Starting phenix.real_space_refine
on Mon Apr 28 06:35:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9epr_19884/04_2025/9epr_19884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9epr_19884/04_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_19884/04_2025/9epr_19884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9epr_19884/04_2025/9epr_19884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9epr_19884/04_2025/9epr_19884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9epr_19884/04_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.91, per 1000 atoms: 0.84
  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: 1.68
  Conformation dependent library (CDL) restraints added in 944.2 milliseconds
  

  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: 0.71
  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: 1.90

  Time building geometry restraints manager: 2.01 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:             3.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.070
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.250
-------------------------------------------------------------------------------
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      :  0.005   0.126   7207  Z= 0.291
  Angle     :  0.931  12.559   9749  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13712 (  312)
  hydrogen bonds       : angle       7.53461 (  903)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.98708 (    2)
  covalent geometry    : bond        0.00447 ( 7205)
  covalent geometry    : angle       0.93110 ( 9747)
  Misc. bond           : bond        0.12609 (    1)

*********************** 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  : 0.744 
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: 0.2033
  time to fit residues: 88.6373
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  : 0.869 
-------------------------------------------------------------------------------
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 = 19520.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106805 restraints weight = 18567.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.108945 restraints weight = 14089.044|
|-----------------------------------------------------------------------------|
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   7207  Z= 0.190
  Angle     :  0.730   7.328   9749  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04694 (  312)
  hydrogen bonds       : angle       6.11880 (  903)
  SS BOND              : bond        0.00299 (    1)
  SS BOND              : angle       0.82404 (    2)
  covalent geometry    : bond        0.00394 ( 7205)
  covalent geometry    : angle       0.72985 ( 9747)
  Misc. bond           : bond        0.00006 (    1)

*********************** 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  : 0.753 
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: 0.9247 (pttp) cc_final: 0.8527 (mmtt)
REVERT: A  221 ILE cc_start: 0.8747 (mt) cc_final: 0.8365 (mt)
REVERT: A  222 ILE cc_start: 0.8949 (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: 0.8441 (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: 0.8170 (t80)
REVERT: A  313 ARG cc_start: 0.9142 (ttm170) cc_final: 0.8834 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9216 (t0) cc_final: 0.8533 (m110)
REVERT: B   42 ARG cc_start: 0.9006 (tmm160) cc_final: 0.8410 (ttp80)
REVERT: B   63 TRP cc_start: 0.8137 (m100) cc_final: 0.7354 (m100)
REVERT: B   79 LEU cc_start: 0.9534 (mp) cc_final: 0.9334 (mp)
REVERT: B  235 PHE cc_start: 0.9331 (t80) cc_final: 0.8890 (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: 0.6873 (m-10) cc_final: 0.6507 (m-10)
REVERT: R   55 MET cc_start: 0.8673 (mmt) cc_final: 0.7941 (mmm)
REVERT: R   68 ASN cc_start: 0.8536 (m-40) cc_final: 0.8278 (m110)
REVERT: R   87 PHE cc_start: 0.8827 (m-10) cc_final: 0.8295 (m-80)
REVERT: R  147 ASP cc_start: 0.8664 (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: 0.7752 (m100) cc_final: 0.6861 (m100)
REVERT: R  206 ASP cc_start: 0.6517 (t0) cc_final: 0.6083 (t0)
REVERT: R  229 ILE cc_start: 0.9322 (mt) cc_final: 0.9090 (mt)
REVERT: R  287 PHE cc_start: 0.8912 (t80) cc_final: 0.8095 (t80)
REVERT: R  305 ARG cc_start: 0.8651 (mpp-170) cc_final: 0.8379 (mpp-170)
REVERT: R  311 MET cc_start: 0.8754 (mpp) cc_final: 0.8542 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2092
  time to fit residues: 64.6629
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  : 0.740 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 83 optimal weight:    0.1980
   chunk 4 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0170
   chunk 41 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 54 optimal weight:    0.1980
   overall best weight:    0.2818

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.144727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.108505 restraints weight = 18496.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.113053 restraints weight = 15351.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.113826 restraints weight = 11495.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7207  Z= 0.125
