Starting phenix.real_space_refine
on Sat Aug 23 03:56:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q5h_18179/08_2025/8q5h_18179.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q5h_18179/08_2025/8q5h_18179.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q5h_18179/08_2025/8q5h_18179.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q5h_18179/08_2025/8q5h_18179.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q5h_18179/08_2025/8q5h_18179.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q5h_18179/08_2025/8q5h_18179.map"
  }
  resolution = 4.5
  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=   0.001 sd=   0.050
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      46      5.16       5
     C    6085      2.51       5
     N    1625      2.21       5
     O    1818      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 9574
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "4"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 530
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 4, 'TRANS': 61}
    Chain: "5"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 835
          Classifications: {'peptide': 102}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 1693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1693
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 197}
    Chain: "B"
      Number of atoms: 1426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1426
          Classifications: {'peptide': 174}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1724
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 5, 'TRANS': 211}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1744
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200}
    Chain: "N"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1622
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 12, 'TRANS': 186}
          Chain breaks: 1
  Time building chain proxies: 2.04, per 1000 atoms: 0.21
  Number of scatterers: 9574
  At special positions: 0
  Unit cell: (208.08, 187.68, 134.64, 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      46     16.00
     O    1818      8.00
     N    1625      7.00
     C    6085      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 348.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2274

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      69.1% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain '4' and resid 131 through 148
    Processing helix  chain '4' and resid 181 through 193
      removed outlier: 3.719A  pdb=" N   VAL 4 193 " --> pdb=" O   LEU 4 189 " (cutoff:3.500A)
    Processing helix  chain '5' and resid 124 through 141
    Processing helix  chain '5' and resid 194 through 204
    Processing helix  chain '5' and resid 207 through 221
    Processing helix  chain '5' and resid 222 through 224
      No H-bonds generated for 'chain '5' and resid 222 through 224'
    Processing helix  chain 'A' and resid 8 through 14
    Processing helix  chain 'A' and resid 16 through 50
      removed outlier: 3.653A  pdb=" N   CYS A  20 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LYS A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLY A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 87
      removed outlier: 3.813A  pdb=" N   HIS A  74 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ASN A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS A  81 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 106
    Processing helix  chain 'A' and resid 110 through 170
      removed outlier: 3.792A  pdb=" N   HIS A 169 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLY A 170 " --> pdb=" O   GLY A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 205
      removed outlier: 3.514A  pdb=" N   SER A 205 " --> pdb=" O   ARG A 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 52
      removed outlier: 4.186A  pdb=" N   LEU B  37 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP B  43 " --> pdb=" O   ASP B  39 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA B  52 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 69 through 98
      removed outlier: 3.627A  pdb=" N   TYR B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ASP B  78 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ARG B  89 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 116
      removed outlier: 3.671A  pdb=" N   VAL B 104 " --> pdb=" O   ASN B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 189
