Starting phenix.real_space_refine
on Wed Sep 17 16:29:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjh_39342/09_2025/8yjh_39342.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjh_39342/09_2025/8yjh_39342.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjh_39342/09_2025/8yjh_39342.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjh_39342/09_2025/8yjh_39342.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjh_39342/09_2025/8yjh_39342.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjh_39342/09_2025/8yjh_39342.cif"
  }
  resolution = 3.68
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      53      5.49       5
     S      63      5.16       5
     C    5965      2.51       5
     N    1631      2.21       5
     O    2023      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9735
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1963
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "C"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1963
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "J"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 308
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "E"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "F"
      Number of atoms: 205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 205
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 2.25, per 1000 atoms: 0.23
  Number of scatterers: 9735
  At special positions: 0
  Unit cell: (106.24, 95.45, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P      53     15.00
     O    2023      8.00
     N    1631      7.00
     C    5965      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " 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: 0.75
  Conformation dependent library (CDL) restraints added in 336.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2106

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      28.9% alpha, 25.4% beta
      14 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 19
      removed outlier: 4.262A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 81
    Processing helix  chain 'B' and resid 141 through 152
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.975A  pdb=" N   LEU B 221 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B 222 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 218 through 222'
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.729A  pdb=" N   LYS C  13 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 141 through 153
    Processing helix  chain 'C' and resid 209 through 217
    Processing helix  chain 'C' and resid 218 through 222
      removed outlier: 3.528A  pdb=" N   LEU C 221 " --> pdb=" O   ALA C 218 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER C 222 " --> pdb=" O   THR C 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 218 through 222'
    Processing helix  chain 'A' and resid 8 through 19
      removed outlier: 4.365A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing helix  chain 'D' and resid 5 through 14
    Processing helix  chain 'D' and resid 35 through 45
      removed outlier: 3.744A  pdb=" N   ALA D  45 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 76
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 3.711A  pdb=" N   GLN D 112 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLN D 113 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 128
    Processing helix  chain 'D' and resid 134 through 149
      removed outlier: 3.561A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
      removed outlier: 3.767A  pdb=" N   SER D 162 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 185
      removed outlier: 3.967A  pdb=" N   THR D 184 " --> pdb=" O   MET D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 216
    Processing helix  chain 'D' and resid 219 through 231
    Processing helix  chain 'D' and resid 242 through 252
      removed outlier: 3.650A  pdb=" N   VAL D 247 " --> pdb=" O   PRO D 243 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASP D 248 " --> pdb=" O   LYS D 244 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LYS D 252 " --> pdb=" O   ASP D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 263
      removed outlier: 3.744A  pdb=" N   ILE D 259 " --> pdb=" O   SER D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 285
      removed outlier: 3.503A  pdb=" N   PHE D 283 " --> pdb=" O   ALA D 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 312
    Processing helix  chain 'D' and resid 317 through 332
      removed outlier: 3.836A  pdb=" N   ILE D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61
    Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71
      removed outlier: 3.713A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B  47 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU B 238 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 112
      removed outlier: 3.563A  pdb=" N   VAL B 111 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 207