  Angle     :  0.669  11.094   9749  Z= 0.350
  Chirality :  0.045   0.233   1087
  Planarity :  0.005   0.047   1220
  Dihedral  :  7.012  70.236    964
  Min Nonbonded Distance : 2.446

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: -2.09 (0.27), residues: 876
  helix:  0.00 (0.27), residues: 334
  sheet: -1.42 (0.42), residues: 140
  loop : -2.63 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 211 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.017   0.002   PHE G  64 
 TYR   0.018   0.001   TYR R  51 
 ARG   0.005   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  312)
  hydrogen bonds       : angle       5.73661 (  903)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       0.29236 (    2)
  covalent geometry    : bond        0.00262 ( 7205)
  covalent geometry    : angle       0.66866 ( 9747)
  Misc. bond           : bond        0.00057 (    1)

*********************** 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
  240 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.820 
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  198 MET cc_start: 0.8334 (tpt) cc_final: 0.7829 (tpt)
REVERT: A  210 LYS cc_start: 0.9142 (pttp) cc_final: 0.8500 (mmtt)
REVERT: A  221 ILE cc_start: 0.8545 (mt) cc_final: 0.8240 (mt)
REVERT: A  263 SER cc_start: 0.8891 (m) cc_final: 0.8475 (t)
REVERT: A  313 ARG cc_start: 0.9080 (ttm170) cc_final: 0.8767 (ttm-80)
REVERT: A  320 TYR cc_start: 0.7270 (m-80) cc_final: 0.5924 (m-80)
REVERT: A  333 GLN cc_start: 0.9382 (mp10) cc_final: 0.9101 (mp10)
REVERT: B   42 ARG cc_start: 0.8869 (tmm160) cc_final: 0.8441 (tmm160)
REVERT: B   43 ILE cc_start: 0.9227 (pt) cc_final: 0.8735 (mm)
REVERT: B   63 TRP cc_start: 0.7887 (m100) cc_final: 0.7209 (m100)
REVERT: B  166 CYS cc_start: 0.7323 (t) cc_final: 0.6844 (m)
REVERT: B  308 LEU cc_start: 0.9166 (mt) cc_final: 0.8617 (tt)
REVERT: B  325 MET cc_start: 0.8678 (tpp) cc_final: 0.8090 (tpt)
REVERT: B  332 TRP cc_start: 0.9171 (m-10) cc_final: 0.8605 (m-10)
REVERT: B  335 PHE cc_start: 0.8119 (m-80) cc_final: 0.7593 (m-80)
REVERT: G   42 ASP cc_start: 0.7795 (m-30) cc_final: 0.7432 (m-30)
REVERT: R   55 MET cc_start: 0.8644 (mmt) cc_final: 0.7956 (mmm)
REVERT: R   68 ASN cc_start: 0.8447 (m-40) cc_final: 0.8176 (m110)
REVERT: R   87 PHE cc_start: 0.8842 (m-10) cc_final: 0.8435 (m-80)
REVERT: R  104 MET cc_start: 0.8498 (ttt) cc_final: 0.8042 (tpp)
REVERT: R  107 MET cc_start: 0.8580 (tpt) cc_final: 0.8123 (tpt)
REVERT: R  150 ASN cc_start: 0.8710 (t0) cc_final: 0.8418 (t0)
REVERT: R  180 TRP cc_start: 0.7645 (m100) cc_final: 0.6775 (m100)
REVERT: R  206 ASP cc_start: 0.6414 (t0) cc_final: 0.6047 (t0)
REVERT: R  229 ILE cc_start: 0.9276 (mt) cc_final: 0.9045 (mt)
REVERT: R  250 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: R  253 LYS cc_start: 0.9448 (tmtt) cc_final: 0.9185 (tptp)
REVERT: R  272 GLU cc_start: 0.9007 (pm20) cc_final: 0.8746 (pm20)
REVERT: R  287 PHE cc_start: 0.8755 (t80) cc_final: 0.8011 (t80)
REVERT: R  305 ARG cc_start: 0.8719 (mpp-170) cc_final: 0.8486 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1742
  time to fit residues: 56.0001
Evaluate side-chains
  188 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 52 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 76 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
R  38 HIS
R 110 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 = 0.4123 r_free = 0.4123 target = 0.142216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.104016 restraints weight = 19124.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108904 restraints weight = 16176.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.109661 restraints weight = 11035.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7207  Z= 0.142
  Angle     :  0.669   8.440   9749  Z= 0.353
  Chirality :  0.046   0.246   1087
  Planarity :  0.005   0.047   1220
  Dihedral  :  6.399  67.573    964
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.28 (0.28), residues: 327
  sheet: -1.29 (0.42), residues: 140
  loop : -2.57 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 211 
 HIS   0.004   0.001   HIS R 335 
 PHE   0.022   0.002   PHE R 298 
 TYR   0.026   0.002   TYR A 320 
 ARG   0.005   0.001   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04004 (  312)
  hydrogen bonds       : angle       5.58891 (  903)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       0.79359 (    2)
  covalent geometry    : bond        0.00303 ( 7205)
  covalent geometry    : angle       0.66944 ( 9747)
  Misc. bond           : bond        0.00001 (    1)

*********************** 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
  225 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.809 
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: 0.8263 (ttp80) cc_final: 0.7937 (ptp-110)