      removed outlier: 3.933A  pdb=" N   VAL B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
      Proline residue:  B 139  - end of helix
      removed outlier: 3.549A  pdb=" N   GLN B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 201
      removed outlier: 4.307A  pdb=" N   GLU B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 150
    Processing helix  chain 'D' and resid 151 through 153
      No H-bonds generated for 'chain 'D' and resid 151 through 153'
    Processing helix  chain 'D' and resid 161 through 183
    Processing helix  chain 'D' and resid 188 through 192
      removed outlier: 3.574A  pdb=" N   CYS D 191 " --> pdb=" O   LEU D 188 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   PHE D 192 " --> pdb=" O   GLN D 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 188 through 192'
    Processing helix  chain 'D' and resid 203 through 245
      removed outlier: 3.796A  pdb=" N   SER D 244 " --> pdb=" O   LEU D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 270
      removed outlier: 3.664A  pdb=" N   LEU D 268 " --> pdb=" O   GLN D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 327
      removed outlier: 3.524A  pdb=" N   ILE D 277 " --> pdb=" O   ASP D 273 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER D 282 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLN D 327 " --> pdb=" O   ARG D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 331 through 338
      removed outlier: 3.597A  pdb=" N   LYS D 335 " --> pdb=" O   SER D 331 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYS D 338 " --> pdb=" O   ARG D 334 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2192 through 2208
    Processing helix  chain 'K' and resid 2211 through 2216
    Processing helix  chain 'K' and resid 2221 through 2250
      removed outlier: 3.506A  pdb=" N   VAL K2232 " --> pdb=" O   GLU K2228 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2251 through 2253
      No H-bonds generated for 'chain 'K' and resid 2251 through 2253'
    Processing helix  chain 'K' and resid 2305 through 2316
      removed outlier: 3.713A  pdb=" N   ILE K2309 " --> pdb=" O   SER K2305 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2321 through 2335
    Processing helix  chain 'N' and resid 43 through 54
    Processing helix  chain 'N' and resid 54 through 62
    Processing helix  chain 'N' and resid 68 through 87
      removed outlier: 3.687A  pdb=" N   ALA N  72 " --> pdb=" O   ILE N  68 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 104 through 151
      removed outlier: 3.864A  pdb=" N   ILE N 108 " --> pdb=" O   MET N 104 " (cutoff:3.500A)
      Proline residue:  N 130  - end of helix
      removed outlier: 3.552A  pdb=" N   LYS N 139 " --> pdb=" O   GLU N 135 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 166 through 213
      removed outlier: 3.533A  pdb=" N   LYS N 189 " --> pdb=" O   SER N 185 " (cutoff:3.500A)
      Proline residue:  N 192  - end of helix
      Proline residue:  N 209  - end of helix
    Processing helix  chain 'N' and resid 214 through 222
    Processing helix  chain 'N' and resid 265 through 270
    Processing sheet with id=AA1, first strand: chain '4' and resid 149 through 151
    Processing sheet with id=AA2, first strand: chain '5' and resid 144 through 149
      removed outlier: 3.567A  pdb=" N   LYS 5 153 " --> pdb=" O   ILE 5 149 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   HIS 5 175 " --> pdb=" O   VAL 5 184 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   VAL 5 184 " --> pdb=" O   HIS 5 175 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 2135 through 2140
      removed outlier: 6.585A  pdb=" N   VAL K2146 " --> pdb=" O   VAL K2138 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   TRP K2140 " --> pdb=" O   GLN K2144 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLN K2144 " --> pdb=" O   TRP K2140 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 2258 through 2259
      removed outlier: 6.553A  pdb=" N   GLU K2279 " --> pdb=" O   ASN K2299 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   ASN K2299 " --> pdb=" O   GLU K2279 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   THR K2281 " --> pdb=" O   ILE K2297 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE K2297 " --> pdb=" O   THR K2281 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'N' and resid 38 through 39
      removed outlier: 5.369A  pdb=" N   VAL N  38 " --> pdb=" O   SER N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    658 hydrogen bonds defined for protein.
