Starting phenix.real_space_refine
on Tue Jan 14 18:22:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9epr_19884/01_2025/9epr_19884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9epr_19884/01_2025/9epr_19884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9epr_19884/01_2025/9epr_19884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9epr_19884/01_2025/9epr_19884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9epr_19884/01_2025/9epr_19884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9epr_19884/01_2025/9epr_19884.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     C    4519      2.51       5
     N    1168      2.21       5
     O    1290      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7046
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1724
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 212}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2392
          Classifications: {'peptide': 312}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 306}
    Chain: "G"
      Number of atoms: 277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 277
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 3, 'TRANS': 30}
    Chain: "R"
      Number of atoms: 2633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2633
          Classifications: {'peptide': 330}
          Link IDs: {'PTRANS': 17, 'TRANS': 312}
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   MET R  76 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET R  76 " occ=0.50
  Time building chain proxies: 5.20, per 1000 atoms: 0.74
  Number of scatterers: 7046
  At special positions: 0
  Unit cell: (116.34, 107.848, 92.5628, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      69     16.00
     O    1290      8.00
     N    1168      7.00
     C    4519      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 123 " - pdb=" SG  CYS R 200 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 9 sheets defined
      41.5% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.719A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 204 through 208
      removed outlier: 3.676A  pdb=" N   ARG A 208 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 3.733A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 309
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 349
      removed outlier: 3.875A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'G' and resid 34 through 48
      removed outlier: 4.212A  pdb=" N   ARG G  47 " --> pdb=" O   TYR G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 51
      No H-bonds generated for 'chain 'G' and resid 49 through 51'
    Processing helix  chain 'R' and resid 22 through 27
    Processing helix  chain 'R' and resid 51 through 78
      removed outlier: 3.908A  pdb=" N   MET R  55 " --> pdb=" O   TYR R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 83 through 101
      removed outlier: 3.832A  pdb=" N   LEU R  88 " --> pdb=" O   PRO R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 107
    Processing helix  chain 'R' and resid 120 through 155
      removed outlier: 4.413A  pdb=" N   GLU R 124 " --> pdb=" O   PRO R 120 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU R 125 " --> pdb=" O   PHE R 121 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LEU R 132 " --> pdb=" O   MET R 128 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   PHE R 133 " --> pdb=" O   ILE R 129 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE R 138 " --> pdb=" O   GLY R 134 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG R 148 " --> pdb=" O   ILE R 144 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   TYR R 149 " --> pdb=" O   THR R 145 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL R 153 " --> pdb=" O   TYR R 149 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LYS R 154 " --> pdb=" O   ASN R 150 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY R 155 " --> pdb=" O   VAL R 151 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 183
      removed outlier: 3.726A  pdb=" N   ALA R 166 " --> pdb=" O   THR R 162 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA R 183 " --> pdb=" O   GLY R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 184 through 187
    Processing helix  chain 'R' and resid 208 through 255
      removed outlier: 3.684A  pdb=" N   VAL R 225 " --> pdb=" O   PHE R 221 " (cutoff:3.500A)
      Proline residue:  R 226  - end of helix
      removed outlier: 4.695A  pdb=" N   GLN R 251 " --> pdb=" O   SER R 247 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ALA R 252 " --> pdb=" O   LEU R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 269
    Processing helix  chain 'R' and resid 270 through 302
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 312 through 324
      removed outlier: 4.113A  pdb=" N   GLY R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA R 320 " --> pdb=" O   GLY R 316 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ALA R 324 " --> pdb=" O   ALA R 320 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 325 through 334
      removed outlier: 3.896A  pdb=" N   ILE R 329 " --> pdb=" O   CYS R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 343
    Processing helix  chain 'R' and resid 344 through 349
      removed outlier: 4.243A  pdb=" N   CYS R 348 " --> pdb=" O   ASP R 344 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.305A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.784A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 7.712A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.585A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.727A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 149
      removed outlier: 3.502A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 202
      removed outlier: 4.441A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 244
      removed outlier: 6.578A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.526A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 191 through 193
      removed outlier: 3.815A  pdb=" N   VAL R 192 " --> pdb=" O   THR R 201 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR R 201 " --> pdb=" O   VAL R 192 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    312 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2214