REVERT: A   35 LYS cc_start: 0.8960 (ptpt) cc_final: 0.8522 (ptmt)
REVERT: A  198 MET cc_start: 0.8786 (tpt) cc_final: 0.8398 (tpt)
REVERT: A  221 ILE cc_start: 0.8796 (mt) cc_final: 0.8480 (mt)
REVERT: A  227 LEU cc_start: 0.8842 (mp) cc_final: 0.8205 (mp)
REVERT: A  263 SER cc_start: 0.8900 (m) cc_final: 0.8390 (t)
REVERT: A  264 ILE cc_start: 0.8833 (mp) cc_final: 0.8603 (mp)
REVERT: A  274 PHE cc_start: 0.8774 (t80) cc_final: 0.8372 (t80)
REVERT: A  313 ARG cc_start: 0.9046 (ttm170) cc_final: 0.8822 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9539 (t0) cc_final: 0.8738 (m110)
REVERT: A  333 GLN cc_start: 0.9468 (mp10) cc_final: 0.9113 (mp10)
REVERT: A  343 ILE cc_start: 0.8807 (mm) cc_final: 0.8562 (tp)
REVERT: B   42 ARG cc_start: 0.8965 (tmm160) cc_final: 0.8726 (tmt-80)
REVERT: B   43 ILE cc_start: 0.9292 (pt) cc_final: 0.8826 (mm)
REVERT: B   52 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7721 (mmm-85)
REVERT: B   63 TRP cc_start: 0.8137 (m100) cc_final: 0.7531 (m100)
REVERT: B  166 CYS cc_start: 0.7371 (t) cc_final: 0.6828 (m)
REVERT: B  234 PHE cc_start: 0.8571 (p90) cc_final: 0.8318 (p90)
REVERT: B  308 LEU cc_start: 0.9213 (mt) cc_final: 0.8533 (tt)
REVERT: B  325 MET cc_start: 0.9183 (tpp) cc_final: 0.8588 (tpp)
REVERT: B  335 PHE cc_start: 0.8242 (m-80) cc_final: 0.7696 (m-80)
REVERT: G   42 ASP cc_start: 0.7819 (m-30) cc_final: 0.7449 (m-30)
REVERT: R   55 MET cc_start: 0.8675 (mmt) cc_final: 0.7969 (mmm)
REVERT: R   68 ASN cc_start: 0.8277 (m-40) cc_final: 0.7921 (m110)
REVERT: R   72 MET cc_start: 0.9016 (tpt) cc_final: 0.8778 (tpt)
REVERT: R   76 MET cc_start: 0.8124 (mmm) cc_final: 0.7710 (tpp)
REVERT: R   87 PHE cc_start: 0.8897 (m-10) cc_final: 0.8544 (m-80)
REVERT: R  104 MET cc_start: 0.8559 (ttt) cc_final: 0.8159 (tpp)
REVERT: R  107 MET cc_start: 0.8453 (tpt) cc_final: 0.8141 (tpt)
REVERT: R  110 ASN cc_start: 0.9195 (m-40) cc_final: 0.8965 (m110)
REVERT: R  150 ASN cc_start: 0.8851 (t0) cc_final: 0.8566 (t0)
REVERT: R  180 TRP cc_start: 0.7724 (m100) cc_final: 0.7060 (m100)
REVERT: R  206 ASP cc_start: 0.6570 (t0) cc_final: 0.6093 (t0)
REVERT: R  229 ILE cc_start: 0.9346 (mt) cc_final: 0.9100 (mt)
REVERT: R  253 LYS cc_start: 0.9487 (tmtt) cc_final: 0.9227 (tptp)
REVERT: R  287 PHE cc_start: 0.8789 (t80) cc_final: 0.8097 (t80)
REVERT: R  305 ARG cc_start: 0.8815 (mpp-170) cc_final: 0.8552 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1907
  time to fit residues: 56.5981
Evaluate side-chains
  186 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 84 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 44 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 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 = 0.4128 r_free = 0.4128 target = 0.143294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.106137 restraints weight = 18334.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.110188 restraints weight = 16545.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.110760 restraints weight = 12416.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7207  Z= 0.141
  Angle     :  0.666   9.075   9749  Z= 0.350
  Chirality :  0.046   0.285   1087
  Planarity :  0.004   0.047   1220
  Dihedral  :  6.485  76.875    964
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  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: -1.64 (0.27), residues: 876
  helix:  0.40 (0.28), residues: 327
  sheet: -0.86 (0.46), residues: 118
  loop : -2.43 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A 211 
 HIS   0.004   0.001   HIS R 335 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.013   0.002   TYR R 191 
 ARG   0.006   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03841 (  312)
  hydrogen bonds       : angle       5.41855 (  903)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       0.72003 (    2)
  covalent geometry    : bond        0.00304 ( 7205)
  covalent geometry    : angle       0.66563 ( 9747)
  Misc. bond           : bond        0.00006 (    1)

*********************** 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
  222 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.742 
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: 0.8986 (ptpt) cc_final: 0.8605 (ptmt)
REVERT: A   50 VAL cc_start: 0.8749 (m) cc_final: 0.8518 (m)
REVERT: A   53 MET cc_start: 0.7687 (ptp) cc_final: 0.7367 (ppp)
REVERT: A  198 MET cc_start: 0.8946 (tpt) cc_final: 0.8515 (tpt)
REVERT: A  210 LYS cc_start: 0.9144 (pptt) cc_final: 0.8276 (mmtt)
REVERT: A  221 ILE cc_start: 0.8725 (mt) cc_final: 0.8433 (mt)
REVERT: A  227 LEU cc_start: 0.8719 (mp) cc_final: 0.8009 (mp)
REVERT: A  263 SER cc_start: 0.8850 (m) cc_final: 0.8373 (t)
REVERT: A  264 ILE cc_start: 0.8782 (mp) cc_final: 0.8557 (mp)
REVERT: A  274 PHE cc_start: 0.8675 (t80) cc_final: 0.8142 (t80)
REVERT: A  313 ARG cc_start: 0.9034 (ttm170) cc_final: 0.8826 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9397 (t0) cc_final: 0.8607 (m110)
REVERT: A  333 GLN cc_start: 0.9313 (mp10) cc_final: 0.9034 (mp10)