    1956 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: 1.10

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2986
        1.34 -     1.45: 1272
        1.45 -     1.57: 5434
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 9762
  Sorted by residual:
  bond pdb=" C   ALA N 167 "
       pdb=" N   PRO N 168 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 1.28e-02 6.10e+03 3.94e+00
  bond pdb=" CG  ARG 5 130 "
       pdb=" CD  ARG 5 130 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.58e+00
  bond pdb=" CA  GLN B  67 "
       pdb=" CB  GLN B  67 "
    ideal  model  delta    sigma   weight residual
    1.523  1.545 -0.022 1.35e-02 5.49e+03 2.56e+00
  bond pdb=" CG1 ILE K2243 "
       pdb=" CD1 ILE K2243 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 1.96e+00
  bond pdb=" N   GLU A 106 "
       pdb=" CA  GLU A 106 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.35e+00
  ... (remaining 9757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 12872
        2.30 -     4.59: 255
        4.59 -     6.89: 33
        6.89 -     9.19: 7
        9.19 -    11.48: 4
  Bond angle restraints: 13171
  Sorted by residual:
  angle pdb=" C   LEU A  98 "
        pdb=" N   LEU A  99 "
        pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.03  130.64   -9.61 1.60e+00 3.91e-01 3.61e+01
  angle pdb=" N   GLN B  67 "
        pdb=" CA  GLN B  67 "
        pdb=" C   GLN B  67 "
      ideal   model   delta    sigma   weight residual
     107.23  114.58   -7.35 1.67e+00 3.59e-01 1.94e+01
  angle pdb=" CG  ARG 5 130 "
        pdb=" CD  ARG 5 130 "
        pdb=" NE  ARG 5 130 "
      ideal   model   delta    sigma   weight residual
     112.00  103.52    8.48 2.20e+00 2.07e-01 1.49e+01
  angle pdb=" CB  MET A  71 "
        pdb=" CG  MET A  71 "
        pdb=" SD  MET A  71 "
      ideal   model   delta    sigma   weight residual
     112.70  124.18  -11.48 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" CB  MET D 211 "
        pdb=" CG  MET D 211 "
        pdb=" SD  MET D 211 "
      ideal   model   delta    sigma   weight residual
     112.70  101.26   11.44 3.00e+00 1.11e-01 1.45e+01
  ... (remaining 13166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 5382
       17.93 -    35.86: 492
       35.86 -    53.80: 75
       53.80 -    71.73: 28
       71.73 -    89.66: 24
  Dihedral angle restraints: 6001
    sinusoidal: 2527
      harmonic: 3474
  Sorted by residual:
  dihedral pdb=" CA  MET 5 171 "
           pdb=" C   MET 5 171 "
           pdb=" N   PHE 5 172 "
           pdb=" CA  PHE 5 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.48   30.52     0      5.00e+00 4.00e-02 3.73e+01
  dihedral pdb=" CA  GLN B  67 "
           pdb=" C   GLN B  67 "
           pdb=" N   LEU B  68 "
           pdb=" CA  LEU B  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.89   26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  LEU A  89 "
           pdb=" C   LEU A  89 "
           pdb=" N   ILE A  90 "
           pdb=" CA  ILE A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 5998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1125
       0.047 -    0.095: 261
       0.095 -    0.142: 61
       0.142 -    0.190: 4
       0.190 -    0.237: 1
  Chirality restraints: 1452
  Sorted by residual:
  chirality pdb=" CA  TYR N 129 "
            pdb=" N   TYR N 129 "
            pdb=" C   TYR N 129 "
            pdb=" CB  TYR N 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  VAL K2180 "
            pdb=" N   VAL K2180 "
            pdb=" C   VAL K2180 "
            pdb=" CB  VAL K2180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" CA  GLU D 150 "
            pdb=" N   GLU D 150 "
            pdb=" C   GLU D 150 "
            pdb=" CB  GLU D 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1449 not shown)

  Planarity restraints: 1709
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG 5 130 "   -0.251 9.50e-02 1.11e+02   1.13e-01 8.70e+00
        pdb=" NE  ARG 5 130 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG 5 130 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG 5 130 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG 5 130 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE N 115 "   -0.018 2.00e-02 2.50e+03   1.99e-02 6.93e+00
