Starting phenix.real_space_refine
on Fri Aug 22 19:09:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9epr_19884/08_2025/9epr_19884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9epr_19884/08_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_19884/08_2025/9epr_19884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9epr_19884/08_2025/9epr_19884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9epr_19884/08_2025/9epr_19884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9epr_19884/08_2025/9epr_19884.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.87, per 1000 atoms: 0.27
  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: 0.56
  Conformation dependent library (CDL) restraints added in 317.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.24
  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: 1.07

  Time building geometry restraints manager: 0.78 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.310
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.860
-------------------------------------------------------------------------------
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 : 12.98
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.94 (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
 ARG   0.004   0.000   ARG R 148 
 TYR   0.018   0.002   TYR B 145 
 PHE   0.018   0.002   PHE A 189 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.009   0.001   HIS R 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 7205)
  covalent geometry    : angle       0.93110 ( 9747)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.98708 (    2)
  hydrogen bonds       : bond        0.13712 (  312)
  hydrogen bonds       : angle       7.53461 (  903)
  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  : 0.298 
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   28 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8100 (tm-30)
REVERT: A   32 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7604 (ptp-110)
REVERT: A   34 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7829 (p)
REVERT: A  197 LYS cc_start: 0.8524 (mttt) cc_final: 0.8227 (mmtm)
REVERT: A  198 MET cc_start: 0.9114 (ttm) cc_final: 0.8881 (tpt)
REVERT: A  209 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8144 (tptt)
REVERT: A  210 LYS cc_start: 0.9284 (pptt) cc_final: 0.9071 (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: 0.8884 (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: 0.8328 (m)
REVERT: A  263 SER cc_start: 0.8893 (m) cc_final: 0.8197 (t)
REVERT: A  264 ILE cc_start: 0.8624 (mp) cc_final: 0.8403 (mp)
REVERT: A  274 PHE cc_start: 0.8171 (t80) cc_final: 0.7904 (t80)
REVERT: A  303 ILE cc_start: 0.8780 (tt) cc_final: 0.8564 (tt)
REVERT: A  313 ARG cc_start: 0.9285 (ttm170) cc_final: 0.8953 (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: 0.8859 (mt)
REVERT: A  345 LYS cc_start: 0.8549 (mttt) cc_final: 0.8347 (mmtt)
REVERT: B   62 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6401 (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: 0.8660 (pp)
REVERT: B   78 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7594 (mmmt)
REVERT: B  103 CYS cc_start: 0.8858 (p) cc_final: 0.8345 (p)
REVERT: B  250 CYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8475 (m)
REVERT: B  277 SER cc_start: 0.6932 (OUTLIER) cc_final: 0.5797 (m)
REVERT: B  280 LYS cc_start: 0.8539 (tptt) cc_final: 0.8140 (mmmm)
REVERT: B  286 LEU cc_start: 0.9375 (mp) cc_final: 0.8781 (mm)
REVERT: B  293 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7410 (p0)
REVERT: B  307 VAL cc_start: 0.8463 (t) cc_final: 0.8200 (p)
REVERT: B  308 LEU cc_start: 0.9126 (mt) cc_final: 0.8673 (tp)
REVERT: B  325 MET cc_start: 0.9303 (tpt) cc_final: 0.9077 (tpp)
REVERT: B  335 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8644 (m-10)
REVERT: G   40 PHE cc_start: 0.6743 (t80) cc_final: 0.6529 (m-80)
REVERT: G   45 GLU cc_start: 0.8941 (mp0) cc_final: 0.8539 (pp20)
REVERT: G   50 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9092 (mp0)
REVERT: G   64 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7519 (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: 0.8400 (t-90)
REVERT: R   45 MET cc_start: 0.5385 (pp-130) cc_final: 0.4635 (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: 0.8398 (mmm)
REVERT: R  104 MET cc_start: 0.8432 (tmm) cc_final: 0.7958 (ptt)
REVERT: R  107 MET cc_start: 0.8928 (tpp) cc_final: 0.8293 (tpt)
REVERT: R  206 ASP cc_start: 0.7103 (t0) cc_final: 0.6846 (t0)
REVERT: R  233 CYS cc_start: 0.8948 (m) cc_final: 0.8748 (p)
REVERT: R  246 LYS cc_start: 0.9763 (tttt) cc_final: 0.9520 (ptmm)
REVERT: R  250 GLU cc_start: 0.9114 (tp30) cc_final: 0.8098 (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: 0.8083 (mmm)
REVERT: R  281 MET cc_start: 0.8947 (ttm) cc_final: 0.8675 (ttt)
REVERT: R  287 PHE cc_start: 0.8474 (t80) cc_final: 0.7670 (t80)
REVERT: R  305 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8013 (mpp-170)
REVERT: R  311 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8038 (mpt)
REVERT: R  334 SER cc_start: 0.8685 (m) cc_final: 0.8463 (m)
  outliers start: 111
  outliers final: 46
  residues processed: 336
  average time/residue: 0.0957
  time to fit residues: 42.0457
Evaluate side-chains
  261 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 199
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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  88 ASN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 110 ASN
R 150 ASN
