
      removed outlier: 4.378A  pdb=" N   PHE N 110 " --> pdb=" O   ARG N  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142
    Processing sheet with id=AB5, first strand: chain 'N' and resid 147 through 149
      removed outlier: 3.567A  pdb=" N   GLU N 247 " --> pdb=" O   VAL N 148 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LEU N 175 " --> pdb=" O   TYR N 191 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   TYR N 191 " --> pdb=" O   LEU N 175 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   TRP N 177 " --> pdb=" O   LEU N 189 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1218 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: 1.39

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1425
        1.32 -     1.44: 2464
        1.44 -     1.57: 4991
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8956
  Sorted by residual:
  bond pdb=" CA  SER B  74 "
       pdb=" CB  SER B  74 "
    ideal  model  delta    sigma   weight residual
    1.535  1.456  0.079 1.71e-02 3.42e+03 2.15e+01
  bond pdb=" N   GLN R  40 "
       pdb=" CA  GLN R  40 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 7.40e-03 1.83e+04 1.66e+01
  bond pdb=" CA  SER B  72 "
       pdb=" CB  SER B  72 "
    ideal  model  delta    sigma   weight residual
    1.534  1.445  0.090 2.47e-02 1.64e+03 1.32e+01
  bond pdb=" CA  SER A  44 "
       pdb=" CB  SER A  44 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.053 1.59e-02 3.96e+03 1.11e+01
  bond pdb=" CA  SER R  92 "
       pdb=" CB  SER R  92 "
    ideal  model  delta    sigma   weight residual
    1.529  1.477  0.052 1.55e-02 4.16e+03 1.10e+01
  ... (remaining 8951 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 11586
        1.66 -     3.31: 447
        3.31 -     4.97: 93
        4.97 -     6.63: 17
        6.63 -     8.28: 5
  Bond angle restraints: 12148
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     112.89  104.61    8.28 1.24e+00 6.50e-01 4.46e+01
  angle pdb=" N   ASP B 312 "
        pdb=" CA  ASP B 312 "
        pdb=" CB  ASP B 312 "
      ideal   model   delta    sigma   weight residual
     114.17  107.50    6.67 1.14e+00 7.69e-01 3.42e+01
  angle pdb=" N   GLN B  75 "
        pdb=" CA  GLN B  75 "
        pdb=" C   GLN B  75 "
      ideal   model   delta    sigma   weight residual
     113.21  106.62    6.59 1.15e+00 7.56e-01 3.28e+01
  angle pdb=" N   GLY B  77 "
        pdb=" CA  GLY B  77 "
        pdb=" C   GLY B  77 "
      ideal   model   delta    sigma   weight residual
     115.72  108.97    6.75 1.51e+00 4.39e-01 2.00e+01
  angle pdb=" N   ALA R  13 "
        pdb=" CA  ALA R  13 "
        pdb=" C   ALA R  13 "
      ideal   model   delta    sigma   weight residual
     111.07  106.29    4.78 1.07e+00 8.73e-01 1.99e+01
  ... (remaining 12143 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4701
       17.98 -    35.95: 528
       35.95 -    53.93: 117
       53.93 -    71.90: 13
       71.90 -    89.88: 3
  Dihedral angle restraints: 5362
    sinusoidal: 2120
      harmonic: 3242
  Sorted by residual:
  dihedral pdb=" C   PRO R 252 "
           pdb=" N   PRO R 252 "
           pdb=" CA  PRO R 252 "
           pdb=" CB  PRO R 252 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -110.61  -10.09     0      2.50e+00 1.60e-01 1.63e+01
  dihedral pdb=" CA  HIS B 311 "
           pdb=" C   HIS B 311 "
           pdb=" N   ASP B 312 "
           pdb=" CA  ASP B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" N   LEU B  79 "
           pdb=" C   LEU B  79 "
           pdb=" CA  LEU B  79 "
           pdb=" CB  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.64    8.16     0      2.50e+00 1.60e-01 1.07e+01
  ... (remaining 5359 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1183
       0.067 -    0.135: 168
       0.135 -    0.202: 22
       0.202 -    0.270: 4
       0.270 -    0.337: 1
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  LEU B  79 "
            pdb=" N   LEU B  79 "
            pdb=" C   LEU B  79 "
            pdb=" CB  LEU B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  VAL B  71 "
            pdb=" N   VAL B  71 "
            pdb=" C   VAL B  71 "
            pdb=" CB  VAL B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  LEU R   9 "
            pdb=" N   LEU R   9 "
            pdb=" C   LEU R   9 "
            pdb=" CB  LEU R   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 1375 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R  86 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   SER R  86 "    0.059 2.00e-02 2.50e+03
        pdb=" O   SER R  86 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PHE R  87 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  62 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.77e+00
        pdb=" N   PRO R  63 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO R  63 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R  63 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R  13 "   -0.012 2.00e-02 2.50e+03   2.54e-02 6.46e+00
        pdb=" C   ALA R  13 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ALA R  13 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR R  14 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 516
        2.73 -     3.27: 8733
        3.27 -     3.81: 14843
        3.81 -     4.36: 17894
        4.36 -     4.90: 31450
  Nonbonded interactions: 73436
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   ALA R 133 "