        pdb=" CG  PHE N 115 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE N 115 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE N 115 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE N 115 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE N 115 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE N 115 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A   4 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO A   5 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A   5 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A   5 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1706 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 127
        2.64 -     3.20: 9229
        3.20 -     3.77: 15325
        3.77 -     4.33: 19328
        4.33 -     4.90: 30707
  Nonbonded interactions: 74716
  Sorted by model distance:
  nonbonded pdb=" O   ARG 5 141 "
            pdb=" NH1 ARG 5 141 "
     model   vdw
     2.072 3.120
  nonbonded pdb=" OH  TYR B  62 "
            pdb=" O   THR B  73 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" OE2 GLU B 156 "
            pdb=" OG  SER D 263 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   THR A  16 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" OG  SER D 160 "
            pdb=" OE1 GLU D 162 "
     model   vdw
     2.152 3.040
  ... (remaining 74711 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.070
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.160
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4656
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9762  Z= 0.181
  Angle     :  0.816  11.481  13171  Z= 0.474
  Chirality :  0.043   0.237   1452
  Planarity :  0.006   0.113   1709
  Dihedral  : 15.487  89.660   3727
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.46 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.25), residues: 1155
  helix:  1.24 (0.19), residues: 748
  sheet: -1.52 (0.61), residues: 77
  loop : -0.89 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG 5 130 
 TYR   0.021   0.001   TYR N 129 
 PHE   0.046   0.002   PHE N 115 
 TRP   0.039   0.002   TRP K2212 
 HIS   0.011   0.001   HIS K2234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9762)
  covalent geometry    : angle       0.81558 (13171)
  hydrogen bonds       : bond        0.10826 (  658)
  hydrogen bonds       : angle       5.38796 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.303 
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: 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: symmetry clash
REVERT: 4  159 MET cc_start: 0.5922 (ppp) cc_final: 0.4886 (ppp)
REVERT: A   68 LEU cc_start: 0.8989 (tp) cc_final: 0.8630 (tt)
REVERT: A  145 GLN cc_start: 0.8148 (mt0) cc_final: 0.7359 (mt0)
REVERT: B   72 MET cc_start: 0.8923 (mtt) cc_final: 0.8570 (tpt)
REVERT: D  220 LEU cc_start: 0.9402 (mt) cc_final: 0.9113 (mt)
REVERT: K 2179 ASP cc_start: 0.8366 (t0) cc_final: 0.7724 (t0)
REVERT: K 2181 ASN cc_start: 0.6364 (p0) cc_final: 0.5178 (p0)
REVERT: K 2241 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7032 (pt0)
REVERT: N  175 CYS cc_start: 0.8391 (m) cc_final: 0.8008 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.1226
  time to fit residues: 41.5640
Evaluate side-chains
  140 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 GLN
** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 ASN
B  47 GLN
B 143 GLN
B 144 GLN
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 GLN
B 183 GLN
D 147 GLN
D 231 HIS
** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.094918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.079870 restraints weight = 83169.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.081357 restraints weight = 58511.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.082508 restraints weight = 40423.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.082493 restraints weight = 35376.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.082604 restraints weight = 32394.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9762  Z= 0.217
  Angle     :  0.786   9.849  13171  Z= 0.405
  Chirality :  0.046   0.171   1452
  Planarity :  0.006   0.078   1709
  Dihedral  :  4.682  31.018   1258