R 251 GLN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.138597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.102076 restraints weight = 19440.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.104636 restraints weight = 19731.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.106818 restraints weight = 14712.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.108276 restraints weight = 11088.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.109964 restraints weight = 9754.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    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 = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7207  Z= 0.210
  Angle     :  0.749   7.063   9749  Z= 0.405
  Chirality :  0.048   0.209   1087
  Planarity :  0.005   0.050   1220
  Dihedral  :  8.870 106.683    964
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.88 (0.26), residues: 876
  helix: -0.81 (0.26), residues: 330
  sheet: -2.06 (0.40), residues: 126
  loop : -2.82 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.021   0.002   TYR R 214 
 PHE   0.027   0.002   PHE G  64 
 TRP   0.051   0.003   TRP A 211 
 HIS   0.007   0.002   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 7205)
  covalent geometry    : angle       0.74907 ( 9747)
  SS BOND              : bond        0.00315 (    1)
  SS BOND              : angle       0.96993 (    2)
  hydrogen bonds       : bond        0.04823 (  312)
  hydrogen bonds       : angle       6.15763 (  903)
  Misc. bond           : bond        0.00078 (    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
  241 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.289 
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  210 LYS cc_start: 0.9259 (pttp) cc_final: 0.8661 (mmtt)
REVERT: A  221 ILE cc_start: 0.8734 (mt) cc_final: 0.8352 (mt)
REVERT: A  222 ILE cc_start: 0.8960 (mt) cc_final: 0.8716 (mt)
REVERT: A  227 LEU cc_start: 0.9238 (mt) cc_final: 0.8760 (mt)
REVERT: A  263 SER cc_start: 0.8970 (m) cc_final: 0.8494 (t)
REVERT: A  264 ILE cc_start: 0.8673 (mp) cc_final: 0.8456 (mp)
REVERT: A  274 PHE cc_start: 0.8715 (t80) cc_final: 0.8219 (t80)
REVERT: A  313 ARG cc_start: 0.9108 (ttm170) cc_final: 0.8806 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9223 (t0) cc_final: 0.8584 (m110)
REVERT: B   42 ARG cc_start: 0.8961 (tmm160) cc_final: 0.8377 (ttp80)
REVERT: B   63 TRP cc_start: 0.8207 (m100) cc_final: 0.7544 (m100)
REVERT: B   89 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8358 (mtpt)
REVERT: B  235 PHE cc_start: 0.9357 (t80) cc_final: 0.8874 (t80)
REVERT: B  280 LYS cc_start: 0.8683 (tptt) cc_final: 0.7403 (mmtt)
REVERT: B  308 LEU cc_start: 0.9262 (mt) cc_final: 0.9032 (mt)
REVERT: G   40 PHE cc_start: 0.7204 (t80) cc_final: 0.6528 (m-80)
REVERT: G   46 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8545 (pt0)
REVERT: R   42 PHE cc_start: 0.6813 (m-10) cc_final: 0.6519 (m-10)
REVERT: R   55 MET cc_start: 0.8684 (mmt) cc_final: 0.7978 (mmm)
REVERT: R   87 PHE cc_start: 0.8814 (m-10) cc_final: 0.8260 (m-80)
REVERT: R  150 ASN cc_start: 0.8553 (t0) cc_final: 0.8308 (t0)
REVERT: R  206 ASP cc_start: 0.6312 (t0) cc_final: 0.6033 (t0)
REVERT: R  233 CYS cc_start: 0.8805 (m) cc_final: 0.8581 (p)
REVERT: R  255 MET cc_start: 0.8646 (mmt) cc_final: 0.8383 (mmp)
REVERT: R  287 PHE cc_start: 0.8871 (t80) cc_final: 0.8077 (t80)
REVERT: R  305 ARG cc_start: 0.8654 (mpp-170) cc_final: 0.8391 (mpp-170)
REVERT: R  311 MET cc_start: 0.8803 (mpp) cc_final: 0.8532 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.0992
  time to fit residues: 31.1978
Evaluate side-chains
  191 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 71 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 85 optimal weight:    0.0770
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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**
R  38 HIS
R 150 ASN
R 244 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 = 0.4101 r_free = 0.4101 target = 0.140811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.103642 restraints weight = 18851.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.106123 restraints weight = 17212.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.107148 restraints weight = 14372.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.109034 restraints weight = 10412.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.111334 restraints weight = 8760.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.4567

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= 0.145
  Angle     :  0.679  10.787   9749  Z= 0.360
  Chirality :  0.046   0.227   1087
  Planarity :  0.005   0.049   1220
  Dihedral  :  7.837  90.538    964
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.27), residues: 876
  helix:  0.00 (0.27), residues: 325
  sheet: -1.41 (0.42), residues: 135
  loop : -2.67 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 314 
 TYR   0.011   0.002   TYR R 218 
 PHE   0.023   0.002   PHE G  64 
 TRP   0.051   0.002   TRP A 211 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7205)
  covalent geometry    : angle       0.67918 ( 9747)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       0.37156 (    2)
  hydrogen bonds       : bond        0.04279 (  312)
  hydrogen bonds       : angle       5.80218 (  903)
  Misc. bond           : bond        0.00010 (    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
  220 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.283 
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   33 GLU cc_start: 0.9123 (pp20) cc_final: 0.8901 (pp20)
REVERT: A  198 MET cc_start: 0.7858 (tpt) cc_final: 0.7597 (tpt)
REVERT: A  210 LYS cc_start: 0.9111 (pttp) cc_final: 0.8545 (mmtt)
REVERT: A  221 ILE cc_start: 0.8592 (mt) cc_final: 0.8278 (mt)