        1.34 -     1.46: 1697
        1.46 -     1.58: 3187
        1.58 -     1.70: 0
        1.70 -     1.81: 107
  Bond restraints: 7205
  Sorted by residual:
  bond pdb=" C10 RET R 401 "
       pdb=" C11 RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.433  1.356  0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" N   ALA R 322 "
       pdb=" CA  ALA R 322 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.035 1.38e-02 5.25e+03 6.36e+00
  bond pdb=" CA  PRO G  58 "
       pdb=" C   PRO G  58 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.027 1.09e-02 8.42e+03 5.98e+00
  bond pdb=" N   LYS R 321A"
       pdb=" CA  LYS R 321A"
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.35e-02 5.49e+03 5.11e+00
  bond pdb=" C14 RET R 401 "
       pdb=" C15 RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.448  1.489 -0.041 2.00e-02 2.50e+03 4.22e+00
  ... (remaining 7200 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 9513
        2.51 -     5.02: 192
        5.02 -     7.54: 32
        7.54 -    10.05: 6
       10.05 -    12.56: 4
  Bond angle restraints: 9747
  Sorted by residual:
  angle pdb=" N   ILE G  57 "
        pdb=" CA  ILE G  57 "
        pdb=" C   ILE G  57 "
      ideal   model   delta    sigma   weight residual
     107.76  116.29   -8.53 1.01e+00 9.80e-01 7.12e+01
  angle pdb=" N   PRO G  58 "
        pdb=" CA  PRO G  58 "
        pdb=" C   PRO G  58 "
      ideal   model   delta    sigma   weight residual
     110.95   98.39   12.56 1.62e+00 3.81e-01 6.01e+01
  angle pdb=" N   TRP R 290 "
        pdb=" CA  TRP R 290 "
        pdb=" C   TRP R 290 "
      ideal   model   delta    sigma   weight residual
     112.23  121.09   -8.86 1.26e+00 6.30e-01 4.94e+01
  angle pdb=" N   GLU G  59 "
        pdb=" CA  GLU G  59 "
        pdb=" C   GLU G  59 "
      ideal   model   delta    sigma   weight residual
     110.80  121.72  -10.92 2.13e+00 2.20e-01 2.63e+01
  angle pdb=" C   ILE G  57 "
        pdb=" CA  ILE G  57 "
        pdb=" CB  ILE G  57 "
      ideal   model   delta    sigma   weight residual
     110.71  105.24    5.47 1.07e+00 8.73e-01 2.62e+01
  ... (remaining 9742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.17: 3919
       24.17 -    48.35: 265
       48.35 -    72.52: 68
       72.52 -    96.69: 5
       96.69 -   120.86: 2
  Dihedral angle restraints: 4259
    sinusoidal: 1681
      harmonic: 2578
  Sorted by residual:
  dihedral pdb=" CA  PRO A 282 "
           pdb=" C   PRO A 282 "
           pdb=" N   LEU A 283 "
           pdb=" CA  LEU A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.53   28.47     0      5.00e+00 4.00e-02 3.24e+01
  dihedral pdb=" CA  LEU A 283 "
           pdb=" C   LEU A 283 "
           pdb=" N   THR A 284 "
           pdb=" CA  THR A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.17  -26.83     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  GLU A 298 "
           pdb=" C   GLU A 298 "
           pdb=" N   ALA A 299 "
           pdb=" CA  ALA A 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 4256 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 759
       0.046 -    0.093: 240
       0.093 -    0.139: 73
       0.139 -    0.185: 11
       0.185 -    0.232: 4
  Chirality restraints: 1087
  Sorted by residual:
  chirality pdb=" CA  TRP R 290 "
            pdb=" N   TRP R 290 "
            pdb=" C   TRP R 290 "
            pdb=" CB  TRP R 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  GLU G  59 "
            pdb=" N   GLU G  59 "
            pdb=" C   GLU G  59 "
            pdb=" CB  GLU G  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  VAL R 192 "
            pdb=" CA  VAL R 192 "
            pdb=" CG1 VAL R 192 "
            pdb=" CG2 VAL R 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1084 not shown)

  Planarity restraints: 1220
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 RET R 401 "   -0.109 2.00e-02 2.50e+03   6.45e-02 5.20e+01
        pdb=" C11 RET R 401 "    0.079 2.00e-02 2.50e+03
        pdb=" C19 RET R 401 "   -0.014 2.00e-02 2.50e+03
        pdb=" C8  RET R 401 "    0.050 2.00e-02 2.50e+03
        pdb=" C9  RET R 401 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 RET R 401 "   -0.033 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        pdb=" C11 RET R 401 "    0.029 2.00e-02 2.50e+03
        pdb=" C12 RET R 401 "    0.037 2.00e-02 2.50e+03
        pdb=" C13 RET R 401 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 320 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.65e+00
        pdb=" C   ALA R 320 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ALA R 320 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS R 321A"   -0.016 2.00e-02 2.50e+03
  ... (remaining 1217 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2255
        2.82 -     3.34: 6617
        3.34 -     3.86: 12698
        3.86 -     4.38: 13892
        4.38 -     4.90: 22138
  Nonbonded interactions: 57600
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 336 "
            pdb=" OG1 THR A 340 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   PHE R 287 "
            pdb=" OG1 THR R 291 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   THR R 106 "
            pdb=" ND2 ASN R 110 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OG  SER B 279 "
            pdb=" O   LEU B 284 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.305 3.040
  ... (remaining 57595 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             4.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     20.250
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   7205  Z= 0.295
  Angle     :  0.931  12.559   9747  Z= 0.559
  Chirality :  0.051   0.232   1087
  Planarity :  0.007   0.065   1220
  Dihedral  : 17.430 120.864   2592
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.76 %
    Favored  : 91.78 %
  Rotamer:
    Outliers : 14.42 %
    Allowed  : 14.55 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.23), residues: 876
  helix: -2.09 (0.23), residues: 321
  sheet: -2.10 (0.43), residues: 110