            pdb=" OG  SER R 137 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   TYR R 238 "
            pdb=" OG  SER R 241 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.253 3.040
  ... (remaining 73431 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:             0.950
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.220
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
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      :  0.005   0.090   8959  Z= 0.319
  Angle     :  0.748   8.283  12154  Z= 0.498
  Chirality :  0.051   0.337   1378
  Planarity :  0.005   0.065   1536
  Dihedral  : 15.215  89.881   3261
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 21.66 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  0.78 (0.26), residues: 1099
  helix:  1.51 (0.26), residues: 381
  sheet:  0.16 (0.32), residues: 272
  loop :  0.01 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG R 217 
 TYR   0.043   0.002   TYR R  14 
 PHE   0.028   0.002   PHE N 240 
 TRP   0.022   0.001   TRP R 254 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 8956)
  covalent geometry    : angle       0.74846 (12148)
  SS BOND              : bond        0.00088 (    3)
  SS BOND              : angle       0.34839 (    6)
  hydrogen bonds       : bond        0.20469 (  429)
  hydrogen bonds       : angle       7.38399 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.211 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 139
  average time/residue: 0.0939
  time to fit residues: 17.6688
Evaluate side-chains
  131 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  268 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.0270
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.2044

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 110 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  25 ASN
R 148 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.161613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115945 restraints weight = 9832.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.30
r_work: 0.3108 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8959  Z= 0.160
  Angle     :  0.537   8.154  12154  Z= 0.286
  Chirality :  0.042   0.143   1378
  Planarity :  0.004   0.064   1536
  Dihedral  :  4.789  57.515   1314
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.17 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1099
  helix:  1.86 (0.26), residues: 379
  sheet:  0.20 (0.31), residues: 272
  loop :  0.29 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.019   0.002   TYR B  59 
 PHE   0.024   0.002   PHE R  18 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8956)
  covalent geometry    : angle       0.53726 (12148)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       0.62344 (    6)
  hydrogen bonds       : bond        0.04424 (  429)
  hydrogen bonds       : angle       4.92736 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  199 ASP cc_start: 0.8144 (m-30) cc_final: 0.7692 (m-30)
REVERT: B   59 TYR cc_start: 0.8472 (m-80) cc_final: 0.7563 (m-80)
REVERT: N   87 ARG cc_start: 0.6903 (ptp-170) cc_final: 0.6675 (ptp-170)
  outliers start: 27
  outliers final: 18
  residues processed: 155
  average time/residue: 0.0911
  time to fit residues: 19.1679
Evaluate side-chains
  147 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 34 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.163167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118641 restraints weight = 9751.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.17
r_work: 0.3122 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8959  Z= 0.117
  Angle     :  0.497   9.541  12154  Z= 0.260
  Chirality :  0.041   0.168   1378
  Planarity :  0.004   0.061   1536
  Dihedral  :  4.476  58.296   1312
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 20.49 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.17 (0.25), residues: 1099
  helix:  2.06 (0.26), residues: 379
  sheet:  0.04 (0.31), residues: 273
  loop :  0.26 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.017   0.001   TYR R 165 
 PHE   0.018   0.001   PHE R  18 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8956)
  covalent geometry    : angle       0.49747 (12148)
  SS BOND              : bond        0.00227 (    3)
  SS BOND              : angle       0.35259 (    6)
  hydrogen bonds       : bond        0.03746 (  429)
  hydrogen bonds       : angle       4.57257 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  199 ASP cc_start: 0.8100 (m-30) cc_final: 0.7696 (m-30)
REVERT: B   59 TYR cc_start: 0.8496 (m-80) cc_final: 0.7632 (m-80)
REVERT: R  106 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7341 (tm-30)
  outliers start: 30
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0783
  time to fit residues: 16.8180
Evaluate side-chains
  151 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0570
   chunk 109 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.8702

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
B  32 GLN
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.162280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116183 restraints weight = 9811.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.23
r_work: 0.3102 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8959  Z= 0.123
  Angle     :  0.492   8.343  12154  Z= 0.256
  Chirality :  0.041   0.177   1378
  Planarity :  0.004   0.059   1536
  Dihedral  :  4.377  53.177   1312