REVERT: A  263 SER cc_start: 0.8928 (m) cc_final: 0.8452 (t)
REVERT: A  264 ILE cc_start: 0.8600 (mp) cc_final: 0.8376 (mp)
REVERT: A  313 ARG cc_start: 0.9078 (ttm170) cc_final: 0.8783 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9173 (t0) cc_final: 0.8479 (m110)
REVERT: A  333 GLN cc_start: 0.9356 (mp10) cc_final: 0.9031 (mp10)
REVERT: B   42 ARG cc_start: 0.8889 (tmm160) cc_final: 0.8245 (ttp80)
REVERT: B   63 TRP cc_start: 0.8066 (m100) cc_final: 0.7405 (m100)
REVERT: B  166 CYS cc_start: 0.7307 (t) cc_final: 0.6844 (m)
REVERT: B  325 MET cc_start: 0.8560 (tpt) cc_final: 0.7985 (tpt)
REVERT: B  332 TRP cc_start: 0.9201 (m-10) cc_final: 0.8384 (m-10)
REVERT: B  335 PHE cc_start: 0.8176 (m-80) cc_final: 0.7617 (m-80)
REVERT: G   42 ASP cc_start: 0.8683 (t0) cc_final: 0.8086 (m-30)
REVERT: R   55 MET cc_start: 0.8643 (mmt) cc_final: 0.7933 (mmm)
REVERT: R   87 PHE cc_start: 0.8821 (m-10) cc_final: 0.8426 (m-80)
REVERT: R  104 MET cc_start: 0.8387 (ttt) cc_final: 0.7924 (tpp)
REVERT: R  150 ASN cc_start: 0.8638 (t0) cc_final: 0.8433 (t0)
REVERT: R  180 TRP cc_start: 0.7765 (m100) cc_final: 0.6958 (m100)
REVERT: R  206 ASP cc_start: 0.6258 (t0) cc_final: 0.5909 (t0)
REVERT: R  230 ILE cc_start: 0.8844 (mt) cc_final: 0.8498 (mm)
REVERT: R  233 CYS cc_start: 0.8810 (m) cc_final: 0.8555 (p)
REVERT: R  251 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8134 (tp-100)
REVERT: R  253 LYS cc_start: 0.9464 (tmtt) cc_final: 0.9254 (tptp)
REVERT: R  255 MET cc_start: 0.8573 (mmt) cc_final: 0.7713 (mmp)
REVERT: R  272 GLU cc_start: 0.8966 (pm20) cc_final: 0.8671 (pm20)
REVERT: R  287 PHE cc_start: 0.8783 (t80) cc_final: 0.7969 (t80)
REVERT: R  305 ARG cc_start: 0.8652 (mpp-170) cc_final: 0.8408 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0864
  time to fit residues: 25.4205
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  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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**
R  91 ASN
R 150 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 = 0.4122 r_free = 0.4122 target = 0.142459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.105352 restraints weight = 18709.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.107593 restraints weight = 16819.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108469 restraints weight = 16405.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.111213 restraints weight = 11642.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.112497 restraints weight = 9455.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.5016

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= 0.134
  Angle     :  0.663   8.929   9749  Z= 0.343
  Chirality :  0.046   0.255   1087
  Planarity :  0.004   0.047   1220
  Dihedral  :  6.582  68.845    964
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.27), residues: 876
  helix:  0.44 (0.28), residues: 329
  sheet: -1.47 (0.41), residues: 141
  loop : -2.62 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 242 
 TYR   0.014   0.002   TYR R 223 
 PHE   0.016   0.002   PHE R 319 
 TRP   0.056   0.002   TRP A 211 
 HIS   0.004   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7205)
  covalent geometry    : angle       0.66337 ( 9747)
  SS BOND              : bond        0.00217 (    1)
  SS BOND              : angle       0.48603 (    2)
  hydrogen bonds       : bond        0.03873 (  312)
  hydrogen bonds       : angle       5.49360 (  903)
  Misc. bond           : bond        0.00015 (    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
  219 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.9007 (ptpt) cc_final: 0.8632 (ptmt)
REVERT: A  221 ILE cc_start: 0.8628 (mt) cc_final: 0.8286 (mt)
REVERT: A  222 ILE cc_start: 0.9037 (mt) cc_final: 0.8804 (mt)
REVERT: A  263 SER cc_start: 0.8838 (m) cc_final: 0.8335 (t)
REVERT: A  264 ILE cc_start: 0.8591 (mp) cc_final: 0.8356 (mp)
REVERT: A  306 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8297 (tp-100)
REVERT: A  313 ARG cc_start: 0.9049 (ttm170) cc_final: 0.8748 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9121 (t0) cc_final: 0.8452 (m110)
REVERT: A  333 GLN cc_start: 0.9303 (mp10) cc_final: 0.9032 (mp10)
REVERT: B   42 ARG cc_start: 0.8796 (tmm160) cc_final: 0.8330 (tmm160)
REVERT: B   63 TRP cc_start: 0.7901 (m100) cc_final: 0.7226 (m100)
REVERT: B   89 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8372 (mtpt)
REVERT: B  166 CYS cc_start: 0.7248 (t) cc_final: 0.6762 (m)
REVERT: B  294 CYS cc_start: 0.9505 (t) cc_final: 0.9198 (t)
REVERT: B  308 LEU cc_start: 0.9041 (mt) cc_final: 0.8549 (tt)
REVERT: B  325 MET cc_start: 0.8937 (tpt) cc_final: 0.8687 (tpp)
REVERT: B  335 PHE cc_start: 0.8225 (m-80) cc_final: 0.7677 (m-80)
REVERT: G   42 ASP cc_start: 0.8636 (t0) cc_final: 0.7997 (m-30)
REVERT: R   36 HIS cc_start: 0.8824 (t-90) cc_final: 0.8615 (t-90)
REVERT: R   55 MET cc_start: 0.8667 (mmt) cc_final: 0.7906 (mmm)
REVERT: R   87 PHE cc_start: 0.8750 (m-10) cc_final: 0.8440 (m-80)
REVERT: R  104 MET cc_start: 0.8501 (ttt) cc_final: 0.8032 (tpp)
REVERT: R  150 ASN cc_start: 0.8642 (t0) cc_final: 0.8427 (t0)
REVERT: R  180 TRP cc_start: 0.7629 (m100) cc_final: 0.6850 (m100)
REVERT: R  218 TYR cc_start: 0.7408 (t80) cc_final: 0.7204 (t80)
REVERT: R  230 ILE cc_start: 0.9015 (mt) cc_final: 0.8562 (mm)
REVERT: R  233 CYS cc_start: 0.8857 (m) cc_final: 0.8624 (p)
REVERT: R  250 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8449 (tm-30)
REVERT: R  251 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8180 (tp-100)
REVERT: R  253 LYS cc_start: 0.9455 (tmtt) cc_final: 0.9219 (tptp)
REVERT: R  255 MET cc_start: 0.8593 (mmt) cc_final: 0.7761 (mmp)