      removed outlier: 4.523A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE C  88 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 71
      removed outlier: 3.863A  pdb=" N   ALA C  26 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY C 245 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU C 251 " --> pdb=" O   LEU C 235 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU C 238 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL C 136 " --> pdb=" O   GLU C 198 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLU C 198 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 127
      removed outlier: 3.753A  pdb=" N   GLY D 348 " --> pdb=" O   GLN C 125 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLY C 127 " --> pdb=" O   VAL D 346 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL D 346 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 208
      removed outlier: 4.863A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU A  99 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A  59 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71
      removed outlier: 3.620A  pdb=" N   MET A  68 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY A  34 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY A 245 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR A 249 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER A 228 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   THR A 224 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 136 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLU A 198 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21
      removed outlier: 3.571A  pdb=" N   ARG D  19 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE D 204 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154
      removed outlier: 6.799A  pdb=" N   LYS D  30 " --> pdb=" O   ALA D 174 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ALA D 176 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   ALA D  32 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2732
        1.34 -     1.46: 2131
        1.46 -     1.58: 4920
        1.58 -     1.70: 102
        1.70 -     1.82: 102
  Bond restraints: 9987
  Sorted by residual:
  bond pdb=" C   THR C 219 "
       pdb=" N   PRO C 220 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 9.40e-03 1.13e+04 8.22e+00
  bond pdb=" CB  ASP C 113 "
       pdb=" CG  ASP C 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.66e+00
  bond pdb=" CB  GLU B 132 "
       pdb=" CG  GLU B 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.579 -0.059 3.00e-02 1.11e+03 3.91e+00
  bond pdb=" CB  ASP A 113 "
       pdb=" CG  ASP A 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.38e+00
  bond pdb=" CB  GLU B 174 "
       pdb=" CG  GLU B 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.31e+00
  ... (remaining 9982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 13130
        2.27 -     4.53: 441
        4.53 -     6.80: 78
        6.80 -     9.06: 37
        9.06 -    11.33: 10
  Bond angle restraints: 13696
  Sorted by residual:
  angle pdb=" CA  GLU B 132 "
        pdb=" CB  GLU B 132 "
        pdb=" CG  GLU B 132 "
      ideal   model   delta    sigma   weight residual
     114.10  123.74   -9.64 2.00e+00 2.50e-01 2.32e+01
  angle pdb=" C   ALA A 242 "
        pdb=" N   ASP A 243 "
        pdb=" CA  ASP A 243 "
      ideal   model   delta    sigma   weight residual
     121.54  130.43   -8.89 1.91e+00 2.74e-01 2.16e+01
  angle pdb=" O   GLN A 131 "
        pdb=" C   GLN A 131 "
        pdb=" N   GLU A 132 "
      ideal   model   delta    sigma   weight residual
     122.39  128.16   -5.77 1.29e+00 6.01e-01 2.00e+01
  angle pdb=" C   LYS B 254 "
        pdb=" N   ILE B 255 "
        pdb=" CA  ILE B 255 "
      ideal   model   delta    sigma   weight residual
     121.70  129.65   -7.95 1.80e+00 3.09e-01 1.95e+01
  angle pdb=" CA  GLU A 132 "
        pdb=" CB  GLU A 132 "
        pdb=" CG  GLU A 132 "
      ideal   model   delta    sigma   weight residual
     114.10  122.26   -8.16 2.00e+00 2.50e-01 1.66e+01
  ... (remaining 13691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 5024
       17.60 -    35.19: 688
       35.19 -    52.79: 280
       52.79 -    70.38: 48
       70.38 -    87.98: 13
  Dihedral angle restraints: 6053
    sinusoidal: 2807
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" CA  MET C 199 "
           pdb=" C   MET C 199 "
           pdb=" N   ASN C 200 "
           pdb=" CA  ASN C 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.09   23.91     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  ASN B  71 "
           pdb=" C   ASN B  71 "
           pdb=" N   LEU B  72 "
           pdb=" CA  LEU B  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.78  -23.22     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  ILE D  33 "
           pdb=" C   ILE D  33 "
           pdb=" N   ASP D  34 "
           pdb=" CA  ASP D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.56   22.44     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 6050 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1181