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.28 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.28 (0.25), residues: 1099
  helix:  2.26 (0.26), residues: 374
  sheet:  0.04 (0.30), residues: 273
  loop :  0.29 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.016   0.001   TYR R 165 
 PHE   0.019   0.001   PHE N  68 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8956)
  covalent geometry    : angle       0.49211 (12148)
  SS BOND              : bond        0.00145 (    3)
  SS BOND              : angle       0.37119 (    6)
  hydrogen bonds       : bond        0.03461 (  429)
  hydrogen bonds       : angle       4.40141 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 144
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8141 (mp)
REVERT: A  199 ASP cc_start: 0.8082 (m-30) cc_final: 0.7639 (m-30)
REVERT: B   59 TYR cc_start: 0.8541 (m-80) cc_final: 0.7720 (m-80)
REVERT: B  338 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8536 (mm)
REVERT: N  161 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7087 (mtp85)
REVERT: R  106 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7401 (tm-30)
  outliers start: 35
  outliers final: 23
  residues processed: 162
  average time/residue: 0.0861
  time to fit residues: 19.2105
Evaluate side-chains
  161 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0470
   chunk 91 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 48 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** 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 = 0.3833 r_free = 0.3833 target = 0.163556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117113 restraints weight = 9750.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.25
r_work: 0.3129 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8959  Z= 0.106
  Angle     :  0.482   9.280  12154  Z= 0.249
  Chirality :  0.041   0.181   1378
  Planarity :  0.003   0.058   1536
  Dihedral  :  4.227  46.695   1312
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 20.81 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1099
  helix:  2.30 (0.26), residues: 380
  sheet:  0.11 (0.30), residues: 283
  loop :  0.30 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 194 
 TYR   0.016   0.001   TYR R 165 
 PHE   0.023   0.001   PHE N  68 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.002   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8956)
  covalent geometry    : angle       0.48173 (12148)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       0.27499 (    6)
  hydrogen bonds       : bond        0.03235 (  429)
  hydrogen bonds       : angle       4.28982 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8144 (mp)
REVERT: A  132 ARG cc_start: 0.8478 (mtm180) cc_final: 0.7960 (ptt180)
REVERT: A  199 ASP cc_start: 0.8012 (m-30) cc_final: 0.7591 (m-30)
REVERT: B   59 TYR cc_start: 0.8561 (m-80) cc_final: 0.7781 (m-80)
REVERT: B  338 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8514 (mm)
REVERT: N  161 ARG cc_start: 0.7720 (ttp-110) cc_final: 0.7087 (mtp85)
REVERT: N  192 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7036 (mtt180)
REVERT: N  231 MET cc_start: 0.9279 (ttt) cc_final: 0.9032 (ttp)
REVERT: R   45 HIS cc_start: 0.7347 (m90) cc_final: 0.6689 (m90)
REVERT: R  106 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7446 (tm-30)
  outliers start: 36
  outliers final: 25
  residues processed: 157
  average time/residue: 0.0897
  time to fit residues: 18.9262
Evaluate side-chains
  158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  192 ARG
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  230 ASN
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 86 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 92 optimal weight:   20.0000
   chunk 97 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.160545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113740 restraints weight = 9761.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.23
r_work: 0.3070 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8959  Z= 0.154
  Angle     :  0.510   9.789  12154  Z= 0.264
  Chirality :  0.042   0.156   1378
  Planarity :  0.004   0.053   1536
  Dihedral  :  4.459  42.816   1312
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.81 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.36 (0.26), residues: 1099
  helix:  2.34 (0.26), residues: 380
  sheet:  0.06 (0.30), residues: 282
  loop :  0.30 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.015   0.001   TYR R 165 
 PHE   0.024   0.001   PHE R  18 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8956)
  covalent geometry    : angle       0.51048 (12148)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       0.47581 (    6)
  hydrogen bonds       : bond        0.03410 (  429)
  hydrogen bonds       : angle       4.39058 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 135
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8134 (mp)
REVERT: A  132 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7985 (ptt180)
REVERT: A  199 ASP cc_start: 0.8103 (m-30) cc_final: 0.7634 (m-30)
REVERT: B   59 TYR cc_start: 0.8626 (m-80) cc_final: 0.7979 (m-80)
REVERT: B  338 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8562 (mm)
REVERT: N  161 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7119 (mtp85)
REVERT: N  192 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7030 (mtt90)
REVERT: R   45 HIS cc_start: 0.7503 (m90) cc_final: 0.6946 (m90)