REVERT: B   42 ARG cc_start: 0.8840 (tmm160) cc_final: 0.8392 (tmm160)
REVERT: B   43 ILE cc_start: 0.9201 (pt) cc_final: 0.8733 (mm)
REVERT: B   52 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7535 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7932 (m100) cc_final: 0.7320 (m100)
REVERT: B  166 CYS cc_start: 0.7279 (t) cc_final: 0.6729 (m)
REVERT: B  308 LEU cc_start: 0.9011 (mt) cc_final: 0.8554 (tt)
REVERT: B  325 MET cc_start: 0.9141 (tpp) cc_final: 0.8512 (tpp)
REVERT: B  335 PHE cc_start: 0.8414 (m-80) cc_final: 0.7868 (m-80)
REVERT: G   40 PHE cc_start: 0.6481 (m-10) cc_final: 0.6206 (m-80)
REVERT: G   42 ASP cc_start: 0.7684 (m-30) cc_final: 0.7440 (m-30)
REVERT: R   55 MET cc_start: 0.8609 (mmt) cc_final: 0.7906 (mmm)
REVERT: R   68 ASN cc_start: 0.8112 (m-40) cc_final: 0.7737 (m110)
REVERT: R   76 MET cc_start: 0.8052 (mmm) cc_final: 0.7838 (tpp)
REVERT: R   87 PHE cc_start: 0.8923 (m-10) cc_final: 0.8325 (m-80)
REVERT: R  104 MET cc_start: 0.8586 (ttt) cc_final: 0.8152 (tpp)
REVERT: R  107 MET cc_start: 0.8381 (tpt) cc_final: 0.8097 (tpt)
REVERT: R  110 ASN cc_start: 0.9132 (m-40) cc_final: 0.8848 (m110)
REVERT: R  150 ASN cc_start: 0.8810 (t0) cc_final: 0.8526 (t0)
REVERT: R  180 TRP cc_start: 0.7536 (m100) cc_final: 0.6894 (m100)
REVERT: R  229 ILE cc_start: 0.9360 (mt) cc_final: 0.9107 (mt)
REVERT: R  250 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8470 (tm-30)
REVERT: R  251 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8322 (tp-100)
REVERT: R  253 LYS cc_start: 0.9435 (tmtt) cc_final: 0.9203 (tptp)
REVERT: R  255 MET cc_start: 0.8943 (mmp) cc_final: 0.7987 (mmp)
REVERT: R  272 GLU cc_start: 0.8969 (pm20) cc_final: 0.8577 (pm20)
REVERT: R  287 PHE cc_start: 0.8791 (t80) cc_final: 0.8120 (t80)
REVERT: R  305 ARG cc_start: 0.8758 (mpp-170) cc_final: 0.8521 (mpp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.1947
  time to fit residues: 57.0696
Evaluate side-chains
  188 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 81 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 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 = 0.4104 r_free = 0.4104 target = 0.140862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.103227 restraints weight = 19300.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.104689 restraints weight = 16486.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.106187 restraints weight = 13971.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7207  Z= 0.164
  Angle     :  0.674   8.304   9749  Z= 0.357
  Chirality :  0.047   0.223   1087
  Planarity :  0.004   0.047   1220
  Dihedral  :  6.745  88.729    964
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.86 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.56 (0.27), residues: 876
  helix:  0.44 (0.28), residues: 328
  sheet: -0.85 (0.46), residues: 117
  loop : -2.34 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 211 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.021   0.002   TYR R 223 
 ARG   0.003   0.000   ARG R 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  312)
  hydrogen bonds       : angle       5.47060 (  903)
  SS BOND              : bond        0.00337 (    1)
  SS BOND              : angle       0.88828 (    2)
  covalent geometry    : bond        0.00342 ( 7205)
  covalent geometry    : angle       0.67386 ( 9747)
  Misc. bond           : bond        0.00016 (    1)

*********************** 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
  216 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.842 
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: A   35 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8466 (ptmt)
REVERT: A  198 MET cc_start: 0.9046 (tpt) cc_final: 0.8664 (tpt)
REVERT: A  210 LYS cc_start: 0.9123 (pptt) cc_final: 0.8194 (mmtt)
REVERT: A  221 ILE cc_start: 0.8829 (mt) cc_final: 0.8553 (mt)
REVERT: A  227 LEU cc_start: 0.8758 (mp) cc_final: 0.8117 (mp)
REVERT: A  263 SER cc_start: 0.8850 (m) cc_final: 0.8388 (t)
REVERT: A  264 ILE cc_start: 0.8808 (mp) cc_final: 0.8557 (mp)
REVERT: A  274 PHE cc_start: 0.8733 (t80) cc_final: 0.8171 (t80)
REVERT: A  306 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8331 (tp-100)
REVERT: A  333 GLN cc_start: 0.9306 (mp10) cc_final: 0.9028 (mp10)
REVERT: A  353 LEU cc_start: 0.8747 (mp) cc_final: 0.8427 (mp)
REVERT: B   42 ARG cc_start: 0.8874 (tmm160) cc_final: 0.8537 (tmm160)
REVERT: B   43 ILE cc_start: 0.9278 (pt) cc_final: 0.9022 (mm)
REVERT: B   52 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7600 (mmm-85)
REVERT: B   63 TRP cc_start: 0.8055 (m100) cc_final: 0.7596 (m100)
REVERT: B  103 CYS cc_start: 0.9107 (p) cc_final: 0.8880 (p)
REVERT: B  166 CYS cc_start: 0.7407 (t) cc_final: 0.6708 (m)
REVERT: B  294 CYS cc_start: 0.9542 (t) cc_final: 0.9260 (t)
REVERT: B  308 LEU cc_start: 0.8890 (mt) cc_final: 0.8552 (tp)
REVERT: B  325 MET cc_start: 0.9261 (tpp) cc_final: 0.8654 (tpp)
REVERT: B  335 PHE cc_start: 0.8557 (m-80) cc_final: 0.7957 (m-80)