REVERT: R  281 MET cc_start: 0.8818 (ttm) cc_final: 0.8476 (ppp)
REVERT: R  287 PHE cc_start: 0.8688 (t80) cc_final: 0.7964 (t80)
REVERT: R  305 ARG cc_start: 0.8703 (mpp-170) cc_final: 0.8401 (mpp-170)
REVERT: R  311 MET cc_start: 0.8797 (mpp) cc_final: 0.8091 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.0851
  time to fit residues: 24.7077
Evaluate side-chains
  193 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0770
   chunk 72 optimal weight:    3.9990
   chunk 51 optimal weight:    0.2980
   chunk 6 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 48 optimal weight:    0.2980
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.2538

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  38 HIS
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.145336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.108532 restraints weight = 18291.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113469 restraints weight = 15467.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113247 restraints weight = 13295.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115812 restraints weight = 9342.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.117054 restraints weight = 7421.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   7207  Z= 0.115
  Angle     :  0.647  10.532   9749  Z= 0.332
  Chirality :  0.045   0.282   1087
  Planarity :  0.004   0.049   1220
  Dihedral  :  6.310  76.356    964
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.28), residues: 876
  helix:  0.85 (0.29), residues: 326
  sheet: -1.22 (0.42), residues: 137
  loop : -2.47 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.017   0.001   TYR R 126 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.028   0.002   TRP A 211 
 HIS   0.003   0.001   HIS R 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7205)
  covalent geometry    : angle       0.64663 ( 9747)
  SS BOND              : bond        0.00213 (    1)
  SS BOND              : angle       0.59163 (    2)
  hydrogen bonds       : bond        0.03562 (  312)
  hydrogen bonds       : angle       5.24656 (  903)
  Misc. bond           : bond        0.00009 (    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
  228 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.455 
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: A   35 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8557 (ptmt)
REVERT: A   39 LEU cc_start: 0.9089 (mt) cc_final: 0.8882 (mt)
REVERT: A  198 MET cc_start: 0.7929 (tpt) cc_final: 0.7138 (tpt)
REVERT: A  210 LYS cc_start: 0.9208 (pptt) cc_final: 0.8050 (mmtt)
REVERT: A  221 ILE cc_start: 0.8394 (mt) cc_final: 0.8072 (mt)
REVERT: A  263 SER cc_start: 0.8844 (m) cc_final: 0.8425 (t)
REVERT: A  264 ILE cc_start: 0.8624 (mp) cc_final: 0.8378 (mp)
REVERT: A  274 PHE cc_start: 0.8657 (t80) cc_final: 0.8257 (t80)
REVERT: A  313 ARG cc_start: 0.9036 (ttm170) cc_final: 0.8748 (ttm-80)
REVERT: A  336 PHE cc_start: 0.9014 (t80) cc_final: 0.8625 (t80)
REVERT: B   42 ARG cc_start: 0.8730 (tmm160) cc_final: 0.8217 (ttp80)
REVERT: B   43 ILE cc_start: 0.9091 (pt) cc_final: 0.8773 (mm)
REVERT: B   63 TRP cc_start: 0.7911 (m100) cc_final: 0.7275 (m100)
REVERT: B  166 CYS cc_start: 0.7134 (t) cc_final: 0.6666 (m)
REVERT: B  235 PHE cc_start: 0.9238 (t80) cc_final: 0.8902 (t80)
REVERT: B  294 CYS cc_start: 0.9488 (t) cc_final: 0.9168 (t)
REVERT: B  308 LEU cc_start: 0.8834 (mt) cc_final: 0.8377 (tt)
REVERT: B  325 MET cc_start: 0.8973 (tpt) cc_final: 0.8675 (tpp)
REVERT: B  335 PHE cc_start: 0.8315 (m-80) cc_final: 0.7636 (m-80)
REVERT: G   40 PHE cc_start: 0.6526 (m-10) cc_final: 0.6164 (m-80)
REVERT: G   42 ASP cc_start: 0.8579 (t0) cc_final: 0.8126 (m-30)
REVERT: R   55 MET cc_start: 0.8589 (mmt) cc_final: 0.7868 (mmm)
REVERT: R   68 ASN cc_start: 0.8164 (m-40) cc_final: 0.7946 (m110)
REVERT: R   87 PHE cc_start: 0.8841 (m-10) cc_final: 0.8407 (m-80)
REVERT: R  104 MET cc_start: 0.8507 (ttt) cc_final: 0.8010 (tpp)
REVERT: R  180 TRP cc_start: 0.7299 (m100) cc_final: 0.6530 (m100)
REVERT: R  206 ASP cc_start: 0.5713 (t0) cc_final: 0.5511 (t0)
REVERT: R  218 TYR cc_start: 0.7353 (t80) cc_final: 0.7118 (t80)
REVERT: R  229 ILE cc_start: 0.9233 (mt) cc_final: 0.8986 (mt)
REVERT: R  230 ILE cc_start: 0.8786 (mt) cc_final: 0.8188 (mt)
REVERT: R  233 CYS cc_start: 0.8877 (m) cc_final: 0.8573 (p)
REVERT: R  250 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: R  253 LYS cc_start: 0.9446 (tmtt) cc_final: 0.9141 (tptp)
REVERT: R  272 GLU cc_start: 0.8944 (pm20) cc_final: 0.8541 (pm20)
REVERT: R  287 PHE cc_start: 0.8704 (t80) cc_final: 0.8131 (t80)
REVERT: R  305 ARG cc_start: 0.8759 (mpp-170) cc_final: 0.8460 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0904
  time to fit residues: 27.4665
Evaluate side-chains
  190 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0770
   chunk 67 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 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 = 0.4135 r_free = 0.4135 target = 0.143747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.105375 restraints weight = 18994.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.110103 restraints weight = 16061.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.110095 restraints weight = 12552.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.111353 restraints weight = 9329.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.112493 restraints weight = 8202.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.5737

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= 0.125
  Angle     :  0.641   9.591   9749  Z= 0.334
  Chirality :  0.044   0.221   1087
  Planarity :  0.004   0.048   1220