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 19.70
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.29 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.60 %
    Favored  : 93.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.24), residues: 1155
  helix:  0.97 (0.18), residues: 753
  sheet: -2.01 (0.55), residues: 82
  loop : -0.94 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG 5 141 
 TYR   0.021   0.002   TYR 4 153 
 PHE   0.046   0.003   PHE N 115 
 TRP   0.023   0.003   TRP K2212 
 HIS   0.012   0.002   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9762)
  covalent geometry    : angle       0.78573 (13171)
  hydrogen bonds       : bond        0.04512 (  658)
  hydrogen bonds       : angle       5.00285 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 174
  time to evaluate  : 0.398 
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: symmetry clash
   revert: symmetry clash
REVERT: 4  159 MET cc_start: 0.5201 (ppp) cc_final: 0.4381 (ppp)
REVERT: 5  199 GLU cc_start: 0.9054 (tp30) cc_final: 0.8795 (tm-30)
REVERT: A  145 GLN cc_start: 0.9111 (mt0) cc_final: 0.8211 (mt0)
REVERT: A  176 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: B   72 MET cc_start: 0.9339 (mtt) cc_final: 0.8695 (tpt)
REVERT: B  137 MET cc_start: 0.6159 (ppp) cc_final: 0.5954 (ppp)
REVERT: B  195 ARG cc_start: 0.8454 (mmt180) cc_final: 0.8096 (mmm-85)
REVERT: D  132 LYS cc_start: 0.7631 (mttt) cc_final: 0.7381 (mppt)
REVERT: K 2155 GLN cc_start: 0.8473 (tt0) cc_final: 0.8156 (tp40)
REVERT: K 2156 LEU cc_start: 0.8747 (tt) cc_final: 0.8098 (tt)
REVERT: K 2179 ASP cc_start: 0.9240 (t0) cc_final: 0.8646 (t0)
REVERT: K 2181 ASN cc_start: 0.7819 (p0) cc_final: 0.7175 (p0)
REVERT: K 2241 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7671 (pt0)
REVERT: N  175 CYS cc_start: 0.8741 (m) cc_final: 0.8406 (p)
REVERT: N  269 TRP cc_start: 0.8649 (m100) cc_final: 0.8020 (m100)
  outliers start: 6
  outliers final: 1
  residues processed: 178
  average time/residue: 0.1270
  time to fit residues: 29.6628
Evaluate side-chains
  120 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 108 optimal weight:    0.2980
   chunk 92 optimal weight:    0.0060
   chunk 111 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 113 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
A 190 ASN
** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 GLN
D 177 HIS
** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2199 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.095935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.081084 restraints weight = 82501.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.082667 restraints weight = 55062.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.083912 restraints weight = 40982.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.084686 restraints weight = 32207.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.085137 restraints weight = 27042.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6379
moved from start:          0.5194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9762  Z= 0.130
  Angle     :  0.663  11.655  13171  Z= 0.339
  Chirality :  0.043   0.166   1452
  Planarity :  0.005   0.052   1709
  Dihedral  :  4.439  31.852   1258
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.77 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.82 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.25), residues: 1155
  helix:  1.27 (0.18), residues: 749
  sheet: -1.85 (0.55), residues: 82
  loop : -0.75 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG 5 127 
 TYR   0.010   0.001   TYR 5 182 
 PHE   0.036   0.002   PHE A  70 
 TRP   0.032   0.002   TRP K2249 
 HIS   0.009   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9762)
  covalent geometry    : angle       0.66332 (13171)
  hydrogen bonds       : bond        0.03973 (  658)
  hydrogen bonds       : angle       4.69780 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.400 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 4  159 MET cc_start: 0.7545 (ppp) cc_final: 0.6677 (ppp)
REVERT: A    6 MET cc_start: 0.2906 (mtp) cc_final: 0.2582 (mtm)
REVERT: A   61 ARG cc_start: 0.8641 (tpt170) cc_final: 0.8406 (tpt170)
REVERT: A   79 PHE cc_start: 0.8943 (m-80) cc_final: 0.8462 (m-80)