REVERT: G   40 PHE cc_start: 0.6627 (m-10) cc_final: 0.6325 (m-80)
REVERT: R   55 MET cc_start: 0.8615 (mmt) cc_final: 0.7968 (mmm)
REVERT: R   68 ASN cc_start: 0.8166 (m-40) cc_final: 0.7892 (m110)
REVERT: R   87 PHE cc_start: 0.8919 (m-10) cc_final: 0.8449 (m-80)
REVERT: R  107 MET cc_start: 0.8481 (tpt) cc_final: 0.8237 (tpt)
REVERT: R  110 ASN cc_start: 0.9079 (m-40) cc_final: 0.8795 (m110)
REVERT: R  150 ASN cc_start: 0.8810 (t0) cc_final: 0.8537 (t0)
REVERT: R  180 TRP cc_start: 0.7589 (m100) cc_final: 0.7136 (m100)
REVERT: R  206 ASP cc_start: 0.6319 (t0) cc_final: 0.6001 (t0)
REVERT: R  229 ILE cc_start: 0.9349 (mt) cc_final: 0.9073 (mt)
REVERT: R  250 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8545 (tm-30)
REVERT: R  251 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8345 (tp-100)
REVERT: R  253 LYS cc_start: 0.9491 (tmtt) cc_final: 0.9263 (tptp)
REVERT: R  255 MET cc_start: 0.8918 (mmp) cc_final: 0.8039 (mmp)
REVERT: R  287 PHE cc_start: 0.8807 (t80) cc_final: 0.8004 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1997
  time to fit residues: 57.3408
Evaluate side-chains
  181 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  44 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 = 0.4140 r_free = 0.4140 target = 0.144497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.107213 restraints weight = 18619.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.111195 restraints weight = 17016.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.111577 restraints weight = 13233.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.5997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7207  Z= 0.127
  Angle     :  0.687  10.465   9749  Z= 0.354
  Chirality :  0.047   0.273   1087
  Planarity :  0.004   0.047   1220
  Dihedral  :  6.329  82.752    964
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  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: -1.45 (0.28), residues: 876
  helix:  0.59 (0.29), residues: 334
  sheet: -1.14 (0.44), residues: 131
  loop : -2.28 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP A 211 
 HIS   0.003   0.001   HIS R 335 
 PHE   0.015   0.001   PHE R 298 
 TYR   0.026   0.002   TYR R  51 
 ARG   0.007   0.001   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03747 (  312)
  hydrogen bonds       : angle       5.27985 (  903)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.54129 (    2)
  covalent geometry    : bond        0.00273 ( 7205)
  covalent geometry    : angle       0.68682 ( 9747)
  Misc. bond           : bond        0.00035 (    1)

*********************** 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
  226 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.741 
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: 0.9002 (ptpt) cc_final: 0.8576 (ptmm)
REVERT: A  198 MET cc_start: 0.9094 (tpt) cc_final: 0.8537 (tpt)
REVERT: A  210 LYS cc_start: 0.9109 (pptt) cc_final: 0.8123 (mmtt)
REVERT: A  221 ILE cc_start: 0.8615 (mt) cc_final: 0.8267 (mt)
REVERT: A  261 ASP cc_start: 0.9056 (m-30) cc_final: 0.8815 (m-30)
REVERT: A  263 SER cc_start: 0.8812 (m) cc_final: 0.8326 (t)
REVERT: A  264 ILE cc_start: 0.8816 (mp) cc_final: 0.8543 (mp)
REVERT: A  306 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8328 (tp-100)
REVERT: B   42 ARG cc_start: 0.8835 (tmm160) cc_final: 0.8416 (tmm160)
REVERT: B   43 ILE cc_start: 0.9107 (pt) cc_final: 0.8692 (mm)
REVERT: B   52 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7485 (mmm-85)
REVERT: B   63 TRP cc_start: 0.7864 (m100) cc_final: 0.7408 (m100)
REVERT: B   75 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8154 (tp-100)
REVERT: B  166 CYS cc_start: 0.7272 (t) cc_final: 0.6686 (m)
REVERT: B  235 PHE cc_start: 0.9231 (t80) cc_final: 0.8730 (t80)
REVERT: B  313 ASN cc_start: 0.8094 (t0) cc_final: 0.7857 (t0)
REVERT: B  325 MET cc_start: 0.9192 (tpp) cc_final: 0.8563 (tpp)
REVERT: B  335 PHE cc_start: 0.8456 (m-80) cc_final: 0.7909 (m-80)
REVERT: G   40 PHE cc_start: 0.6595 (m-10) cc_final: 0.6387 (m-80)
REVERT: R   38 HIS cc_start: 0.8447 (t70) cc_final: 0.8210 (t-90)
REVERT: R   42 PHE cc_start: 0.6650 (m-10) cc_final: 0.6126 (m-10)
REVERT: R   55 MET cc_start: 0.8509 (mmt) cc_final: 0.7869 (mmm)
REVERT: R   68 ASN cc_start: 0.8212 (m-40) cc_final: 0.7868 (m110)
REVERT: R   87 PHE cc_start: 0.8942 (m-10) cc_final: 0.8339 (m-80)
REVERT: R  104 MET cc_start: 0.8479 (ttt) cc_final: 0.8155 (tpp)
REVERT: R  110 ASN cc_start: 0.9047 (m-40) cc_final: 0.8839 (m110)
REVERT: R  150 ASN cc_start: 0.8751 (t0) cc_final: 0.8499 (t0)
REVERT: R  180 TRP cc_start: 0.7452 (m100) cc_final: 0.6821 (m100)
REVERT: R  206 ASP cc_start: 0.6269 (t0) cc_final: 0.5992 (t0)
REVERT: R  229 ILE cc_start: 0.9316 (mt) cc_final: 0.9044 (mt)
REVERT: R  250 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: R  251 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8341 (tp-100)
REVERT: R  253 LYS cc_start: 0.9470 (tmtt) cc_final: 0.9236 (tptp)