  loop : -3.22 (0.25), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.009   0.001   HIS R 335 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.018   0.002   TYR B 145 
 ARG   0.004   0.000   ARG R 148 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 262
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8097 (tm-30)
REVERT: A   32 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7600 (ptp-110)
REVERT: A   34 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7830 (p)
REVERT: A  198 MET cc_start: 0.9114 (ttm) cc_final: 0.8887 (tpt)
REVERT: A  209 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8145 (tptt)
REVERT: A  210 LYS cc_start: 0.9284 (pptt) cc_final: 0.9070 (pptt)
REVERT: A  221 ILE cc_start: 0.8818 (mt) cc_final: 0.8261 (mt)
REVERT: A  227 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8883 (mp)
REVERT: A  240 MET cc_start: 0.6905 (tpp) cc_final: 0.6599 (tpp)
REVERT: A  262 THR cc_start: 0.8738 (p) cc_final: 0.8330 (m)
REVERT: A  263 SER cc_start: 0.8893 (m) cc_final: 0.8203 (t)
REVERT: A  264 ILE cc_start: 0.8624 (mp) cc_final: 0.8400 (mp)
REVERT: A  274 PHE cc_start: 0.8171 (t80) cc_final: 0.7900 (t80)
REVERT: A  303 ILE cc_start: 0.8780 (tt) cc_final: 0.8565 (tt)
REVERT: A  313 ARG cc_start: 0.9285 (ttm170) cc_final: 0.8954 (tpp80)
REVERT: A  321 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8798 (t)
REVERT: A  344 ILE cc_start: 0.9098 (mt) cc_final: 0.8860 (mt)
REVERT: A  345 LYS cc_start: 0.8549 (mttt) cc_final: 0.8345 (mmtt)
REVERT: B   62 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6398 (m90)
REVERT: B   63 TRP cc_start: 0.8291 (m100) cc_final: 0.7415 (m100)
REVERT: B   68 ARG cc_start: 0.8911 (mtp180) cc_final: 0.8692 (mmm-85)
REVERT: B   70 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8657 (pp)
REVERT: B   78 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7592 (mmmt)
REVERT: B  103 CYS cc_start: 0.8858 (p) cc_final: 0.8346 (p)
REVERT: B  250 CYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8465 (m)
REVERT: B  277 SER cc_start: 0.6932 (OUTLIER) cc_final: 0.5805 (m)
REVERT: B  280 LYS cc_start: 0.8539 (tptt) cc_final: 0.8139 (mmmm)
REVERT: B  286 LEU cc_start: 0.9375 (mp) cc_final: 0.8782 (mm)
REVERT: B  293 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7443 (p0)
REVERT: B  325 MET cc_start: 0.9303 (tpt) cc_final: 0.9080 (tpp)
REVERT: B  335 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8660 (m-10)
REVERT: G   40 PHE cc_start: 0.6743 (t80) cc_final: 0.6450 (m-80)
REVERT: G   45 GLU cc_start: 0.8941 (mp0) cc_final: 0.8538 (pp20)
REVERT: G   50 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9091 (mp0)
REVERT: G   64 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7515 (p90)
REVERT: R   30 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (p0)
REVERT: R   36 HIS cc_start: 0.8623 (t-90) cc_final: 0.8389 (t-90)
REVERT: R   45 MET cc_start: 0.5385 (pp-130) cc_final: 0.4643 (ptt)
REVERT: R   55 MET cc_start: 0.8619 (mmt) cc_final: 0.7990 (mmm)
REVERT: R   76 MET cc_start: 0.8920 (mmt) cc_final: 0.8406 (mmm)
REVERT: R  104 MET cc_start: 0.8432 (tmm) cc_final: 0.7957 (ptt)
REVERT: R  107 MET cc_start: 0.8928 (tpp) cc_final: 0.8296 (tpt)
REVERT: R  206 ASP cc_start: 0.7103 (t0) cc_final: 0.6866 (t0)
REVERT: R  246 LYS cc_start: 0.9763 (tttt) cc_final: 0.9519 (ptmm)
REVERT: R  250 GLU cc_start: 0.9114 (tp30) cc_final: 0.8099 (tm-30)
REVERT: R  251 GLN cc_start: 0.9119 (tp40) cc_final: 0.8353 (tp-100)
REVERT: R  255 MET cc_start: 0.8900 (mmt) cc_final: 0.8082 (mmm)
REVERT: R  281 MET cc_start: 0.8947 (ttm) cc_final: 0.8672 (ttt)
REVERT: R  287 PHE cc_start: 0.8474 (t80) cc_final: 0.7671 (t80)
REVERT: R  305 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8010 (mpp-170)
REVERT: R  311 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8036 (mpt)
REVERT: R  334 SER cc_start: 0.8685 (m) cc_final: 0.8464 (m)
  outliers start: 111
  outliers final: 46
  residues processed: 336
  average time/residue: 0.2134
  time to fit residues: 92.3048
Evaluate side-chains
  258 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 196
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 66 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
B  32 GLN
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  38 HIS
R 251 GLN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.139689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.103516 restraints weight = 19520.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106829 restraints weight = 18566.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.108950 restraints weight = 14083.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3662 r_free = 0.3662    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7205  Z= 0.256
  Angle     :  0.730   7.328   9747  Z= 0.394
  Chirality :  0.048   0.191   1087
  Planarity :  0.005   0.050   1220
  Dihedral  :  8.734 103.804    964
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.26), residues: 876
  helix: -0.78 (0.26), residues: 331
  sheet: -1.99 (0.41), residues: 126
  loop : -2.82 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 211 
 HIS   0.006   0.002   HIS B  62 
 PHE   0.028   0.002   PHE G  64 
 TYR   0.019   0.002   TYR R 214 
 ARG   0.006   0.001   ARG B  49 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.9248 (pttp) cc_final: 0.8526 (mmtt)
REVERT: A  221 ILE cc_start: 0.8747 (mt) cc_final: 0.8366 (mt)
REVERT: A  222 ILE cc_start: 0.8950 (mt) cc_final: 0.8694 (mt)
REVERT: A  227 LEU cc_start: 0.9211 (mt) cc_final: 0.8743 (mt)
REVERT: A  263 SER cc_start: 0.8941 (m) cc_final: 0.8442 (t)
REVERT: A  264 ILE cc_start: 0.8663 (mp) cc_final: 0.8456 (mp)
REVERT: A  274 PHE cc_start: 0.8656 (t80) cc_final: 0.8171 (t80)
REVERT: A  313 ARG cc_start: 0.9142 (ttm170) cc_final: 0.8834 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9217 (t0) cc_final: 0.8533 (m110)
REVERT: B   42 ARG cc_start: 0.9007 (tmm160) cc_final: 0.8410 (ttp80)
REVERT: B   63 TRP cc_start: 0.8137 (m100) cc_final: 0.7355 (m100)
REVERT: B   79 LEU cc_start: 0.9534 (mp) cc_final: 0.9333 (mp)
REVERT: B  235 PHE cc_start: 0.9331 (t80) cc_final: 0.8889 (t80)
REVERT: B  280 LYS cc_start: 0.8677 (tptt) cc_final: 0.8211 (mmmt)