REVERT: R  106 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7479 (tm-30)
  outliers start: 43
  outliers final: 31
  residues processed: 161
  average time/residue: 0.0888
  time to fit residues: 19.4319
Evaluate side-chains
  165 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  115 TYR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  192 ARG
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  230 ASN
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0470
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.9282

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.161306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114828 restraints weight = 9787.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.22
r_work: 0.3089 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8959  Z= 0.127
  Angle     :  0.499   8.975  12154  Z= 0.259
  Chirality :  0.041   0.189   1378
  Planarity :  0.003   0.051   1536
  Dihedral  :  4.356  37.094   1312
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 21.02 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.42 (0.26), residues: 1099
  helix:  2.38 (0.26), residues: 380
  sheet:  0.07 (0.30), residues: 287
  loop :  0.39 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.015   0.001   TYR R 165 
 PHE   0.020   0.001   PHE N  68 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8956)
  covalent geometry    : angle       0.49942 (12148)
  SS BOND              : bond        0.00141 (    3)
  SS BOND              : angle       0.35091 (    6)
  hydrogen bonds       : bond        0.03247 (  429)
  hydrogen bonds       : angle       4.31434 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8120 (mp)
REVERT: A  132 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7974 (ptt180)
REVERT: A  199 ASP cc_start: 0.8110 (m-30) cc_final: 0.7674 (m-30)
REVERT: B   59 TYR cc_start: 0.8629 (m-80) cc_final: 0.7947 (m-80)
REVERT: B  259 GLN cc_start: 0.8484 (pt0) cc_final: 0.8209 (pt0)
REVERT: B  338 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8542 (mm)
REVERT: N  161 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7107 (mtp85)
REVERT: N  192 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6895 (mtt90)
REVERT: R   45 HIS cc_start: 0.7483 (m90) cc_final: 0.6888 (m90)
REVERT: R  106 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7458 (tm-30)
  outliers start: 42
  outliers final: 31
  residues processed: 156
  average time/residue: 0.0837
  time to fit residues: 18.0997
Evaluate side-chains
  163 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  115 TYR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  192 ARG
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  230 ASN
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0070
   chunk 109 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0670
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.163905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.117818 restraints weight = 9730.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.22
r_work: 0.3140 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8959  Z= 0.096
  Angle     :  0.479   8.706  12154  Z= 0.247
  Chirality :  0.040   0.191   1378
  Planarity :  0.003   0.050   1536
  Dihedral  :  4.041  27.147   1312
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.13 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.53 (0.26), residues: 1099
  helix:  2.51 (0.26), residues: 380
  sheet:  0.12 (0.30), residues: 287
  loop :  0.40 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.014   0.001   TYR R 165 
 PHE   0.022   0.001   PHE R  18 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8956)
  covalent geometry    : angle       0.47933 (12148)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       0.24056 (    6)
  hydrogen bonds       : bond        0.03018 (  429)
  hydrogen bonds       : angle       4.14162 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: A  132 ARG cc_start: 0.8441 (mtm180) cc_final: 0.8047 (ptt180)
REVERT: B   59 TYR cc_start: 0.8603 (m-80) cc_final: 0.7867 (m-80)
REVERT: B  338 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8516 (mm)
REVERT: N  161 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7072 (mtp85)
REVERT: N  192 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7081 (mtt180)
REVERT: N  231 MET cc_start: 0.9265 (ttt) cc_final: 0.9043 (ttp)
REVERT: R   12 MET cc_start: 0.7504 (ptm) cc_final: 0.7233 (ptm)
REVERT: R   45 HIS cc_start: 0.7336 (m90) cc_final: 0.6681 (m90)
REVERT: R  106 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7440 (tm-30)
REVERT: R  187 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7727 (mp)
  outliers start: 40
  outliers final: 27
  residues processed: 159
  average time/residue: 0.0944
  time to fit residues: 20.4556
Evaluate side-chains
  155 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  192 ARG
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  187 LEU
Chi-restraints excluded: chain R residue  230 ASN
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0370
   chunk 67 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.162825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.116403 restraints weight = 9682.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.22
r_work: 0.3118 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8959  Z= 0.115
  Angle     :  0.494   9.824  12154  Z= 0.255
  Chirality :  0.041   0.174   1378
  Planarity :  0.003   0.051   1536
  Dihedral  :  4.067  27.171   1312