REVERT: R  255 MET cc_start: 0.8907 (mmp) cc_final: 0.8071 (mmp)
REVERT: R  272 GLU cc_start: 0.9086 (pm20) cc_final: 0.8807 (pm20)
REVERT: R  281 MET cc_start: 0.8848 (ttm) cc_final: 0.8593 (ppp)
REVERT: R  287 PHE cc_start: 0.8634 (t80) cc_final: 0.7859 (t80)
REVERT: R  308 LEU cc_start: 0.9292 (tp) cc_final: 0.9080 (tp)
REVERT: R  330 VAL cc_start: 0.9065 (t) cc_final: 0.8800 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1938
  time to fit residues: 58.4364
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  : 0.867 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0670
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:    0.1980
   chunk 58 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.145293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.107183 restraints weight = 19015.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.112124 restraints weight = 17100.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.112783 restraints weight = 12073.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.6184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7207  Z= 0.123
  Angle     :  0.667  10.008   9749  Z= 0.343
  Chirality :  0.046   0.300   1087
  Planarity :  0.005   0.046   1220
  Dihedral  :  6.029  80.174    964
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.26 %
    Favored  : 99.61 %
  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: -1.23 (0.28), residues: 876
  helix:  0.85 (0.29), residues: 329
  sheet: -1.00 (0.44), residues: 135
  loop : -2.20 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 211 
 HIS   0.010   0.001   HIS B 266 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.021   0.002   TYR R  51 
 ARG   0.007   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  312)
  hydrogen bonds       : angle       5.16691 (  903)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       0.63932 (    2)
  covalent geometry    : bond        0.00264 ( 7205)
  covalent geometry    : angle       0.66713 ( 9747)
  Misc. bond           : bond        0.00034 (    1)

*********************** 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
  219 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 218
  time to evaluate  : 0.986 
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: 0.9010 (ptpt) cc_final: 0.8502 (ptmm)
REVERT: A  198 MET cc_start: 0.9107 (tpt) cc_final: 0.8492 (tpt)
REVERT: A  210 LYS cc_start: 0.9153 (pptt) cc_final: 0.8100 (mmtt)
REVERT: A  221 ILE cc_start: 0.8638 (mt) cc_final: 0.8311 (mt)
REVERT: A  227 LEU cc_start: 0.8653 (mp) cc_final: 0.7957 (mp)
REVERT: A  261 ASP cc_start: 0.9103 (m-30) cc_final: 0.8861 (m-30)
REVERT: A  263 SER cc_start: 0.8823 (m) cc_final: 0.8354 (t)
REVERT: A  264 ILE cc_start: 0.8841 (mp) cc_final: 0.8577 (mp)
REVERT: A  274 PHE cc_start: 0.8626 (t80) cc_final: 0.8131 (t80)
REVERT: A  306 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8299 (tp-100)
REVERT: B   42 ARG cc_start: 0.8804 (tmm160) cc_final: 0.8312 (tmm160)
REVERT: B   43 ILE cc_start: 0.8961 (pt) cc_final: 0.8437 (mm)
REVERT: B   63 TRP cc_start: 0.7758 (m100) cc_final: 0.7329 (m100)
REVERT: B  166 CYS cc_start: 0.7231 (t) cc_final: 0.6593 (m)
REVERT: B  235 PHE cc_start: 0.9252 (t80) cc_final: 0.8864 (t80)
REVERT: B  325 MET cc_start: 0.9222 (tpp) cc_final: 0.8601 (tpp)
REVERT: B  335 PHE cc_start: 0.8426 (m-80) cc_final: 0.7853 (m-80)
REVERT: G   40 PHE cc_start: 0.6599 (m-10) cc_final: 0.6236 (m-80)
REVERT: G   42 ASP cc_start: 0.8017 (m-30) cc_final: 0.7750 (m-30)
REVERT: R   55 MET cc_start: 0.8512 (mmt) cc_final: 0.7859 (mmm)
REVERT: R   68 ASN cc_start: 0.7987 (m-40) cc_final: 0.7571 (m110)
REVERT: R   87 PHE cc_start: 0.8894 (m-10) cc_final: 0.8413 (m-80)
REVERT: R  104 MET cc_start: 0.8481 (ttt) cc_final: 0.8127 (tpp)
REVERT: R  110 ASN cc_start: 0.8993 (m-40) cc_final: 0.8778 (m110)
REVERT: R  150 ASN cc_start: 0.8737 (t0) cc_final: 0.8493 (t0)
REVERT: R  180 TRP cc_start: 0.7507 (m100) cc_final: 0.6845 (m100)
REVERT: R  206 ASP cc_start: 0.6347 (t0) cc_final: 0.6021 (t0)
REVERT: R  229 ILE cc_start: 0.9274 (mt) cc_final: 0.8989 (mt)
REVERT: R  250 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: R  251 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8325 (tp-100)
REVERT: R  253 LYS cc_start: 0.9470 (tmtt) cc_final: 0.9224 (tptp)
REVERT: R  255 MET cc_start: 0.8923 (mmp) cc_final: 0.8120 (mmp)
REVERT: R  272 GLU cc_start: 0.9102 (pm20) cc_final: 0.8834 (pm20)
REVERT: R  281 MET cc_start: 0.8862 (ttm) cc_final: 0.8577 (ppp)
REVERT: R  287 PHE cc_start: 0.8632 (t80) cc_final: 0.7868 (t80)
REVERT: R  308 LEU cc_start: 0.9290 (tp) cc_final: 0.9062 (tp)
REVERT: R  330 VAL cc_start: 0.9056 (t) cc_final: 0.8786 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1909
  time to fit residues: 56.4687
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  : 0.813 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0870
   chunk 50 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0870
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