REVERT: G   40 PHE cc_start: 0.7106 (t80) cc_final: 0.6440 (m-80)
REVERT: R   42 PHE cc_start: 0.6874 (m-10) cc_final: 0.6508 (m-10)
REVERT: R   55 MET cc_start: 0.8673 (mmt) cc_final: 0.7942 (mmm)
REVERT: R   68 ASN cc_start: 0.8537 (m-40) cc_final: 0.8279 (m110)
REVERT: R   87 PHE cc_start: 0.8827 (m-10) cc_final: 0.8295 (m-80)
REVERT: R  147 ASP cc_start: 0.8665 (t70) cc_final: 0.8442 (t0)
REVERT: R  150 ASN cc_start: 0.8604 (t0) cc_final: 0.8320 (t0)
REVERT: R  180 TRP cc_start: 0.7751 (m100) cc_final: 0.6859 (m100)
REVERT: R  206 ASP cc_start: 0.6518 (t0) cc_final: 0.6084 (t0)
REVERT: R  229 ILE cc_start: 0.9322 (mt) cc_final: 0.9091 (mt)
REVERT: R  287 PHE cc_start: 0.8913 (t80) cc_final: 0.8095 (t80)
REVERT: R  305 ARG cc_start: 0.8652 (mpp-170) cc_final: 0.8379 (mpp-170)
REVERT: R  311 MET cc_start: 0.8754 (mpp) cc_final: 0.8541 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2272
  time to fit residues: 69.7551
Evaluate side-chains
  192 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 83 optimal weight:    0.0020
   chunk 4 optimal weight:    0.0980
   chunk 57 optimal weight:    0.5980
   chunk 41 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 54 optimal weight:    0.1980
   overall best weight:    0.3388

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R  38 HIS
R 110 ASN
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.144201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.108063 restraints weight = 18556.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.112258 restraints weight = 15385.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113608 restraints weight = 10579.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7205  Z= 0.181
  Angle     :  0.669  10.656   9747  Z= 0.351
  Chirality :  0.045   0.235   1087
  Planarity :  0.005   0.047   1220
  Dihedral  :  7.087  70.957    964
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.27), residues: 876
  helix:  0.00 (0.27), residues: 334
  sheet: -1.43 (0.42), residues: 140
  loop : -2.64 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 211 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.017   0.001   PHE G  64 
 TYR   0.016   0.001   TYR R  51 
 ARG   0.005   0.001   ARG B 314 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.8375 (tpt) cc_final: 0.7867 (tpt)
REVERT: A  210 LYS cc_start: 0.9143 (pttp) cc_final: 0.8498 (mmtt)
REVERT: A  221 ILE cc_start: 0.8501 (mt) cc_final: 0.8185 (mt)
REVERT: A  263 SER cc_start: 0.8888 (m) cc_final: 0.8469 (t)
REVERT: A  313 ARG cc_start: 0.9075 (ttm170) cc_final: 0.8765 (ttm-80)
REVERT: A  320 TYR cc_start: 0.7323 (m-80) cc_final: 0.5939 (m-80)
REVERT: A  333 GLN cc_start: 0.9389 (mp10) cc_final: 0.9101 (mp10)
REVERT: B   42 ARG cc_start: 0.8866 (tmm160) cc_final: 0.8435 (tmm160)
REVERT: B   43 ILE cc_start: 0.9239 (pt) cc_final: 0.8765 (mm)
REVERT: B   59 TYR cc_start: 0.7999 (m-80) cc_final: 0.7792 (m-80)
REVERT: B   63 TRP cc_start: 0.7944 (m100) cc_final: 0.7254 (m100)
REVERT: B  166 CYS cc_start: 0.7286 (t) cc_final: 0.6832 (m)
REVERT: B  308 LEU cc_start: 0.9166 (mt) cc_final: 0.8624 (tt)
REVERT: B  325 MET cc_start: 0.8736 (tpp) cc_final: 0.8150 (tpt)
REVERT: B  332 TRP cc_start: 0.9175 (m-10) cc_final: 0.8602 (m-10)
REVERT: B  335 PHE cc_start: 0.8170 (m-80) cc_final: 0.7634 (m-80)
REVERT: G   42 ASP cc_start: 0.7784 (m-30) cc_final: 0.7420 (m-30)
REVERT: R   55 MET cc_start: 0.8636 (mmt) cc_final: 0.7949 (mmm)
REVERT: R   68 ASN cc_start: 0.8468 (m-40) cc_final: 0.8171 (m110)
REVERT: R   87 PHE cc_start: 0.8833 (m-10) cc_final: 0.8428 (m-80)
REVERT: R  104 MET cc_start: 0.8456 (ttt) cc_final: 0.8002 (tpp)
REVERT: R  107 MET cc_start: 0.8602 (tpt) cc_final: 0.8176 (tpt)
REVERT: R  150 ASN cc_start: 0.8715 (t0) cc_final: 0.8419 (t0)
REVERT: R  180 TRP cc_start: 0.7655 (m100) cc_final: 0.6814 (m100)
REVERT: R  206 ASP cc_start: 0.6433 (t0) cc_final: 0.6163 (t0)
REVERT: R  229 ILE cc_start: 0.9296 (mt) cc_final: 0.9069 (mt)
REVERT: R  250 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: R  253 LYS cc_start: 0.9450 (tmtt) cc_final: 0.9192 (tptp)
REVERT: R  272 GLU cc_start: 0.9000 (pm20) cc_final: 0.8699 (pm20)
REVERT: R  287 PHE cc_start: 0.8685 (t80) cc_final: 0.7922 (t80)
REVERT: R  305 ARG cc_start: 0.8723 (mpp-170) cc_final: 0.8490 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1890
  time to fit residues: 60.0997
Evaluate side-chains
  190 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0570
   chunk 27 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 76 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
R  38 HIS
R 110 ASN
R 244 HIS
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.142539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.104758 restraints weight = 18848.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.110274 restraints weight = 15500.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.110188 restraints weight = 11706.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.5169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7205  Z= 0.188
  Angle     :  0.665   9.705   9747  Z= 0.350
  Chirality :  0.046   0.252   1087
  Planarity :  0.005   0.047   1220
  Dihedral  :  6.349  67.643    964
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.27), residues: 876
  helix:  0.29 (0.28), residues: 327
  sheet: -1.35 (0.42), residues: 140
  loop : -2.56 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 211 
 HIS   0.004   0.001   HIS R 343 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.028   0.002   TYR A 320 
 ARG   0.005   0.001   ARG A 242 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7878 (ptp-110)
REVERT: A   35 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8423 (ptmt)
REVERT: A  198 MET cc_start: 0.8710 (tpt) cc_final: 0.8281 (tpt)
REVERT: A  221 ILE cc_start: 0.8784 (mt) cc_final: 0.8448 (mt)
REVERT: A  227 LEU cc_start: 0.8828 (mp) cc_final: 0.8189 (mp)
REVERT: A  263 SER cc_start: 0.8913 (m) cc_final: 0.8401 (t)
REVERT: A  274 PHE cc_start: 0.8745 (t80) cc_final: 0.8337 (t80)
REVERT: A  313 ARG cc_start: 0.9042 (ttm170) cc_final: 0.8821 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9526 (t160) cc_final: 0.8713 (m110)