  Dihedral  :  6.278  81.864    964
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.28), residues: 876
  helix:  0.86 (0.29), residues: 327
  sheet: -1.27 (0.41), residues: 143
  loop : -2.25 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.010   0.002   TYR R 191 
 PHE   0.016   0.001   PHE R 298 
 TRP   0.021   0.001   TRP R 315 
 HIS   0.004   0.001   HIS R  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7205)
  covalent geometry    : angle       0.64131 ( 9747)
  SS BOND              : bond        0.00317 (    1)
  SS BOND              : angle       0.70771 (    2)
  hydrogen bonds       : bond        0.03521 (  312)
  hydrogen bonds       : angle       5.21491 (  903)
  Misc. bond           : bond        0.00024 (    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
  219 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 218
  time to evaluate  : 0.283 
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: A   35 LYS cc_start: 0.8987 (ptpt) cc_final: 0.8433 (ptmt)
REVERT: A   50 VAL cc_start: 0.8720 (m) cc_final: 0.8519 (m)
REVERT: A   53 MET cc_start: 0.7807 (ptp) cc_final: 0.7482 (ppp)
REVERT: A  198 MET cc_start: 0.8080 (tpt) cc_final: 0.7275 (tpt)
REVERT: A  210 LYS cc_start: 0.9236 (pptt) cc_final: 0.7978 (mmtt)
REVERT: A  221 ILE cc_start: 0.8561 (mt) cc_final: 0.8244 (mt)
REVERT: A  222 ILE cc_start: 0.9099 (mt) cc_final: 0.8877 (mt)
REVERT: A  227 LEU cc_start: 0.8710 (mp) cc_final: 0.7988 (mp)
REVERT: A  263 SER cc_start: 0.8911 (m) cc_final: 0.8377 (t)
REVERT: A  264 ILE cc_start: 0.8727 (mp) cc_final: 0.8484 (mp)
REVERT: A  274 PHE cc_start: 0.8752 (t80) cc_final: 0.8350 (t80)
REVERT: A  306 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8391 (tp-100)
REVERT: A  313 ARG cc_start: 0.9045 (ttm170) cc_final: 0.8779 (ttm-80)
REVERT: A  331 ASN cc_start: 0.9334 (t0) cc_final: 0.8589 (m110)
REVERT: A  333 GLN cc_start: 0.9159 (mp10) cc_final: 0.8940 (mp10)
REVERT: B   63 TRP cc_start: 0.8145 (m100) cc_final: 0.7605 (m100)
REVERT: B   72 SER cc_start: 0.9363 (m) cc_final: 0.9155 (m)
REVERT: B  166 CYS cc_start: 0.7329 (t) cc_final: 0.6821 (m)
REVERT: B  235 PHE cc_start: 0.9374 (t80) cc_final: 0.8868 (t80)
REVERT: B  294 CYS cc_start: 0.9571 (t) cc_final: 0.9248 (t)
REVERT: B  308 LEU cc_start: 0.8579 (mt) cc_final: 0.8328 (tp)
REVERT: B  325 MET cc_start: 0.9159 (tpt) cc_final: 0.8899 (tpp)
REVERT: B  335 PHE cc_start: 0.8421 (m-80) cc_final: 0.7779 (m-80)
REVERT: G   40 PHE cc_start: 0.6720 (m-10) cc_final: 0.6436 (m-80)
REVERT: G   42 ASP cc_start: 0.8952 (t0) cc_final: 0.8524 (m-30)
REVERT: R   36 HIS cc_start: 0.8977 (t-90) cc_final: 0.8752 (t-90)
REVERT: R   55 MET cc_start: 0.8622 (mmt) cc_final: 0.7924 (mmm)
REVERT: R   68 ASN cc_start: 0.8210 (m-40) cc_final: 0.7974 (m110)
REVERT: R   87 PHE cc_start: 0.8861 (m-10) cc_final: 0.8478 (m-80)
REVERT: R  110 ASN cc_start: 0.9215 (m-40) cc_final: 0.8990 (m110)
REVERT: R  150 ASN cc_start: 0.8863 (t0) cc_final: 0.8300 (t0)
REVERT: R  154 LYS cc_start: 0.8099 (mptt) cc_final: 0.7118 (mtpt)
REVERT: R  171 LEU cc_start: 0.8317 (mp) cc_final: 0.8103 (mp)
REVERT: R  180 TRP cc_start: 0.7444 (m100) cc_final: 0.6695 (m100)
REVERT: R  218 TYR cc_start: 0.7430 (t80) cc_final: 0.7117 (t80)
REVERT: R  250 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: R  255 MET cc_start: 0.8965 (mmp) cc_final: 0.8756 (mmp)
REVERT: R  272 GLU cc_start: 0.8973 (pm20) cc_final: 0.8629 (pm20)
REVERT: R  281 MET cc_start: 0.8714 (ttm) cc_final: 0.8409 (ppp)
REVERT: R  287 PHE cc_start: 0.8696 (t80) cc_final: 0.8010 (t80)
REVERT: R  305 ARG cc_start: 0.8823 (mpp-170) cc_final: 0.8577 (mpp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 219
  average time/residue: 0.0955
  time to fit residues: 27.4962
Evaluate side-chains
  189 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 85 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
** R  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 ASN
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.140507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.102775 restraints weight = 18610.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.105962 restraints weight = 16107.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.106733 restraints weight = 13384.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.107982 restraints weight = 9723.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.109299 restraints weight = 8646.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.5818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7207  Z= 0.174
  Angle     :  0.701   9.993   9749  Z= 0.368
  Chirality :  0.047   0.273   1087
  Planarity :  0.005   0.047   1220
  Dihedral  :  6.426  78.610    964
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.30 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.28), residues: 876
  helix:  0.49 (0.28), residues: 328
  sheet: -1.17 (0.42), residues: 140
  loop : -2.19 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 208 
 TYR   0.028   0.002   TYR R 126 
 PHE   0.018   0.002   PHE R 298 
 TRP   0.018   0.002   TRP B 339 
 HIS   0.008   0.001   HIS R  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7205)
  covalent geometry    : angle       0.70077 ( 9747)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       1.11042 (    2)
  hydrogen bonds       : bond        0.03898 (  312)
  hydrogen bonds       : angle       5.37028 (  903)
  Misc. bond           : bond        0.00017 (    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
  212 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 0.305 
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: A   32 ARG cc_start: 0.8097 (ptp-110) cc_final: 0.7792 (ptp90)