REVERT: A   93 ILE cc_start: 0.8072 (pt) cc_final: 0.7687 (mm)
REVERT: A  156 LEU cc_start: 0.9117 (mm) cc_final: 0.8828 (pp)
REVERT: A  175 ARG cc_start: 0.8316 (tpt170) cc_final: 0.7943 (mmm160)
REVERT: A  179 VAL cc_start: 0.8936 (t) cc_final: 0.8431 (m)
REVERT: B   72 MET cc_start: 0.9320 (mtt) cc_final: 0.8616 (tpt)
REVERT: B  137 MET cc_start: 0.6363 (ppp) cc_final: 0.6114 (ppp)
REVERT: B  191 HIS cc_start: 0.7013 (t-170) cc_final: 0.6563 (t70)
REVERT: D  126 VAL cc_start: 0.6935 (t) cc_final: 0.6695 (t)
REVERT: D  132 LYS cc_start: 0.7554 (mttt) cc_final: 0.7344 (mppt)
REVERT: D  292 MET cc_start: 0.8226 (tmm) cc_final: 0.7399 (ppp)
REVERT: K 2155 GLN cc_start: 0.8311 (tt0) cc_final: 0.7920 (tp40)
REVERT: K 2156 LEU cc_start: 0.8616 (tt) cc_final: 0.8113 (tt)
REVERT: K 2175 ARG cc_start: 0.7041 (ttt180) cc_final: 0.6524 (mmm160)
REVERT: K 2179 ASP cc_start: 0.9122 (t0) cc_final: 0.8399 (t0)
REVERT: K 2181 ASN cc_start: 0.7603 (p0) cc_final: 0.6480 (p0)
REVERT: K 2239 LEU cc_start: 0.9286 (tp) cc_final: 0.8824 (tt)
REVERT: K 2241 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7766 (pt0)
REVERT: K 2328 LYS cc_start: 0.7653 (pttp) cc_final: 0.7199 (ttpp)
REVERT: N  175 CYS cc_start: 0.8709 (m) cc_final: 0.8241 (p)
REVERT: N  269 TRP cc_start: 0.8505 (m100) cc_final: 0.7936 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1043
  time to fit residues: 23.9646
Evaluate side-chains
  127 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 101 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
4 165 HIS
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 ASN
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 HIS
** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 GLN
** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K2332 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.091198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.076194 restraints weight = 84996.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.077764 restraints weight = 56831.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.078881 restraints weight = 42324.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.079502 restraints weight = 33878.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.080136 restraints weight = 28985.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6635
moved from start:          0.6511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9762  Z= 0.187
  Angle     :  0.719   9.730  13171  Z= 0.379
  Chirality :  0.045   0.165   1452
  Planarity :  0.005   0.052   1709
  Dihedral  :  4.660  31.564   1258
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.29 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.99 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.25), residues: 1155
  helix:  1.08 (0.18), residues: 747
  sheet: -1.78 (0.55), residues: 78
  loop : -0.86 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG 5 130 
 TYR   0.024   0.002   TYR 4 153 
 PHE   0.059   0.003   PHE B  80 
 TRP   0.044   0.002   TRP K2249 
 HIS   0.006   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 9762)
  covalent geometry    : angle       0.71889 (13171)
  hydrogen bonds       : bond        0.04140 (  658)
  hydrogen bonds       : angle       4.98088 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 0.465 
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: 4  159 MET cc_start: 0.7268 (ppp) cc_final: 0.7053 (ppp)
REVERT: 5  192 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6129 (pp20)
REVERT: A   79 PHE cc_start: 0.9128 (m-80) cc_final: 0.8304 (m-80)
REVERT: A  175 ARG cc_start: 0.8379 (tpt170) cc_final: 0.8165 (mmm160)
REVERT: A  179 VAL cc_start: 0.9307 (t) cc_final: 0.8922 (m)
REVERT: A  181 LEU cc_start: 0.8891 (mt) cc_final: 0.8688 (mt)
REVERT: B   72 MET cc_start: 0.9287 (mtt) cc_final: 0.8681 (tpt)
REVERT: B  137 MET cc_start: 0.6288 (ppp) cc_final: 0.5969 (ppp)
REVERT: D  132 LYS cc_start: 0.7360 (mttt) cc_final: 0.6977 (mppt)
REVERT: D  133 ARG cc_start: 0.8465 (mmm160) cc_final: 0.7592 (mtt180)
REVERT: D  292 MET cc_start: 0.8416 (tmm) cc_final: 0.7692 (ppp)
REVERT: K 2179 ASP cc_start: 0.9163 (t0) cc_final: 0.8283 (t0)
REVERT: K 2181 ASN cc_start: 0.7339 (p0) cc_final: 0.7030 (p0)