REVERT: A  333 GLN cc_start: 0.9456 (mp10) cc_final: 0.9109 (mp10)
REVERT: A  343 ILE cc_start: 0.8802 (mm) cc_final: 0.8559 (tp)
REVERT: B   42 ARG cc_start: 0.8960 (tmm160) cc_final: 0.8725 (tmt-80)
REVERT: B   43 ILE cc_start: 0.9272 (pt) cc_final: 0.8801 (mm)
REVERT: B   52 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7528 (mmm-85)
REVERT: B   63 TRP cc_start: 0.8104 (m100) cc_final: 0.7434 (m100)
REVERT: B  166 CYS cc_start: 0.7413 (t) cc_final: 0.6878 (m)
REVERT: B  308 LEU cc_start: 0.9195 (mt) cc_final: 0.8517 (tt)
REVERT: B  325 MET cc_start: 0.9146 (tpp) cc_final: 0.8557 (tpp)
REVERT: B  335 PHE cc_start: 0.8258 (m-80) cc_final: 0.7663 (m-80)
REVERT: G   42 ASP cc_start: 0.7866 (m-30) cc_final: 0.7510 (m-30)
REVERT: R   55 MET cc_start: 0.8690 (mmt) cc_final: 0.7992 (mmm)
REVERT: R   68 ASN cc_start: 0.8214 (m-40) cc_final: 0.7898 (m110)
REVERT: R   76 MET cc_start: 0.8155 (mmm) cc_final: 0.7954 (tpp)
REVERT: R   87 PHE cc_start: 0.8870 (m-10) cc_final: 0.8336 (m-80)
REVERT: R  104 MET cc_start: 0.8480 (ttt) cc_final: 0.8101 (tpp)
REVERT: R  107 MET cc_start: 0.8473 (tpt) cc_final: 0.8193 (tpt)
REVERT: R  150 ASN cc_start: 0.8858 (t0) cc_final: 0.8592 (t0)
REVERT: R  180 TRP cc_start: 0.7718 (m100) cc_final: 0.7066 (m100)
REVERT: R  206 ASP cc_start: 0.6646 (t0) cc_final: 0.6284 (t0)
REVERT: R  229 ILE cc_start: 0.9343 (mt) cc_final: 0.9093 (mt)
REVERT: R  253 LYS cc_start: 0.9485 (tmtt) cc_final: 0.9221 (tptp)
REVERT: R  287 PHE cc_start: 0.8821 (t80) cc_final: 0.8199 (t80)
REVERT: R  305 ARG cc_start: 0.8790 (mpp-170) cc_final: 0.8540 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2046
  time to fit residues: 59.0259
Evaluate side-chains
  184 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.3980
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 84 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  38 HIS
R 110 ASN
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.143054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.105801 restraints weight = 18450.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.109731 restraints weight = 16356.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.110239 restraints weight = 12674.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.5508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7205  Z= 0.194
  Angle     :  0.663   8.215   9747  Z= 0.351
  Chirality :  0.046   0.282   1087
  Planarity :  0.004   0.048   1220
  Dihedral  :  6.538  80.608    964
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.69 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.27), residues: 876
  helix:  0.41 (0.28), residues: 328
  sheet: -0.88 (0.46), residues: 118
  loop : -2.47 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 211 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.014   0.002   TYR R 191 
 ARG   0.004   0.001   ARG B  46 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8987 (ptpt) cc_final: 0.8611 (ptmt)
REVERT: A  198 MET cc_start: 0.8952 (tpt) cc_final: 0.8517 (tpt)
REVERT: A  210 LYS cc_start: 0.9132 (pptt) cc_final: 0.8284 (mmtt)
REVERT: A  221 ILE cc_start: 0.8695 (mt) cc_final: 0.8414 (mt)
REVERT: A  227 LEU cc_start: 0.8725 (mp) cc_final: 0.8031 (mp)
REVERT: A  263 SER cc_start: 0.8851 (m) cc_final: 0.8375 (t)
REVERT: A  264 ILE cc_start: 0.8846 (mp) cc_final: 0.8629 (mp)
REVERT: A  274 PHE cc_start: 0.8673 (t80) cc_final: 0.8139 (t80)
REVERT: A  313 ARG cc_start: 0.9054 (ttm170) cc_final: 0.8833 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9336 (t0) cc_final: 0.8566 (m110)
REVERT: A  333 GLN cc_start: 0.9308 (mp10) cc_final: 0.9035 (mp10)
REVERT: B   42 ARG cc_start: 0.8837 (tmm160) cc_final: 0.8366 (tmm160)
REVERT: B   43 ILE cc_start: 0.9203 (pt) cc_final: 0.8698 (mm)
REVERT: B   52 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7530 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7949 (m100) cc_final: 0.7412 (m100)
REVERT: B  166 CYS cc_start: 0.7285 (t) cc_final: 0.6723 (m)
REVERT: B  313 ASN cc_start: 0.8125 (t0) cc_final: 0.7908 (t0)
REVERT: B  325 MET cc_start: 0.9139 (tpp) cc_final: 0.8497 (tpp)
REVERT: B  335 PHE cc_start: 0.8436 (m-80) cc_final: 0.7874 (m-80)
REVERT: G   40 PHE cc_start: 0.6498 (m-10) cc_final: 0.6298 (m-80)
REVERT: R   38 HIS cc_start: 0.8480 (t70) cc_final: 0.8205 (t-90)
REVERT: R   42 PHE cc_start: 0.6678 (m-10) cc_final: 0.5976 (m-10)
REVERT: R   55 MET cc_start: 0.8635 (mmt) cc_final: 0.7928 (mmm)
REVERT: R   68 ASN cc_start: 0.8030 (m-40) cc_final: 0.7681 (m110)
REVERT: R  110 ASN cc_start: 0.9135 (m-40) cc_final: 0.8897 (m110)
REVERT: R  150 ASN cc_start: 0.8814 (t0) cc_final: 0.8532 (t0)
REVERT: R  180 TRP cc_start: 0.7507 (m100) cc_final: 0.6846 (m100)
REVERT: R  206 ASP cc_start: 0.6466 (t0) cc_final: 0.6008 (t0)
REVERT: R  229 ILE cc_start: 0.9360 (mt) cc_final: 0.9097 (mt)
REVERT: R  251 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8353 (tp-100)
REVERT: R  253 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9210 (tptp)
REVERT: R  255 MET cc_start: 0.8947 (mmp) cc_final: 0.7968 (mmp)
REVERT: R  272 GLU cc_start: 0.8994 (pm20) cc_final: 0.8610 (pm20)
REVERT: R  287 PHE cc_start: 0.8797 (t80) cc_final: 0.8131 (t80)
REVERT: R  305 ARG cc_start: 0.8772 (mpp-170) cc_final: 0.8541 (mpp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2047
  time to fit residues: 59.0602
Evaluate side-chains
  182 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0020
   overall best weight:    1.0390

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.141073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.102056 restraints weight = 18897.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.105558 restraints weight = 14528.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.106925 restraints weight = 11661.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7205  Z= 0.217
  Angle     :  0.682   9.512   9747  Z= 0.361
  Chirality :  0.047   0.222   1087
  Planarity :  0.005   0.049   1220
  Dihedral  :  6.806  89.761    964
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.28), residues: 876
  helix:  0.46 (0.28), residues: 328
  sheet: -0.82 (0.47), residues: 117
  loop : -2.31 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 211 