       0.054 -    0.108: 290
       0.108 -    0.162: 80
       0.162 -    0.216: 21
       0.216 -    0.270: 6
  Chirality restraints: 1578
  Sorted by residual:
  chirality pdb=" CA  THR A 219 "
            pdb=" N   THR A 219 "
            pdb=" C   THR A 219 "
            pdb=" CB  THR A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL A 236 "
            pdb=" CA  VAL A 236 "
            pdb=" CG1 VAL A 236 "
            pdb=" CG2 VAL A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  ILE D  44 "
            pdb=" CA  ILE D  44 "
            pdb=" CG1 ILE D  44 "
            pdb=" CG2 ILE D  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1575 not shown)

  Planarity restraints: 1583
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 274 "   -0.020 2.00e-02 2.50e+03   2.32e-02 1.35e+01
        pdb=" CG  TRP D 274 "    0.062 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 274 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 274 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 274 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 132 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.92e+00
        pdb=" C   GLU A 132 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLU A 132 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 133 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A   5 "   -0.236 9.50e-02 1.11e+02   1.07e-01 8.83e+00
        pdb=" NE  ARG A   5 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A   5 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG A   5 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A   5 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1580 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1834
        2.79 -     3.31: 8023
        3.31 -     3.84: 17211
        3.84 -     4.37: 19369
        4.37 -     4.90: 32874
  Nonbonded interactions: 79311
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 192 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   THR C 216 "
            pdb=" OG1 THR C 219 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OH  TYR C 211 "
            pdb=" O   SER D  25 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" O   ASN B  71 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.366 3.040
  ... (remaining 79306 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 1 through 254)
  selection = (chain 'C' and resid 1 through 254)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.390
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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   0.062   9988  Z= 0.237
  Angle     :  1.042  11.331  13698  Z= 0.537
  Chirality :  0.056   0.270   1578
  Planarity :  0.007   0.107   1583
  Dihedral  : 18.972  87.975   3944
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.68 (0.21), residues: 1107
  helix: -2.74 (0.20), residues: 307
  sheet: -2.02 (0.27), residues: 331
  loop : -2.36 (0.23), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A   5 
 TYR   0.022   0.003   TYR B 133 
 PHE   0.037   0.003   PHE D  27 
 TRP   0.062   0.004   TRP D 274 
 HIS   0.007   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 9987)
  covalent geometry    : angle       1.04158 (13696)
  SS BOND              : bond        0.00363 (    1)
  SS BOND              : angle       2.40126 (    2)
  hydrogen bonds       : bond        0.19943 (  431)
  hydrogen bonds       : angle       9.94013 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.377 
Fit side-chains
REVERT: B  184 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6491 (tm-30)
REVERT: C  201 GLU cc_start: 0.7192 (pt0) cc_final: 0.6920 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0716
  time to fit residues: 18.0645
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0870
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
C 246 HIS
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.142065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.110774 restraints weight = 14626.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.113834 restraints weight = 10979.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.114482 restraints weight = 7446.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114739 restraints weight = 6953.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.116575 restraints weight = 6311.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9988  Z= 0.184
  Angle     :  0.625   5.775  13698  Z= 0.337
  Chirality :  0.045   0.170   1578
  Planarity :  0.004   0.036   1583
  Dihedral  : 19.328  73.389   1802
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.88 %
    Favored  : 89.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.22), residues: 1107
  helix: -0.70 (0.27), residues: 304
  sheet: -1.80 (0.27), residues: 327
  loop : -1.95 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A   5 
 TYR   0.014   0.002   TYR B 133 
 PHE   0.012   0.002   PHE D 126 
 TRP   0.025   0.002   TRP D 274 
 HIS   0.010   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9987)