B  75 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.145384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.107635 restraints weight = 19228.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.109620 restraints weight = 17159.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.111265 restraints weight = 13720.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.6382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7207  Z= 0.122
  Angle     :  0.671   9.748   9749  Z= 0.345
  Chirality :  0.045   0.279   1087
  Planarity :  0.004   0.046   1220
  Dihedral  :  5.837  76.964    964
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -1.12 (0.28), residues: 876
  helix:  0.92 (0.29), residues: 328
  sheet: -0.85 (0.45), residues: 131
  loop : -2.14 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 211 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.024   0.002   TYR R 126 
 ARG   0.007   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  312)
  hydrogen bonds       : angle       5.09221 (  903)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       0.48446 (    2)
  covalent geometry    : bond        0.00263 ( 7205)
  covalent geometry    : angle       0.67141 ( 9747)
  Misc. bond           : bond        0.00041 (    1)

*********************** 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
  216 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 1.013 
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: 0.9020 (ptpt) cc_final: 0.8543 (ptmt)
REVERT: A  198 MET cc_start: 0.9188 (tpt) cc_final: 0.8763 (tpt)
REVERT: A  221 ILE cc_start: 0.8648 (mt) cc_final: 0.8221 (mt)
REVERT: A  227 LEU cc_start: 0.8648 (mp) cc_final: 0.7953 (mp)
REVERT: A  261 ASP cc_start: 0.9068 (m-30) cc_final: 0.8768 (m-30)
REVERT: A  262 THR cc_start: 0.8396 (p) cc_final: 0.8086 (m)
REVERT: A  263 SER cc_start: 0.8793 (m) cc_final: 0.8366 (t)
REVERT: A  264 ILE cc_start: 0.8870 (mp) cc_final: 0.8620 (mp)
REVERT: A  274 PHE cc_start: 0.8599 (t80) cc_final: 0.8094 (t80)
REVERT: A  306 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8307 (tp-100)
REVERT: A  343 ILE cc_start: 0.8764 (mm) cc_final: 0.8516 (tp)
REVERT: B   54 HIS cc_start: 0.8159 (m-70) cc_final: 0.7766 (p-80)
REVERT: B   58 ILE cc_start: 0.9532 (mt) cc_final: 0.9284 (mt)
REVERT: B   63 TRP cc_start: 0.7735 (m100) cc_final: 0.7251 (m100)
REVERT: B  166 CYS cc_start: 0.7319 (t) cc_final: 0.6603 (m)
REVERT: B  235 PHE cc_start: 0.9214 (t80) cc_final: 0.8834 (t80)
REVERT: B  325 MET cc_start: 0.9241 (tpp) cc_final: 0.8620 (tpp)
REVERT: G   40 PHE cc_start: 0.6587 (m-10) cc_final: 0.6275 (m-80)
REVERT: R   27 LEU cc_start: 0.9043 (tt) cc_final: 0.8808 (tt)
REVERT: R   55 MET cc_start: 0.8520 (mmt) cc_final: 0.7884 (mmm)
REVERT: R   68 ASN cc_start: 0.7905 (m-40) cc_final: 0.7423 (m110)
REVERT: R   87 PHE cc_start: 0.8943 (m-10) cc_final: 0.8418 (m-80)
REVERT: R  104 MET cc_start: 0.8440 (ttt) cc_final: 0.8155 (tpp)
REVERT: R  110 ASN cc_start: 0.8998 (m-40) cc_final: 0.8729 (m110)
REVERT: R  154 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7046 (mptt)
REVERT: R  180 TRP cc_start: 0.7452 (m100) cc_final: 0.6814 (m100)
REVERT: R  181 THR cc_start: 0.9060 (p) cc_final: 0.8858 (p)
REVERT: R  206 ASP cc_start: 0.6491 (t0) cc_final: 0.6230 (t0)
REVERT: R  229 ILE cc_start: 0.9281 (mt) cc_final: 0.9016 (mt)
REVERT: R  250 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8442 (tm-30)
REVERT: R  251 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8330 (tp-100)
REVERT: R  253 LYS cc_start: 0.9465 (tmtt) cc_final: 0.9217 (tptp)
REVERT: R  255 MET cc_start: 0.8930 (mmp) cc_final: 0.8125 (mmp)
REVERT: R  272 GLU cc_start: 0.9162 (pm20) cc_final: 0.8893 (pm20)
REVERT: R  287 PHE cc_start: 0.8644 (t80) cc_final: 0.7868 (t80)
REVERT: R  311 MET cc_start: 0.8610 (mmm) cc_final: 0.7882 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2038
  time to fit residues: 60.4000
Evaluate side-chains
  177 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 87 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** 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 = 0.4130 r_free = 0.4130 target = 0.144110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.106204 restraints weight = 19100.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.111162 restraints weight = 17685.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.111719 restraints weight = 12182.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.6433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7207  Z= 0.135
  Angle     :  0.689   9.343   9749  Z= 0.357
  Chirality :  0.046   0.281   1087
  Planarity :  0.005   0.070   1220
  Dihedral  :  5.790  76.162    964
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  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: -1.10 (0.28), residues: 876
  helix:  0.88 (0.29), residues: 329
  sheet: -0.39 (0.49), residues: 112
  loop : -2.21 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 211 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.015   0.002   TYR R  51 