 HIS   0.005   0.001   HIS R  50 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.013   0.002   TYR R 191 
 ARG   0.003   0.000   ARG A  15 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.9010 (ptpt) cc_final: 0.8420 (ptmt)
REVERT: A  198 MET cc_start: 0.9033 (tpt) cc_final: 0.8643 (tpt)
REVERT: A  210 LYS cc_start: 0.9176 (pptt) cc_final: 0.8249 (mmtt)
REVERT: A  221 ILE cc_start: 0.8809 (mt) cc_final: 0.8552 (mt)
REVERT: A  227 LEU cc_start: 0.8800 (mp) cc_final: 0.8178 (mp)
REVERT: A  263 SER cc_start: 0.8864 (m) cc_final: 0.8395 (t)
REVERT: A  264 ILE cc_start: 0.8807 (mp) cc_final: 0.8563 (mp)
REVERT: A  274 PHE cc_start: 0.8774 (t80) cc_final: 0.8260 (t80)
REVERT: A  306 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8322 (tp-100)
REVERT: A  333 GLN cc_start: 0.9334 (mp10) cc_final: 0.9055 (mp10)
REVERT: A  353 LEU cc_start: 0.8696 (mp) cc_final: 0.8365 (mp)
REVERT: B   43 ILE cc_start: 0.9281 (pt) cc_final: 0.8882 (mm)
REVERT: B   52 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7608 (mmm-85)
REVERT: B   63 TRP cc_start: 0.8120 (m100) cc_final: 0.7702 (m100)
REVERT: B   89 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8297 (mtpt)
REVERT: B  103 CYS cc_start: 0.9105 (p) cc_final: 0.8889 (p)
REVERT: B  166 CYS cc_start: 0.7382 (t) cc_final: 0.6752 (m)
REVERT: B  235 PHE cc_start: 0.9382 (t80) cc_final: 0.8765 (t80)
REVERT: B  262 MET cc_start: 0.3146 (ttp) cc_final: 0.2912 (tmm)
REVERT: B  325 MET cc_start: 0.9272 (tpp) cc_final: 0.8634 (tpp)
REVERT: B  335 PHE cc_start: 0.8530 (m-80) cc_final: 0.7924 (m-80)
REVERT: R   31 MET cc_start: 0.6730 (mmt) cc_final: 0.6347 (mmm)
REVERT: R   55 MET cc_start: 0.8602 (mmt) cc_final: 0.7937 (mmm)
REVERT: R   68 ASN cc_start: 0.8219 (m-40) cc_final: 0.7877 (m110)
REVERT: R   87 PHE cc_start: 0.8537 (m-80) cc_final: 0.7915 (m-80)
REVERT: R  104 MET cc_start: 0.8432 (ttt) cc_final: 0.8131 (tpp)
REVERT: R  110 ASN cc_start: 0.9061 (m-40) cc_final: 0.8836 (m110)
REVERT: R  150 ASN cc_start: 0.8762 (t0) cc_final: 0.8485 (t0)
REVERT: R  180 TRP cc_start: 0.7554 (m100) cc_final: 0.7084 (m100)
REVERT: R  206 ASP cc_start: 0.6608 (t0) cc_final: 0.6132 (t0)
REVERT: R  229 ILE cc_start: 0.9379 (mt) cc_final: 0.9112 (mt)
REVERT: R  251 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8369 (tp-100)
REVERT: R  253 LYS cc_start: 0.9479 (tmtt) cc_final: 0.9253 (tptp)
REVERT: R  255 MET cc_start: 0.8956 (mmp) cc_final: 0.8081 (mmp)
REVERT: R  287 PHE cc_start: 0.8774 (t80) cc_final: 0.7971 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2232
  time to fit residues: 63.1489
Evaluate side-chains
  179 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 85 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  38 HIS
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.143567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.106352 restraints weight = 18873.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108342 restraints weight = 17973.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.109179 restraints weight = 15576.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.5926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7205  Z= 0.183
  Angle     :  0.677   9.032   9747  Z= 0.354
  Chirality :  0.046   0.272   1087
  Planarity :  0.005   0.048   1220
  Dihedral  :  6.453  84.527    964
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.04 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.28), residues: 876
  helix:  0.62 (0.28), residues: 327
  sheet: -0.65 (0.49), residues: 112
  loop : -2.23 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A 211 
 HIS   0.003   0.001   HIS R 335 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.013   0.002   TYR R 218 
 ARG   0.008   0.001   ARG A  32 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.9033 (ptpt) cc_final: 0.8593 (ptmt)
REVERT: A  198 MET cc_start: 0.9088 (tpt) cc_final: 0.8644 (tpt)
REVERT: A  210 LYS cc_start: 0.9088 (pptt) cc_final: 0.8071 (mmtt)
REVERT: A  221 ILE cc_start: 0.8708 (mt) cc_final: 0.8348 (mt)
REVERT: A  227 LEU cc_start: 0.8678 (mp) cc_final: 0.8044 (mp)
REVERT: A  263 SER cc_start: 0.8824 (m) cc_final: 0.8358 (t)
REVERT: A  264 ILE cc_start: 0.8783 (mp) cc_final: 0.8513 (mp)
REVERT: A  274 PHE cc_start: 0.8653 (t80) cc_final: 0.8128 (t80)
REVERT: A  337 ASP cc_start: 0.9557 (m-30) cc_final: 0.9348 (m-30)
REVERT: A  343 ILE cc_start: 0.8823 (mm) cc_final: 0.8583 (tp)
REVERT: B   52 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7535 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7866 (m100) cc_final: 0.7409 (m100)
REVERT: B  166 CYS cc_start: 0.7271 (t) cc_final: 0.6676 (m)
REVERT: B  235 PHE cc_start: 0.9251 (t80) cc_final: 0.8802 (t80)
REVERT: B  325 MET cc_start: 0.9237 (tpp) cc_final: 0.8597 (tpp)
REVERT: B  335 PHE cc_start: 0.8509 (m-80) cc_final: 0.7986 (m-80)
REVERT: G   40 PHE cc_start: 0.6593 (m-10) cc_final: 0.6330 (m-80)
REVERT: R   31 MET cc_start: 0.6804 (mmt) cc_final: 0.6423 (mmm)
REVERT: R   55 MET cc_start: 0.8560 (mmt) cc_final: 0.7913 (mmm)
REVERT: R   68 ASN cc_start: 0.8104 (m-40) cc_final: 0.7810 (m110)
REVERT: R   87 PHE cc_start: 0.8614 (m-80) cc_final: 0.7861 (m-80)
REVERT: R  104 MET cc_start: 0.8421 (ttt) cc_final: 0.8092 (tpp)
REVERT: R  110 ASN cc_start: 0.9010 (m-40) cc_final: 0.8767 (m110)
REVERT: R  150 ASN cc_start: 0.8726 (t0) cc_final: 0.8454 (t0)
REVERT: R  180 TRP cc_start: 0.7495 (m100) cc_final: 0.6814 (m100)
REVERT: R  229 ILE cc_start: 0.9327 (mt) cc_final: 0.9014 (mt)
REVERT: R  251 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8361 (tp-100)
REVERT: R  253 LYS cc_start: 0.9501 (tmtt) cc_final: 0.9270 (tptp)
REVERT: R  255 MET cc_start: 0.8892 (mmp) cc_final: 0.8059 (mmp)
REVERT: R  281 MET cc_start: 0.8899 (ttm) cc_final: 0.8659 (ppp)
REVERT: R  287 PHE cc_start: 0.8662 (t80) cc_final: 0.7890 (t80)
REVERT: R  330 VAL cc_start: 0.9050 (t) cc_final: 0.8784 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1949
  time to fit residues: 56.5654
Evaluate side-chains
  184 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0670
   chunk 37 optimal weight:    0.0050
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.5332