REVERT: A   35 LYS cc_start: 0.9034 (ptpt) cc_final: 0.8731 (ptpt)
REVERT: A  221 ILE cc_start: 0.8661 (mt) cc_final: 0.8436 (mt)
REVERT: A  227 LEU cc_start: 0.8798 (mp) cc_final: 0.8056 (mp)
REVERT: A  263 SER cc_start: 0.8870 (m) cc_final: 0.8359 (t)
REVERT: A  264 ILE cc_start: 0.8729 (mp) cc_final: 0.8505 (mp)
REVERT: A  274 PHE cc_start: 0.8813 (t80) cc_final: 0.8340 (t80)
REVERT: A  306 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8391 (tp-100)
REVERT: A  313 ARG cc_start: 0.9079 (ttm170) cc_final: 0.8833 (ttm-80)
REVERT: B   42 ARG cc_start: 0.8915 (tmm160) cc_final: 0.8344 (tmm160)
REVERT: B   59 TYR cc_start: 0.8450 (m-80) cc_final: 0.8201 (m-80)
REVERT: B   63 TRP cc_start: 0.8268 (m100) cc_final: 0.7829 (m100)
REVERT: B   72 SER cc_start: 0.9361 (m) cc_final: 0.9142 (m)
REVERT: B  103 CYS cc_start: 0.9161 (p) cc_final: 0.8945 (p)
REVERT: B  166 CYS cc_start: 0.7330 (t) cc_final: 0.6714 (m)
REVERT: B  235 PHE cc_start: 0.9424 (t80) cc_final: 0.8832 (t80)
REVERT: B  294 CYS cc_start: 0.9580 (t) cc_final: 0.9240 (t)
REVERT: B  308 LEU cc_start: 0.8637 (mt) cc_final: 0.8332 (tp)
REVERT: B  325 MET cc_start: 0.9264 (tpt) cc_final: 0.9038 (tpp)
REVERT: B  335 PHE cc_start: 0.8521 (m-80) cc_final: 0.7923 (m-80)
REVERT: G   40 PHE cc_start: 0.6663 (m-10) cc_final: 0.6447 (m-80)
REVERT: R   31 MET cc_start: 0.6570 (mmt) cc_final: 0.6059 (mmm)
REVERT: R   36 HIS cc_start: 0.8984 (t-90) cc_final: 0.8661 (t-90)
REVERT: R   45 MET cc_start: 0.5613 (tmm) cc_final: 0.5122 (tmm)
REVERT: R   55 MET cc_start: 0.8634 (mmt) cc_final: 0.7927 (mmm)
REVERT: R   87 PHE cc_start: 0.8922 (m-10) cc_final: 0.8522 (m-80)
REVERT: R  104 MET cc_start: 0.8439 (ttt) cc_final: 0.8164 (tpp)
REVERT: R  150 ASN cc_start: 0.8866 (t0) cc_final: 0.8644 (t0)
REVERT: R  180 TRP cc_start: 0.7616 (m100) cc_final: 0.7111 (m100)
REVERT: R  206 ASP cc_start: 0.6070 (t0) cc_final: 0.5835 (t0)
REVERT: R  250 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8334 (tm-30)
REVERT: R  287 PHE cc_start: 0.8710 (t80) cc_final: 0.8025 (t80)
REVERT: R  305 ARG cc_start: 0.8698 (mpp-170) cc_final: 0.8460 (mpp-170)
REVERT: R  308 LEU cc_start: 0.9407 (tp) cc_final: 0.9170 (tt)
REVERT: R  311 MET cc_start: 0.8345 (mmm) cc_final: 0.7973 (mmm)
REVERT: R  330 VAL cc_start: 0.9149 (t) cc_final: 0.8780 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0963
  time to fit residues: 26.6965
Evaluate side-chains
  176 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.0970
   chunk 75 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0010
   chunk 45 optimal weight:    7.9990
   chunk 9 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0670
   chunk 78 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    0.2722

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 311 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 = 0.4167 r_free = 0.4167 target = 0.146004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.108541 restraints weight = 18456.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.111784 restraints weight = 16729.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.112606 restraints weight = 13981.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.114241 restraints weight = 10111.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.115280 restraints weight = 8812.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.6168

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= 0.119
  Angle     :  0.678  10.643   9749  Z= 0.349
  Chirality :  0.046   0.293   1087
  Planarity :  0.004   0.047   1220
  Dihedral  :  6.056  77.902    964
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.28), residues: 876
  helix:  0.78 (0.29), residues: 326
  sheet: -0.83 (0.43), residues: 135
  loop : -2.12 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  15 
 TYR   0.010   0.001   TYR R 338 
 PHE   0.021   0.001   PHE R 298 
 TRP   0.020   0.001   TRP R 315 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7205)
  covalent geometry    : angle       0.67800 ( 9747)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.76222 (    2)
  hydrogen bonds       : bond        0.03549 (  312)
  hydrogen bonds       : angle       5.18977 (  903)
  Misc. bond           : bond        0.00052 (    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
  221 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8604 (ptmt)
REVERT: A   39 LEU cc_start: 0.9121 (mt) cc_final: 0.8830 (mt)
REVERT: A  221 ILE cc_start: 0.8367 (mt) cc_final: 0.7832 (mt)
REVERT: A  222 ILE cc_start: 0.8987 (mt) cc_final: 0.8748 (mt)
REVERT: A  261 ASP cc_start: 0.9002 (m-30) cc_final: 0.8779 (m-30)
REVERT: A  263 SER cc_start: 0.8810 (m) cc_final: 0.8285 (t)
REVERT: A  264 ILE cc_start: 0.8712 (mp) cc_final: 0.8360 (mp)
REVERT: A  274 PHE cc_start: 0.8612 (t80) cc_final: 0.8142 (t80)
REVERT: A  306 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8261 (tp-100)
REVERT: A  313 ARG cc_start: 0.9032 (ttm170) cc_final: 0.8743 (ttm-80)
REVERT: A  336 PHE cc_start: 0.9083 (t80) cc_final: 0.8613 (t80)
REVERT: B   63 TRP cc_start: 0.7772 (m100) cc_final: 0.7297 (m100)
REVERT: B  166 CYS cc_start: 0.7176 (t) cc_final: 0.6635 (m)
REVERT: B  235 PHE cc_start: 0.9304 (t80) cc_final: 0.8821 (t80)
REVERT: B  294 CYS cc_start: 0.9429 (t) cc_final: 0.9012 (t)
REVERT: B  308 LEU cc_start: 0.8548 (mt) cc_final: 0.8280 (tp)
REVERT: B  325 MET cc_start: 0.9106 (tpt) cc_final: 0.8850 (tpp)
REVERT: B  335 PHE cc_start: 0.8483 (m-80) cc_final: 0.7837 (m-80)
REVERT: G   42 ASP cc_start: 0.8884 (t0) cc_final: 0.8172 (m-30)
REVERT: R   29 GLU cc_start: 0.8279 (pp20) cc_final: 0.7973 (pm20)