  covalent geometry    : angle       0.62451 (13696)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       1.17608 (    2)
  hydrogen bonds       : bond        0.03959 (  431)
  hydrogen bonds       : angle       6.59806 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7785 (t0) cc_final: 0.7525 (t0)
REVERT: B  184 GLN cc_start: 0.7025 (tm-30) cc_final: 0.6809 (tm-30)
REVERT: C    1 MET cc_start: 0.7599 (tpp) cc_final: 0.7381 (tpp)
REVERT: C  201 GLU cc_start: 0.7338 (pt0) cc_final: 0.7102 (pt0)
REVERT: A   68 MET cc_start: 0.8057 (ptp) cc_final: 0.7824 (ptp)
REVERT: A  135 CYS cc_start: 0.8144 (p) cc_final: 0.7869 (p)
REVERT: D  127 THR cc_start: 0.8840 (p) cc_final: 0.8546 (t)
REVERT: D  202 LEU cc_start: 0.7498 (mm) cc_final: 0.7173 (mt)
REVERT: D  326 LYS cc_start: 0.8007 (pttm) cc_final: 0.7399 (mmtp)
  outliers start: 11
  outliers final: 7
  residues processed: 147
  average time/residue: 0.0791
  time to fit residues: 17.4958
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue  256 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.138875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.106969 restraints weight = 14670.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.109681 restraints weight = 9794.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.111581 restraints weight = 7359.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.112474 restraints weight = 6026.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.113693 restraints weight = 5338.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9988  Z= 0.185
  Angle     :  0.598   8.413  13698  Z= 0.316
  Chirality :  0.044   0.236   1578
  Planarity :  0.003   0.040   1583
  Dihedral  : 18.872  75.954   1802
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.25 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.01 (0.23), residues: 1107
  helix: -0.08 (0.28), residues: 307
  sheet: -1.77 (0.26), residues: 329
  loop : -1.72 (0.25), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   5 
 TYR   0.017   0.002   TYR B 133 
 PHE   0.010   0.002   PHE D 126 
 TRP   0.020   0.002   TRP D 274 
 HIS   0.005   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9987)
  covalent geometry    : angle       0.59778 (13696)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       0.68377 (    2)
  hydrogen bonds       : bond        0.03728 (  431)
  hydrogen bonds       : angle       6.12879 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.269 
Fit side-chains
REVERT: B   36 ASN cc_start: 0.8463 (m-40) cc_final: 0.8216 (m-40)
REVERT: B  177 ASN cc_start: 0.7803 (t0) cc_final: 0.7548 (t0)
REVERT: B  199 MET cc_start: 0.7370 (tmm) cc_final: 0.7093 (tmm)
REVERT: C    1 MET cc_start: 0.7627 (tpp) cc_final: 0.7350 (tpp)
REVERT: A   68 MET cc_start: 0.7993 (ptp) cc_final: 0.7772 (ptp)
REVERT: A  135 CYS cc_start: 0.8156 (p) cc_final: 0.7827 (p)
REVERT: D   40 TYR cc_start: 0.7861 (m-10) cc_final: 0.7484 (m-10)
REVERT: D   44 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: D  139 ASP cc_start: 0.7013 (m-30) cc_final: 0.6798 (m-30)
REVERT: D  202 LEU cc_start: 0.7664 (mm) cc_final: 0.7446 (mt)
REVERT: D  326 LYS cc_start: 0.8202 (pttm) cc_final: 0.7548 (mmtp)
  outliers start: 19
  outliers final: 11
  residues processed: 139
  average time/residue: 0.0858
  time to fit residues: 17.6148
Evaluate side-chains
  128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0030
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.140151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.108628 restraints weight = 14591.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.111352 restraints weight = 9648.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.113338 restraints weight = 7223.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.114752 restraints weight = 5876.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115674 restraints weight = 5057.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9988  Z= 0.140
  Angle     :  0.558   8.540  13698  Z= 0.296
  Chirality :  0.043   0.226   1578
  Planarity :  0.003   0.033   1583
  Dihedral  : 18.667  75.709   1802
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.90 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.24), residues: 1107
  helix:  0.43 (0.29), residues: 306
  sheet: -1.88 (0.27), residues: 301
  loop : -1.49 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 211 
 TYR   0.014   0.002   TYR A 250 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.041   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9987)
  covalent geometry    : angle       0.55809 (13696)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.55883 (    2)
  hydrogen bonds       : bond        0.03131 (  431)
  hydrogen bonds       : angle       5.77096 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.233 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7834 (t0) cc_final: 0.7613 (t0)
REVERT: B  184 GLN cc_start: 0.7207 (pp30) cc_final: 0.6877 (pp30)
REVERT: A  135 CYS cc_start: 0.8097 (p) cc_final: 0.7835 (p)