 ARG   0.006   0.001   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  312)
  hydrogen bonds       : angle       5.09125 (  903)
  SS BOND              : bond        0.00299 (    1)
  SS BOND              : angle       0.75516 (    2)
  covalent geometry    : bond        0.00288 ( 7205)
  covalent geometry    : angle       0.68920 ( 9747)
  Misc. bond           : bond        0.00043 (    1)

********************** 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
  211 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.950 
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   22 ASN cc_start: 0.9481 (m110) cc_final: 0.9278 (m110)
REVERT: A   35 LYS cc_start: 0.9002 (ptpt) cc_final: 0.8516 (ptmm)
REVERT: A   39 LEU cc_start: 0.9254 (mt) cc_final: 0.9039 (mt)
REVERT: A  198 MET cc_start: 0.9175 (tpt) cc_final: 0.8786 (tpt)
REVERT: A  221 ILE cc_start: 0.8604 (mt) cc_final: 0.8172 (mt)
REVERT: A  227 LEU cc_start: 0.8676 (mp) cc_final: 0.7957 (mp)
REVERT: A  261 ASP cc_start: 0.9126 (m-30) cc_final: 0.8857 (m-30)
REVERT: A  262 THR cc_start: 0.8393 (p) cc_final: 0.8127 (m)
REVERT: A  263 SER cc_start: 0.8812 (m) cc_final: 0.8398 (t)
REVERT: A  264 ILE cc_start: 0.8814 (mp) cc_final: 0.8550 (mp)
REVERT: A  274 PHE cc_start: 0.8630 (t80) cc_final: 0.8139 (t80)
REVERT: A  302 TYR cc_start: 0.8934 (t80) cc_final: 0.8630 (t80)
REVERT: B   63 TRP cc_start: 0.7817 (m100) cc_final: 0.7259 (m100)
REVERT: B  105 TYR cc_start: 0.8537 (t80) cc_final: 0.7984 (t80)
REVERT: B  166 CYS cc_start: 0.7296 (t) cc_final: 0.6594 (m)
REVERT: B  235 PHE cc_start: 0.9265 (t80) cc_final: 0.8767 (t80)
REVERT: B  325 MET cc_start: 0.9218 (tpp) cc_final: 0.8607 (tpp)
REVERT: B  335 PHE cc_start: 0.9079 (m-80) cc_final: 0.8334 (m-80)
REVERT: G   40 PHE cc_start: 0.6604 (m-10) cc_final: 0.6321 (m-80)
REVERT: G   42 ASP cc_start: 0.7979 (m-30) cc_final: 0.7704 (m-30)
REVERT: R   31 MET cc_start: 0.7647 (mmm) cc_final: 0.7354 (mmm)
REVERT: R   55 MET cc_start: 0.8489 (mmt) cc_final: 0.7854 (mmm)
REVERT: R   68 ASN cc_start: 0.8089 (m-40) cc_final: 0.7689 (m110)
REVERT: R   87 PHE cc_start: 0.8864 (m-10) cc_final: 0.8327 (m-80)
REVERT: R  104 MET cc_start: 0.8396 (ttt) cc_final: 0.8030 (tpp)
REVERT: R  110 ASN cc_start: 0.9019 (m-40) cc_final: 0.8583 (m-40)
REVERT: R  150 ASN cc_start: 0.8618 (t0) cc_final: 0.8372 (t0)
REVERT: R  180 TRP cc_start: 0.7531 (m100) cc_final: 0.6888 (m100)
REVERT: R  206 ASP cc_start: 0.6406 (t0) cc_final: 0.6205 (t0)
REVERT: R  229 ILE cc_start: 0.9282 (mt) cc_final: 0.8973 (mt)
REVERT: R  250 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8441 (tm-30)
REVERT: R  251 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8294 (tp-100)
REVERT: R  253 LYS cc_start: 0.9442 (tmtt) cc_final: 0.9193 (tptp)
REVERT: R  255 MET cc_start: 0.8922 (mmp) cc_final: 0.8142 (mmp)
REVERT: R  272 GLU cc_start: 0.9139 (pm20) cc_final: 0.8862 (pm20)
REVERT: R  280 PHE cc_start: 0.8095 (t80) cc_final: 0.7823 (t80)
REVERT: R  287 PHE cc_start: 0.8552 (t80) cc_final: 0.7797 (t80)
REVERT: R  308 LEU cc_start: 0.9274 (tp) cc_final: 0.9062 (tp)
REVERT: R  311 MET cc_start: 0.8810 (mmm) cc_final: 0.8577 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2173
  time to fit residues: 62.2233
Evaluate side-chains
  173 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 10 optimal weight:   20.0000
   chunk 45 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 70 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 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 = 0.4140 r_free = 0.4140 target = 0.144390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.105550 restraints weight = 18917.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.109191 restraints weight = 14047.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.110620 restraints weight = 10943.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.6613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7207  Z= 0.130
  Angle     :  0.679   9.152   9749  Z= 0.353
  Chirality :  0.046   0.284   1087
  Planarity :  0.005   0.063   1220
  Dihedral  :  5.741  75.580    964
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  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: -1.14 (0.28), residues: 876
  helix:  0.85 (0.29), residues: 337
  sheet: -0.42 (0.49), residues: 110
  loop : -2.27 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 211 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.015   0.002   TYR R  51 
 ARG   0.005   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  312)
  hydrogen bonds       : angle       5.11990 (  903)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.77744 (    2)
  covalent geometry    : bond        0.00278 ( 7205)
  covalent geometry    : angle       0.67941 ( 9747)
  Misc. bond           : bond        0.00048 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3921.26 seconds
wall clock time: 70 minutes 26.45 seconds (4226.45 seconds total)