REVERT: R   31 MET cc_start: 0.6520 (mmt) cc_final: 0.6135 (mmm)
REVERT: R   55 MET cc_start: 0.8555 (mmt) cc_final: 0.7797 (mmm)
REVERT: R   68 ASN cc_start: 0.8261 (m-40) cc_final: 0.7933 (m110)
REVERT: R   87 PHE cc_start: 0.8841 (m-10) cc_final: 0.8284 (m-80)
REVERT: R  104 MET cc_start: 0.8493 (ttt) cc_final: 0.8123 (tpp)
REVERT: R  110 ASN cc_start: 0.9009 (m-40) cc_final: 0.8734 (m110)
REVERT: R  150 ASN cc_start: 0.8767 (t0) cc_final: 0.7408 (t0)
REVERT: R  154 LYS cc_start: 0.8168 (mptt) cc_final: 0.7406 (mttp)
REVERT: R  180 TRP cc_start: 0.7441 (m100) cc_final: 0.6785 (m100)
REVERT: R  206 ASP cc_start: 0.5903 (t0) cc_final: 0.5613 (t0)
REVERT: R  218 TYR cc_start: 0.7417 (t80) cc_final: 0.7135 (t80)
REVERT: R  250 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: R  255 MET cc_start: 0.9141 (mmp) cc_final: 0.8914 (mmp)
REVERT: R  272 GLU cc_start: 0.9006 (pm20) cc_final: 0.8499 (pm20)
REVERT: R  281 MET cc_start: 0.8600 (tmm) cc_final: 0.8306 (ppp)
REVERT: R  287 PHE cc_start: 0.8601 (t80) cc_final: 0.7840 (t80)
REVERT: R  305 ARG cc_start: 0.8740 (mpp-170) cc_final: 0.8470 (mpp-170)
REVERT: R  342 LEU cc_start: 0.8796 (mm) cc_final: 0.8586 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0860
  time to fit residues: 25.0844
Evaluate side-chains
  185 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0270
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS
R 150 ASN
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.144007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.106608 restraints weight = 18419.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.111221 restraints weight = 16293.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.112208 restraints weight = 11584.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.112720 restraints weight = 9076.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.114390 restraints weight = 8284.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.6291

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     :  0.685  10.031   9749  Z= 0.353
  Chirality :  0.046   0.283   1087
  Planarity :  0.004   0.046   1220
  Dihedral  :  5.885  73.306    964
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.28), residues: 876
  helix:  0.76 (0.29), residues: 326
  sheet: -0.76 (0.42), residues: 136
  loop : -2.15 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  15 
 TYR   0.011   0.001   TYR R 191 
 PHE   0.021   0.002   PHE R 298 
 TRP   0.017   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7205)
  covalent geometry    : angle       0.68451 ( 9747)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.87302 (    2)
  hydrogen bonds       : bond        0.03544 (  312)
  hydrogen bonds       : angle       5.20006 (  903)
  Misc. bond           : bond        0.00064 (    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
  209 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.9079 (ptpt) cc_final: 0.8711 (ptmm)
REVERT: A  221 ILE cc_start: 0.8585 (mt) cc_final: 0.8254 (mt)
REVERT: A  263 SER cc_start: 0.8772 (m) cc_final: 0.8282 (t)
REVERT: A  264 ILE cc_start: 0.8619 (mp) cc_final: 0.8378 (mp)
REVERT: A  306 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8269 (tp-100)
REVERT: A  313 ARG cc_start: 0.9043 (ttm170) cc_final: 0.8743 (ttm-80)
REVERT: B   63 TRP cc_start: 0.7869 (m100) cc_final: 0.7240 (m100)
REVERT: B   71 VAL cc_start: 0.9370 (t) cc_final: 0.9166 (t)
REVERT: B   75 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8136 (tp-100)
REVERT: B  105 TYR cc_start: 0.8136 (t80) cc_final: 0.7785 (t80)
REVERT: B  166 CYS cc_start: 0.7131 (t) cc_final: 0.6476 (m)
REVERT: B  235 PHE cc_start: 0.9377 (t80) cc_final: 0.8585 (t80)
REVERT: B  253 PHE cc_start: 0.9018 (m-10) cc_final: 0.8779 (m-80)
REVERT: B  294 CYS cc_start: 0.9443 (t) cc_final: 0.9002 (t)
REVERT: B  308 LEU cc_start: 0.8609 (mt) cc_final: 0.8297 (tp)
REVERT: B  325 MET cc_start: 0.9164 (tpt) cc_final: 0.8922 (tpp)
REVERT: B  335 PHE cc_start: 0.8547 (m-80) cc_final: 0.7901 (m-80)
REVERT: G   46 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8760 (mt-10)
REVERT: R   29 GLU cc_start: 0.8419 (pp20) cc_final: 0.8099 (pm20)
REVERT: R   31 MET cc_start: 0.6642 (mmt) cc_final: 0.6320 (mmm)
REVERT: R   45 MET cc_start: 0.4774 (tmm) cc_final: 0.4485 (tmm)
REVERT: R   55 MET cc_start: 0.8534 (mmt) cc_final: 0.7797 (mmm)
REVERT: R   68 ASN cc_start: 0.8149 (m-40) cc_final: 0.7895 (m110)
REVERT: R   87 PHE cc_start: 0.8790 (m-10) cc_final: 0.8420 (m-80)
REVERT: R  104 MET cc_start: 0.8451 (ttt) cc_final: 0.8063 (tpp)
REVERT: R  146 LEU cc_start: 0.9176 (tp) cc_final: 0.8614 (tp)
REVERT: R  180 TRP cc_start: 0.7469 (m100) cc_final: 0.6822 (m100)
REVERT: R  206 ASP cc_start: 0.6050 (t0) cc_final: 0.5782 (t0)
REVERT: R  229 ILE cc_start: 0.9131 (mt) cc_final: 0.8876 (mt)
REVERT: R  250 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: R  255 MET cc_start: 0.9144 (mmp) cc_final: 0.8873 (mmp)
REVERT: R  272 GLU cc_start: 0.9009 (pm20) cc_final: 0.8488 (pm20)
REVERT: R  280 PHE cc_start: 0.8006 (t80) cc_final: 0.7607 (t80)
REVERT: R  287 PHE cc_start: 0.8529 (t80) cc_final: 0.7834 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0923
  time to fit residues: 25.4885
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  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS
R 150 ASN
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.142903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.105332 restraints weight = 18960.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.110617 restraints weight = 17058.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.110393 restraints weight = 13563.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.112580 restraints weight = 10112.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.113736 restraints weight = 8272.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.6419