REVERT: A  141 SER cc_start: 0.8302 (p) cc_final: 0.8077 (t)
REVERT: D   40 TYR cc_start: 0.7938 (m-10) cc_final: 0.7538 (m-10)
REVERT: D   44 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8555 (mp)
REVERT: D  127 THR cc_start: 0.8949 (p) cc_final: 0.8654 (t)
REVERT: D  326 LYS cc_start: 0.8228 (pttm) cc_final: 0.7646 (mmtp)
  outliers start: 23
  outliers final: 14
  residues processed: 141
  average time/residue: 0.0837
  time to fit residues: 17.4701
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 74 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.138475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.106949 restraints weight = 14514.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.109600 restraints weight = 9616.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.111507 restraints weight = 7225.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.112849 restraints weight = 5900.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.113769 restraints weight = 5124.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9988  Z= 0.166
  Angle     :  0.588   9.933  13698  Z= 0.306
  Chirality :  0.044   0.240   1578
  Planarity :  0.003   0.030   1583
  Dihedral  : 18.583  72.850   1802
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.04 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.24), residues: 1107
  helix:  0.62 (0.29), residues: 305
  sheet: -1.87 (0.27), residues: 301
  loop : -1.37 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.015   0.002   TYR A 250 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.023   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9987)
  covalent geometry    : angle       0.58789 (13696)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.89568 (    2)
  hydrogen bonds       : bond        0.03267 (  431)
  hydrogen bonds       : angle       5.67804 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7867 (t0) cc_final: 0.7649 (t0)
REVERT: B  184 GLN cc_start: 0.7425 (pp30) cc_final: 0.7087 (pp30)
REVERT: B  199 MET cc_start: 0.7340 (tmm) cc_final: 0.7112 (tpt)
REVERT: C   91 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6202 (mtm110)
REVERT: A  135 CYS cc_start: 0.8137 (p) cc_final: 0.7865 (p)
REVERT: A  141 SER cc_start: 0.8317 (p) cc_final: 0.8057 (t)
REVERT: D   40 TYR cc_start: 0.7939 (m-10) cc_final: 0.7549 (m-10)
REVERT: D   44 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8539 (mp)
REVERT: D  127 THR cc_start: 0.9001 (p) cc_final: 0.8709 (t)
REVERT: D  326 LYS cc_start: 0.8347 (pttm) cc_final: 0.7681 (mmtp)
  outliers start: 27
  outliers final: 17
  residues processed: 142
  average time/residue: 0.0813
  time to fit residues: 17.4099
Evaluate side-chains
  138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 74 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 96 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.147075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.116502 restraints weight = 14629.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.119756 restraints weight = 10354.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.121012 restraints weight = 7452.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.121101 restraints weight = 6627.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.121403 restraints weight = 6395.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9988  Z= 0.151
  Angle     :  0.568  10.176  13698  Z= 0.298
  Chirality :  0.043   0.233   1578
  Planarity :  0.003   0.029   1583
  Dihedral  : 18.476  72.605   1802
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.48 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.25), residues: 1107
  helix:  0.75 (0.29), residues: 305
  sheet: -1.82 (0.27), residues: 309
  loop : -1.27 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 211 
 TYR   0.015   0.002   TYR A 250 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.022   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9987)
  covalent geometry    : angle       0.56840 (13696)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.79443 (    2)
  hydrogen bonds       : bond        0.03102 (  431)
  hydrogen bonds       : angle       5.55787 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.305 
Fit side-chains
REVERT: B  119 MET cc_start: 0.7469 (pmm) cc_final: 0.6227 (pmm)
REVERT: B  177 ASN cc_start: 0.7870 (t0) cc_final: 0.7659 (t0)
REVERT: B  184 GLN cc_start: 0.7506 (pp30) cc_final: 0.7174 (pp30)
REVERT: C   91 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6211 (mtm110)
REVERT: A  141 SER cc_start: 0.8279 (p) cc_final: 0.8032 (t)
REVERT: D   44 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: D  127 THR cc_start: 0.8987 (p) cc_final: 0.8734 (t)
REVERT: D  326 LYS cc_start: 0.8374 (pttm) cc_final: 0.7731 (mmtp)
  outliers start: 30
  outliers final: 21
  residues processed: 142
  average time/residue: 0.0794
  time to fit residues: 16.8531
Evaluate side-chains