REVERT: N  175 CYS cc_start: 0.8924 (m) cc_final: 0.8532 (p)
REVERT: N  269 TRP cc_start: 0.8361 (m100) cc_final: 0.7799 (m100)
  outliers start: 3
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1102
  time to fit residues: 23.6732
Evaluate side-chains
  116 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
4 141 GLN
4 165 HIS
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 152 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.085005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.070070 restraints weight = 89776.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.071496 restraints weight = 60279.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.072362 restraints weight = 45307.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.073209 restraints weight = 36803.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.073661 restraints weight = 31259.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.8422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   9762  Z= 0.244
  Angle     :  0.830   9.318  13171  Z= 0.436
  Chirality :  0.049   0.263   1452
  Planarity :  0.006   0.048   1709
  Dihedral  :  5.229  29.926   1258
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 25.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.24 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.24), residues: 1155
  helix:  0.69 (0.18), residues: 750
  sheet: -1.90 (0.52), residues: 83
  loop : -1.35 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K2173 
 TYR   0.044   0.003   TYR 4 153 
 PHE   0.037   0.003   PHE A  28 
 TRP   0.033   0.004   TRP K2249 
 HIS   0.014   0.002   HIS K2220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 9762)
  covalent geometry    : angle       0.82987 (13171)
  hydrogen bonds       : bond        0.04580 (  658)
  hydrogen bonds       : angle       5.39814 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.350 
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: 4  159 MET cc_start: 0.8231 (ppp) cc_final: 0.6979 (ppp)
REVERT: A    6 MET cc_start: 0.4936 (mtm) cc_final: 0.4546 (mtt)
REVERT: A   79 PHE cc_start: 0.9021 (m-80) cc_final: 0.8579 (m-80)
REVERT: A  175 ARG cc_start: 0.8632 (tpt170) cc_final: 0.8294 (tpt170)
REVERT: B   41 MET cc_start: 0.2219 (ppp) cc_final: 0.1840 (ppp)
REVERT: B   66 TYR cc_start: 0.9101 (t80) cc_final: 0.8884 (t80)
REVERT: B   72 MET cc_start: 0.9279 (mtt) cc_final: 0.8639 (tpt)
REVERT: B  137 MET cc_start: 0.6782 (ppp) cc_final: 0.6305 (ppp)
REVERT: D  132 LYS cc_start: 0.7136 (mttt) cc_final: 0.6907 (mmmt)
REVERT: D  133 ARG cc_start: 0.8479 (mmm160) cc_final: 0.7824 (mtt180)
REVERT: D  231 HIS cc_start: 0.8906 (t70) cc_final: 0.8220 (t70)
REVERT: D  288 MET cc_start: 0.8306 (ptm) cc_final: 0.8041 (ptt)
REVERT: K 2201 LEU cc_start: 0.8998 (mt) cc_final: 0.8732 (mt)
REVERT: K 2245 TYR cc_start: 0.8415 (t80) cc_final: 0.8098 (t80)
REVERT: K 2324 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7562 (tttt)
REVERT: N  175 CYS cc_start: 0.9003 (m) cc_final: 0.8662 (p)
REVERT: N  207 MET cc_start: 0.7548 (mtt) cc_final: 0.7223 (mtt)
REVERT: N  269 TRP cc_start: 0.8812 (m100) cc_final: 0.8100 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1082
  time to fit residues: 19.9664
Evaluate side-chains
  98 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
4 165 HIS
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 GLN
B  83 GLN
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K2199 HIS
K2325 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.084873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.070245 restraints weight = 89688.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.071865 restraints weight = 60817.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.072626 restraints weight = 43636.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.073085 restraints weight = 35489.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.073597 restraints weight = 30663.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.9012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9762  Z= 0.184
  Angle     :  0.738  10.610  13171  Z= 0.388
  Chirality :  0.046   0.181   1452
  Planarity :  0.005   0.046   1709
  Dihedral  :  5.005  30.021   1258
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 20.54