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.144551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.107177 restraints weight = 18637.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.108418 restraints weight = 17056.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.110500 restraints weight = 13963.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.6143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7205  Z= 0.170
  Angle     :  0.671   8.951   9747  Z= 0.349
  Chirality :  0.046   0.301   1087
  Planarity :  0.004   0.048   1220
  Dihedral  :  6.171  83.197    964
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.78 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.28), residues: 876
  helix:  0.75 (0.29), residues: 328
  sheet: -0.50 (0.49), residues: 116
  loop : -2.22 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 211 
 HIS   0.010   0.001   HIS B 266 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.017   0.002   TYR R 338 
 ARG   0.008   0.000   ARG A 313 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8543 (ptmt)
REVERT: A  198 MET cc_start: 0.9111 (tpt) cc_final: 0.8661 (tpt)
REVERT: A  210 LYS cc_start: 0.9161 (pptt) cc_final: 0.7887 (mmpt)
REVERT: A  221 ILE cc_start: 0.8708 (mt) cc_final: 0.8344 (mt)
REVERT: A  227 LEU cc_start: 0.8621 (mp) cc_final: 0.7994 (mp)
REVERT: A  261 ASP cc_start: 0.9054 (m-30) cc_final: 0.8791 (m-30)
REVERT: A  263 SER cc_start: 0.8832 (m) cc_final: 0.8401 (t)
REVERT: A  264 ILE cc_start: 0.8855 (mp) cc_final: 0.8600 (mp)
REVERT: A  274 PHE cc_start: 0.8570 (t80) cc_final: 0.8069 (t80)
REVERT: A  306 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8180 (tp-100)
REVERT: A  343 ILE cc_start: 0.8822 (mm) cc_final: 0.8581 (tp)
REVERT: B   52 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7588 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7758 (m100) cc_final: 0.7352 (m100)
REVERT: B   75 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7983 (tp-100)
REVERT: B  166 CYS cc_start: 0.7233 (t) cc_final: 0.6548 (m)
REVERT: B  235 PHE cc_start: 0.9202 (t80) cc_final: 0.8794 (t80)
REVERT: B  325 MET cc_start: 0.9241 (tpp) cc_final: 0.8590 (tpp)
REVERT: B  335 PHE cc_start: 0.8463 (m-80) cc_final: 0.7922 (m-80)
REVERT: G   40 PHE cc_start: 0.6574 (m-10) cc_final: 0.6311 (m-80)
REVERT: R   31 MET cc_start: 0.6974 (mmt) cc_final: 0.6595 (mmm)
REVERT: R   55 MET cc_start: 0.8534 (mmt) cc_final: 0.7856 (mmm)
REVERT: R   68 ASN cc_start: 0.8080 (m-40) cc_final: 0.7750 (m110)
REVERT: R   87 PHE cc_start: 0.8447 (m-80) cc_final: 0.7815 (m-80)
REVERT: R  104 MET cc_start: 0.8468 (ttt) cc_final: 0.8098 (tpp)
REVERT: R  110 ASN cc_start: 0.8979 (m-40) cc_final: 0.8687 (m110)
REVERT: R  150 ASN cc_start: 0.8666 (t0) cc_final: 0.8412 (t0)
REVERT: R  180 TRP cc_start: 0.7463 (m100) cc_final: 0.6801 (m100)
REVERT: R  206 ASP cc_start: 0.6003 (t0) cc_final: 0.5729 (t0)
REVERT: R  229 ILE cc_start: 0.9287 (mt) cc_final: 0.9010 (mt)
REVERT: R  251 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8321 (tp-100)
REVERT: R  253 LYS cc_start: 0.9479 (tmtt) cc_final: 0.9231 (tptp)
REVERT: R  255 MET cc_start: 0.8867 (mmp) cc_final: 0.8066 (mmp)
REVERT: R  272 GLU cc_start: 0.9117 (pm20) cc_final: 0.8839 (pm20)
REVERT: R  281 MET cc_start: 0.8891 (ttm) cc_final: 0.8594 (ppp)
REVERT: R  287 PHE cc_start: 0.8623 (t80) cc_final: 0.7856 (t80)
REVERT: R  308 LEU cc_start: 0.9262 (tp) cc_final: 0.9042 (tp)
REVERT: R  330 VAL cc_start: 0.9022 (t) cc_final: 0.8775 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2014
  time to fit residues: 57.6485
Evaluate side-chains
  180 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    0.0060
   chunk 64 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 85 optimal weight:    0.2980
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.145642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.108364 restraints weight = 18665.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.110119 restraints weight = 17008.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.111406 restraints weight = 14466.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.6353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7205  Z= 0.170
  Angle     :  0.670  11.004   9747  Z= 0.346
  Chirality :  0.045   0.277   1087
  Planarity :  0.005   0.071   1220
  Dihedral  :  5.937  80.199    964
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.28), residues: 876
  helix:  0.81 (0.29), residues: 326
  sheet: -0.38 (0.50), residues: 112
  loop : -2.22 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 211 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.015   0.001   PHE A 334 
 TYR   0.012   0.001   TYR R 218 
 ARG   0.007   0.000   ARG A 313 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9465 (m110) cc_final: 0.9263 (m110)
REVERT: A   35 LYS cc_start: 0.9016 (ptpt) cc_final: 0.8517 (ptmt)
REVERT: A  198 MET cc_start: 0.9148 (tpt) cc_final: 0.8690 (tpt)
REVERT: A  210 LYS cc_start: 0.9087 (pptt) cc_final: 0.7793 (mmtt)
REVERT: A  221 ILE cc_start: 0.8714 (mt) cc_final: 0.8382 (mt)
REVERT: A  261 ASP cc_start: 0.9043 (m-30) cc_final: 0.8806 (m-30)
REVERT: A  263 SER cc_start: 0.8822 (m) cc_final: 0.8381 (t)
REVERT: A  264 ILE cc_start: 0.8877 (mp) cc_final: 0.8625 (mp)
REVERT: A  274 PHE cc_start: 0.8575 (t80) cc_final: 0.8076 (t80)
REVERT: A  306 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8193 (tp-100)
REVERT: B   52 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7561 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7818 (m100) cc_final: 0.7406 (m100)
REVERT: B  166 CYS cc_start: 0.7252 (t) cc_final: 0.6556 (m)
REVERT: B  235 PHE cc_start: 0.9217 (t80) cc_final: 0.8710 (t80)
REVERT: B  325 MET cc_start: 0.9251 (tpp) cc_final: 0.8586 (tpp)
REVERT: B  335 PHE cc_start: 0.8462 (m-80) cc_final: 0.7876 (m-80)
REVERT: G   40 PHE cc_start: 0.6554 (m-10) cc_final: 0.6279 (m-80)
REVERT: G   42 ASP cc_start: 0.7959 (m-30) cc_final: 0.7717 (m-30)
REVERT: R   27 LEU cc_start: 0.9132 (tt) cc_final: 0.8815 (tt)
REVERT: R   29 GLU cc_start: 0.8426 (pp20) cc_final: 0.8134 (pm20)
REVERT: R   31 MET cc_start: 0.6960 (mmt) cc_final: 0.6629 (mmm)