  141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  256 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 110 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.144035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.113091 restraints weight = 14750.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.116998 restraints weight = 10714.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.117819 restraints weight = 7607.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.117862 restraints weight = 6543.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.118114 restraints weight = 6599.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9988  Z= 0.223
  Angle     :  0.633  11.119  13698  Z= 0.328
  Chirality :  0.045   0.244   1578
  Planarity :  0.003   0.030   1583
  Dihedral  : 18.559  73.175   1802
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.89 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.46 (0.25), residues: 1107
  helix:  0.60 (0.29), residues: 305
  sheet: -1.88 (0.27), residues: 305
  loop : -1.25 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 211 
 TYR   0.018   0.002   TYR A 250 
 PHE   0.012   0.002   PHE D 126 
 TRP   0.021   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 9987)
  covalent geometry    : angle       0.63256 (13696)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       1.31956 (    2)
  hydrogen bonds       : bond        0.03583 (  431)
  hydrogen bonds       : angle       5.79419 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.391 
Fit side-chains
REVERT: B  119 MET cc_start: 0.7523 (pmm) cc_final: 0.7306 (pmm)
REVERT: B  177 ASN cc_start: 0.7914 (t0) cc_final: 0.7657 (t0)
REVERT: B  184 GLN cc_start: 0.7605 (pp30) cc_final: 0.7321 (pp30)
REVERT: C   91 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6278 (mtm110)
REVERT: C  175 LEU cc_start: 0.9045 (tp) cc_final: 0.8818 (tt)
REVERT: A  135 CYS cc_start: 0.8202 (p) cc_final: 0.7923 (p)
REVERT: D   44 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: D  127 THR cc_start: 0.9056 (p) cc_final: 0.8787 (t)
REVERT: D  152 TYR cc_start: 0.8605 (p90) cc_final: 0.8254 (p90)
  outliers start: 32
  outliers final: 25
  residues processed: 142
  average time/residue: 0.0860
  time to fit residues: 18.1228
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  199 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  270 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.146055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.115668 restraints weight = 14789.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.118543 restraints weight = 9986.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.120473 restraints weight = 7558.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.121815 restraints weight = 6220.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.122613 restraints weight = 5410.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9988  Z= 0.159
  Angle     :  0.594  10.066  13698  Z= 0.311
  Chirality :  0.044   0.179   1578
  Planarity :  0.003   0.029   1583
  Dihedral  : 18.482  73.724   1802
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.44 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.25), residues: 1107
  helix:  0.74 (0.30), residues: 305
  sheet: -1.90 (0.27), residues: 294
  loop : -1.24 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.016   0.002   TYR A 250 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.020   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9987)
  covalent geometry    : angle       0.59412 (13696)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.94186 (    2)
  hydrogen bonds       : bond        0.03188 (  431)
  hydrogen bonds       : angle       5.62636 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.360 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7926 (t0) cc_final: 0.7697 (t0)
REVERT: C   91 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6253 (mtm110)
REVERT: A  141 SER cc_start: 0.8272 (p) cc_final: 0.8021 (t)
REVERT: D   44 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8563 (mp)
REVERT: D  127 THR cc_start: 0.9149 (p) cc_final: 0.8932 (t)
REVERT: D  152 TYR cc_start: 0.8578 (p90) cc_final: 0.8219 (p90)
REVERT: D  326 LYS cc_start: 0.8632 (pttt) cc_final: 0.7598 (mmtp)
  outliers start: 28
  outliers final: 24
  residues processed: 144
  average time/residue: 0.0810
  time to fit residues: 17.5187
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  199 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain D residue  284 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 13 optimal weight:    0.1980
   chunk 43 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.146378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.115126 restraints weight = 14781.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.118538 restraints weight = 10417.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.119306 restraints weight = 7465.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.119861 restraints weight = 6718.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.120283 restraints weight = 6348.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9988  Z= 0.157