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= 0.143
  Angle     :  0.693   9.652   9749  Z= 0.360
  Chirality :  0.046   0.278   1087
  Planarity :  0.004   0.046   1220
  Dihedral  :  5.750  67.029    964
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.39 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.28), residues: 876
  helix:  0.62 (0.28), residues: 328
  sheet: -0.85 (0.42), residues: 135
  loop : -2.07 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  15 
 TYR   0.014   0.002   TYR R 191 
 PHE   0.016   0.001   PHE A 334 
 TRP   0.016   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7205)
  covalent geometry    : angle       0.69336 ( 9747)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.90148 (    2)
  hydrogen bonds       : bond        0.03658 (  312)
  hydrogen bonds       : angle       5.21202 (  903)
  Misc. bond           : bond        0.00058 (    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
  209 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.309 
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   35 LYS cc_start: 0.9115 (ptpt) cc_final: 0.8736 (ptmm)
REVERT: A  221 ILE cc_start: 0.8684 (mt) cc_final: 0.8384 (mt)
REVERT: A  227 LEU cc_start: 0.8728 (mp) cc_final: 0.8010 (mp)
REVERT: A  263 SER cc_start: 0.8794 (m) cc_final: 0.8320 (t)
REVERT: A  264 ILE cc_start: 0.8629 (mp) cc_final: 0.8382 (mp)
REVERT: A  274 PHE cc_start: 0.8666 (t80) cc_final: 0.8213 (t80)
REVERT: A  306 GLN cc_start: 0.8543 (tp-100) cc_final: 0.8287 (tp-100)
REVERT: A  313 ARG cc_start: 0.9036 (ttm170) cc_final: 0.8763 (ttm-80)
REVERT: B   63 TRP cc_start: 0.8008 (m100) cc_final: 0.7380 (m100)
REVERT: B   71 VAL cc_start: 0.9367 (t) cc_final: 0.9092 (t)
REVERT: B  105 TYR cc_start: 0.8195 (t80) cc_final: 0.7776 (t80)
REVERT: B  166 CYS cc_start: 0.7144 (t) cc_final: 0.6459 (m)
REVERT: B  235 PHE cc_start: 0.9298 (t80) cc_final: 0.8602 (t80)
REVERT: B  253 PHE cc_start: 0.8883 (m-10) cc_final: 0.8467 (m-10)
REVERT: B  294 CYS cc_start: 0.9382 (t) cc_final: 0.8890 (t)
REVERT: B  308 LEU cc_start: 0.8616 (mt) cc_final: 0.8332 (tp)
REVERT: B  325 MET cc_start: 0.9219 (tpt) cc_final: 0.8590 (tpp)
REVERT: B  335 PHE cc_start: 0.8584 (m-80) cc_final: 0.7934 (m-80)
REVERT: R   29 GLU cc_start: 0.8477 (pp20) cc_final: 0.8151 (pm20)
REVERT: R   31 MET cc_start: 0.6793 (mmt) cc_final: 0.6560 (mmm)
REVERT: R   45 MET cc_start: 0.4905 (tmm) cc_final: 0.4569 (tmm)
REVERT: R   55 MET cc_start: 0.8532 (mmt) cc_final: 0.7837 (mmm)
REVERT: R   68 ASN cc_start: 0.8133 (m-40) cc_final: 0.7856 (m110)
REVERT: R   87 PHE cc_start: 0.8812 (m-10) cc_final: 0.8434 (m-80)
REVERT: R  104 MET cc_start: 0.8419 (ttt) cc_final: 0.8041 (tpp)
REVERT: R  150 ASN cc_start: 0.8804 (t160) cc_final: 0.8339 (t0)
REVERT: R  154 LYS cc_start: 0.8209 (mptt) cc_final: 0.6910 (mtpt)
REVERT: R  180 TRP cc_start: 0.7493 (m100) cc_final: 0.6824 (m100)
REVERT: R  206 ASP cc_start: 0.6333 (t0) cc_final: 0.6065 (t0)
REVERT: R  229 ILE cc_start: 0.9280 (mt) cc_final: 0.9045 (mt)
REVERT: R  250 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: R  255 MET cc_start: 0.9150 (mmp) cc_final: 0.8871 (mmp)
REVERT: R  272 GLU cc_start: 0.8982 (pm20) cc_final: 0.8476 (pm20)
REVERT: R  280 PHE cc_start: 0.8021 (t80) cc_final: 0.7569 (t80)
REVERT: R  287 PHE cc_start: 0.8683 (t80) cc_final: 0.7954 (t80)
REVERT: R  308 LEU cc_start: 0.9316 (tp) cc_final: 0.9095 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0903
  time to fit residues: 25.3124
Evaluate side-chains
  171 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0370
   chunk 84 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0050
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.4472

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 311 HIS
R 150 ASN
R 263 ASN
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.145556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.107733 restraints weight = 18784.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.112333 restraints weight = 16182.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.112975 restraints weight = 12557.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.113581 restraints weight = 9368.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.114968 restraints weight = 8565.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.6645

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= 0.120
  Angle     :  0.676  10.029   9749  Z= 0.348
  Chirality :  0.045   0.279   1087
  Planarity :  0.004   0.048   1220
  Dihedral  :  5.441  62.532    964
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.52 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.28), residues: 876
  helix:  0.74 (0.29), residues: 330
  sheet: -0.60 (0.44), residues: 130
  loop : -1.99 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  15 
 TYR   0.010   0.001   TYR R 191 
 PHE   0.016   0.001   PHE R 298 
 TRP   0.019   0.002   TRP R 315 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7205)
  covalent geometry    : angle       0.67635 ( 9747)
  SS BOND              : bond        0.00195 (    1)
  SS BOND              : angle       0.78173 (    2)
  hydrogen bonds       : bond        0.03492 (  312)
  hydrogen bonds       : angle       5.04819 (  903)
  Misc. bond           : bond        0.00050 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1593.54 seconds
wall clock time: 28 minutes 18.70 seconds (1698.70 seconds total)