REVERT: R   55 MET cc_start: 0.8552 (mmt) cc_final: 0.7850 (mmm)
REVERT: R   68 ASN cc_start: 0.7898 (m-40) cc_final: 0.7423 (m110)
REVERT: R   87 PHE cc_start: 0.8586 (m-80) cc_final: 0.7742 (m-80)
REVERT: R  104 MET cc_start: 0.8343 (ttt) cc_final: 0.8032 (tpp)
REVERT: R  110 ASN cc_start: 0.8940 (m-40) cc_final: 0.8436 (m-40)
REVERT: R  154 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7062 (mptt)
REVERT: R  180 TRP cc_start: 0.7469 (m100) cc_final: 0.6843 (m100)
REVERT: R  229 ILE cc_start: 0.9276 (mt) cc_final: 0.9013 (mt)
REVERT: R  251 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8327 (tp-100)
REVERT: R  253 LYS cc_start: 0.9484 (tmtt) cc_final: 0.9239 (tptp)
REVERT: R  255 MET cc_start: 0.8918 (mmp) cc_final: 0.8132 (mmp)
REVERT: R  272 GLU cc_start: 0.9157 (pm20) cc_final: 0.8886 (pm20)
REVERT: R  280 PHE cc_start: 0.8126 (t80) cc_final: 0.7873 (t80)
REVERT: R  281 MET cc_start: 0.8909 (ttm) cc_final: 0.8611 (ppp)
REVERT: R  287 PHE cc_start: 0.8581 (t80) cc_final: 0.7816 (t80)
REVERT: R  330 VAL cc_start: 0.9039 (t) cc_final: 0.8797 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2208
  time to fit residues: 62.1472
Evaluate side-chains
  178 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0020
   chunk 21 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  38 HIS
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.144747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.106945 restraints weight = 19410.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.108863 restraints weight = 17363.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.109938 restraints weight = 16719.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.6468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7205  Z= 0.184
  Angle     :  0.687  10.480   9747  Z= 0.354
  Chirality :  0.046   0.282   1087
  Planarity :  0.004   0.060   1220
  Dihedral  :  5.884  78.022    964
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.28), residues: 876
  helix:  0.72 (0.29), residues: 333
  sheet: -0.36 (0.50), residues: 110
  loop : -2.13 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 211 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.014   0.001   PHE A 334 
 TYR   0.012   0.002   TYR R 191 
 ARG   0.004   0.000   ARG A 313 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9474 (m110) cc_final: 0.9271 (m110)
REVERT: A   35 LYS cc_start: 0.9053 (ptpt) cc_final: 0.8567 (ptmm)
REVERT: A   39 LEU cc_start: 0.9234 (mt) cc_final: 0.9032 (mt)
REVERT: A  198 MET cc_start: 0.9161 (tpt) cc_final: 0.8748 (tpt)
REVERT: A  210 LYS cc_start: 0.9199 (pptt) cc_final: 0.7909 (mmpt)
REVERT: A  221 ILE cc_start: 0.8750 (mt) cc_final: 0.8411 (mt)
REVERT: A  261 ASP cc_start: 0.9076 (m-30) cc_final: 0.8834 (m-30)
REVERT: A  263 SER cc_start: 0.8819 (m) cc_final: 0.8380 (t)
REVERT: A  264 ILE cc_start: 0.8868 (mp) cc_final: 0.8614 (mp)
REVERT: A  306 GLN cc_start: 0.8471 (tp-100) cc_final: 0.8212 (tp-100)
REVERT: B   52 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7600 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7908 (m100) cc_final: 0.7301 (m100)
REVERT: B  105 TYR cc_start: 0.8188 (t80) cc_final: 0.7796 (t80)
REVERT: B  166 CYS cc_start: 0.7294 (t) cc_final: 0.6582 (m)
REVERT: B  235 PHE cc_start: 0.9249 (t80) cc_final: 0.8786 (t80)
REVERT: B  262 MET cc_start: 0.4218 (ppp) cc_final: 0.4013 (ppp)
REVERT: B  325 MET cc_start: 0.9281 (tpp) cc_final: 0.8627 (tpp)
REVERT: B  335 PHE cc_start: 0.8485 (m-80) cc_final: 0.7895 (m-80)
REVERT: G   40 PHE cc_start: 0.6643 (m-10) cc_final: 0.6311 (m-80)
REVERT: G   42 ASP cc_start: 0.7949 (m-30) cc_final: 0.7704 (m-30)
REVERT: R   29 GLU cc_start: 0.8530 (pp20) cc_final: 0.8231 (pm20)
REVERT: R   31 MET cc_start: 0.7163 (mmt) cc_final: 0.6928 (mmm)
REVERT: R   55 MET cc_start: 0.8546 (mmt) cc_final: 0.7879 (mmm)
REVERT: R   68 ASN cc_start: 0.7868 (m-40) cc_final: 0.7438 (m110)
REVERT: R   87 PHE cc_start: 0.8470 (m-80) cc_final: 0.7802 (m-80)
REVERT: R  104 MET cc_start: 0.8415 (ttt) cc_final: 0.8054 (tpp)
REVERT: R  110 ASN cc_start: 0.8995 (m-40) cc_final: 0.8515 (m-40)
REVERT: R  150 ASN cc_start: 0.8831 (t0) cc_final: 0.8588 (t0)
REVERT: R  180 TRP cc_start: 0.7460 (m100) cc_final: 0.6800 (m100)
REVERT: R  229 ILE cc_start: 0.9307 (mt) cc_final: 0.9037 (mt)
REVERT: R  251 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8390 (tp-100)
REVERT: R  253 LYS cc_start: 0.9507 (tmtt) cc_final: 0.9272 (tptp)
REVERT: R  255 MET cc_start: 0.8944 (mmp) cc_final: 0.8207 (mmp)
REVERT: R  272 GLU cc_start: 0.9161 (pm20) cc_final: 0.8913 (pm20)
REVERT: R  280 PHE cc_start: 0.8140 (t80) cc_final: 0.7874 (t80)
REVERT: R  281 MET cc_start: 0.8964 (ttm) cc_final: 0.8656 (ppp)
REVERT: R  287 PHE cc_start: 0.8654 (t80) cc_final: 0.7881 (t80)
REVERT: R  311 MET cc_start: 0.8705 (mmm) cc_final: 0.8386 (tpt)
REVERT: R  330 VAL cc_start: 0.9020 (t) cc_final: 0.8767 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2032
  time to fit residues: 56.3119
Evaluate side-chains
  183 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0770
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 77 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.145882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.108219 restraints weight = 18816.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.112971 restraints weight = 16840.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.113328 restraints weight = 12646.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.6604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7205  Z= 0.165
  Angle     :  0.660  10.601   9747  Z= 0.340
  Chirality :  0.045   0.274   1087
  Planarity :  0.004   0.057   1220
  Dihedral  :  5.699  76.117    964
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.28), residues: 876
  helix:  0.75 (0.29), residues: 334
  sheet: -0.48 (0.49), residues: 112
  loop : -2.12 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 211 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.028   0.001   PHE A 250 
 TYR   0.012   0.001   TYR R 218 
 ARG   0.004   0.000   ARG A 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2785.85 seconds
wall clock time: 52 minutes 25.27 seconds (3145.27 seconds total)