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.77 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.52 (0.26), residues: 1099
  helix:  2.55 (0.26), residues: 380
  sheet:  0.16 (0.30), residues: 287
  loop :  0.34 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.014   0.001   TYR R 165 
 PHE   0.021   0.001   PHE R  18 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8956)
  covalent geometry    : angle       0.49426 (12148)
  SS BOND              : bond        0.00147 (    3)
  SS BOND              : angle       0.30665 (    6)
  hydrogen bonds       : bond        0.03120 (  429)
  hydrogen bonds       : angle       4.18000 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (mp)
REVERT: A  132 ARG cc_start: 0.8452 (mtm180) cc_final: 0.8048 (ptt180)
REVERT: B   59 TYR cc_start: 0.8653 (m-80) cc_final: 0.7972 (m-80)
REVERT: B  338 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8503 (mm)
REVERT: N  161 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.7062 (mtp85)
REVERT: N  192 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6975 (mtt180)
REVERT: R   12 MET cc_start: 0.7492 (ptm) cc_final: 0.7252 (ptm)
REVERT: R   45 HIS cc_start: 0.7368 (m90) cc_final: 0.6683 (m90)
REVERT: R  106 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7459 (tm-30)
REVERT: R  187 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7743 (mp)
  outliers start: 36
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0913
  time to fit residues: 18.0564
Evaluate side-chains
  155 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  192 ARG
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  187 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  230 ASN
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 66 optimal weight:    0.4980
   chunk 109 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.162676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116378 restraints weight = 9685.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.20
r_work: 0.3119 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8959  Z= 0.117
  Angle     :  0.495   9.404  12154  Z= 0.256
  Chirality :  0.041   0.179   1378
  Planarity :  0.003   0.051   1536
  Dihedral  :  4.091  26.914   1312
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.56 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.52 (0.26), residues: 1099
  helix:  2.62 (0.26), residues: 375
  sheet:  0.13 (0.30), residues: 276
  loop :  0.29 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.013   0.001   TYR R 165 
 PHE   0.022   0.001   PHE R  18 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8956)
  covalent geometry    : angle       0.49541 (12148)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       0.29234 (    6)
  hydrogen bonds       : bond        0.03119 (  429)
  hydrogen bonds       : angle       4.19360 ( 1218)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 119
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8059 (mp)
REVERT: A  132 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8037 (ptt180)
REVERT: B  338 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8501 (mm)
REVERT: N  161 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7071 (mtp85)
REVERT: N  192 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.6994 (mtt180)
REVERT: R   12 MET cc_start: 0.7508 (ptm) cc_final: 0.7257 (ptm)
REVERT: R   45 HIS cc_start: 0.7377 (m90) cc_final: 0.6712 (m90)
REVERT: R  106 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7455 (tm-30)
REVERT: R  187 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7771 (mp)
  outliers start: 37
  outliers final: 31
  residues processed: 142
  average time/residue: 0.0942
  time to fit residues: 18.1251
Evaluate side-chains
  153 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  115 TYR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  192 ARG
Chi-restraints excluded: chain N residue  193 MET
Chi-restraints excluded: chain N residue  198 SER
Chi-restraints excluded: chain R residue  106 GLU
Chi-restraints excluded: chain R residue  187 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  230 ASN
Chi-restraints excluded: chain R residue  257 ILE
Chi-restraints excluded: chain R residue  260 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.160527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113832 restraints weight = 9745.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.23
r_work: 0.3079 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8959  Z= 0.157
  Angle     :  0.522   9.842  12154  Z= 0.271
  Chirality :  0.042   0.182   1378
  Planarity :  0.004   0.051   1536
  Dihedral  :  4.308  27.547   1312
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.56 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 aren not related in a simple way.
  whole:  1.44 (0.26), residues: 1099
  helix:  2.48 (0.26), residues: 381
  sheet:  0.08 (0.30), residues: 274
  loop :  0.29 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.013   0.001   TYR R 165 
 PHE   0.022   0.001   PHE R  18 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8956)
  covalent geometry    : angle       0.52221 (12148)
  SS BOND              : bond        0.00110 (    3)
  SS BOND              : angle       0.48406 (    6)
  hydrogen bonds       : bond        0.03310 (  429)
  hydrogen bonds       : angle       4.30811 ( 1218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2259.37 seconds
wall clock time: 39 minutes 19.13 seconds (2359.13 seconds total)