  Angle     :  0.600   9.867  13698  Z= 0.312
  Chirality :  0.044   0.192   1578
  Planarity :  0.003   0.029   1583
  Dihedral  : 18.427  74.466   1802
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.54 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.25), residues: 1107
  helix:  0.75 (0.30), residues: 309
  sheet: -1.81 (0.26), residues: 307
  loop : -1.17 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.014   0.002   TYR A 250 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.019   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9987)
  covalent geometry    : angle       0.59965 (13696)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       1.08871 (    2)
  hydrogen bonds       : bond        0.03188 (  431)
  hydrogen bonds       : angle       5.58058 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.380 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7969 (t0) cc_final: 0.7768 (t0)
REVERT: C   91 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6225 (mtm110)
REVERT: D   44 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8579 (mp)
REVERT: D  127 THR cc_start: 0.9050 (p) cc_final: 0.8812 (t)
REVERT: D  326 LYS cc_start: 0.8594 (pttt) cc_final: 0.7550 (mmtp)
  outliers start: 28
  outliers final: 24
  residues processed: 141
  average time/residue: 0.0865
  time to fit residues: 18.0636
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  199 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 110 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.145869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.114611 restraints weight = 14717.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.117693 restraints weight = 9642.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.119851 restraints weight = 7182.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.121295 restraints weight = 5842.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.122100 restraints weight = 5039.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9988  Z= 0.166
  Angle     :  0.614   9.725  13698  Z= 0.319
  Chirality :  0.044   0.170   1578
  Planarity :  0.003   0.030   1583
  Dihedral  : 18.419  75.008   1802
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.34 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.25), residues: 1107
  helix:  0.67 (0.30), residues: 311
  sheet: -1.77 (0.27), residues: 304
  loop : -1.17 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 149 
 TYR   0.014   0.002   TYR A 250 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.019   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 9987)
  covalent geometry    : angle       0.61396 (13696)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       1.15856 (    2)
  hydrogen bonds       : bond        0.03216 (  431)
  hydrogen bonds       : angle       5.57909 ( 1208)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.363 
Fit side-chains
REVERT: C   91 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6210 (mtm110)
REVERT: A  146 ARG cc_start: 0.7778 (tpm170) cc_final: 0.7480 (ttm-80)
REVERT: D   44 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8586 (mp)
REVERT: D  127 THR cc_start: 0.9101 (p) cc_final: 0.8884 (t)
REVERT: D  152 TYR cc_start: 0.8550 (p90) cc_final: 0.8206 (p90)
REVERT: D  326 LYS cc_start: 0.8598 (pttt) cc_final: 0.7540 (mmtp)
  outliers start: 28
  outliers final: 22
  residues processed: 142
  average time/residue: 0.0906
  time to fit residues: 18.8095
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  199 MET
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.147055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.116080 restraints weight = 14715.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.119659 restraints weight = 10376.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120547 restraints weight = 7269.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.121015 restraints weight = 6542.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121333 restraints weight = 6190.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9988  Z= 0.146
  Angle     :  0.602   9.453  13698  Z= 0.313
  Chirality :  0.043   0.168   1578
  Planarity :  0.003   0.028   1583
  Dihedral  : 18.368  75.413   1802
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.06 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1107
  helix:  0.75 (0.30), residues: 311
  sheet: -1.72 (0.27), residues: 303
  loop : -1.12 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  91 
 TYR   0.013   0.001   TYR A 250 
 PHE   0.009   0.001   PHE D 126 
 TRP   0.018   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9987)
  covalent geometry    : angle       0.60237 (13696)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       0.99142 (    2)
  hydrogen bonds       : bond        0.03092 (  431)
  hydrogen bonds       : angle       5.49190 ( 1208)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1509.13 seconds
wall clock time: 27 minutes 3.88 seconds (1623.88 seconds total)