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.64 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.71 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.25), residues: 1155
  helix:  0.85 (0.18), residues: 749
  sheet: -1.74 (0.52), residues: 85
  loop : -1.24 (0.38), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  23 
 TYR   0.021   0.002   TYR 4 153 
 PHE   0.027   0.002   PHE A  28 
 TRP   0.023   0.002   TRP K2249 
 HIS   0.006   0.001   HIS 4 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9762)
  covalent geometry    : angle       0.73780 (13171)
  hydrogen bonds       : bond        0.04268 (  658)
  hydrogen bonds       : angle       5.22340 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.408 
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: 4  159 MET cc_start: 0.8343 (ppp) cc_final: 0.6961 (ppp)
REVERT: A   79 PHE cc_start: 0.9121 (m-80) cc_final: 0.8625 (m-80)
REVERT: A  175 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8180 (tpt170)
REVERT: B   41 MET cc_start: 0.1707 (ppp) cc_final: 0.1323 (ppp)
REVERT: B   66 TYR cc_start: 0.9201 (t80) cc_final: 0.8914 (t80)
REVERT: B   72 MET cc_start: 0.9267 (mtt) cc_final: 0.8699 (tpt)
REVERT: B  137 MET cc_start: 0.6338 (ppp) cc_final: 0.5967 (ppp)
REVERT: B  195 ARG cc_start: 0.8996 (mmt180) cc_final: 0.8597 (mmt180)
REVERT: D  132 LYS cc_start: 0.7220 (mttt) cc_final: 0.7001 (mmmt)
REVERT: D  133 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8130 (mtt180)
REVERT: K 2179 ASP cc_start: 0.8930 (t0) cc_final: 0.8552 (t0)
REVERT: K 2201 LEU cc_start: 0.9043 (mt) cc_final: 0.8777 (mt)
REVERT: K 2256 MET cc_start: 0.6968 (ptt) cc_final: 0.6748 (ptp)
REVERT: K 2324 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7517 (pttt)
REVERT: N  175 CYS cc_start: 0.8979 (m) cc_final: 0.8570 (p)
REVERT: N  269 TRP cc_start: 0.8637 (m100) cc_final: 0.7886 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1212
  time to fit residues: 22.8326
Evaluate side-chains
  102 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 86 optimal weight:    0.3980
   chunk 63 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
4 141 GLN
4 145 GLN
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  87 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.084172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.069524 restraints weight = 88530.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.070938 restraints weight = 59008.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.071833 restraints weight = 43705.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.072605 restraints weight = 35324.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.073127 restraints weight = 29944.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.9524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9762  Z= 0.171
  Angle     :  0.737  10.531  13171  Z= 0.387
  Chirality :  0.046   0.192   1452
  Planarity :  0.005   0.042   1709
  Dihedral  :  4.986  29.260   1258
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 20.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.98 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.25), residues: 1155
  helix:  0.80 (0.18), residues: 747
  sheet: -1.77 (0.53), residues: 85
  loop : -1.13 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG 5 130 
 TYR   0.022   0.002   TYR 4 153 
 PHE   0.034   0.002   PHE A  28 
 TRP   0.016   0.002   TRP K2249 
 HIS   0.006   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9762)
  covalent geometry    : angle       0.73660 (13171)
  hydrogen bonds       : bond        0.04141 (  658)
  hydrogen bonds       : angle       5.17648 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.339 
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: 4  159 MET cc_start: 0.8409 (ppp) cc_final: 0.7015 (ppp)
REVERT: 4  180 LEU cc_start: 0.7846 (tp) cc_final: 0.7617 (tp)
REVERT: 5  131 LEU cc_start: 0.9007 (mt) cc_final: 0.8781 (pp)
REVERT: A    1 MET cc_start: 0.4297 (mmm) cc_final: 0.4068 (mmm)
REVERT: A   79 PHE cc_start: 0.9158 (m-80) cc_final: 0.8643 (m-80)
REVERT: A  175 ARG cc_start: 0.8680 (tpt170) cc_final: 0.8225 (tpt90)
REVERT: B   41 MET cc_start: 0.0624 (ppp) cc_final: 0.0319 (ppp)
REVERT: B   66 TYR cc_start: 0.9227 (t80) cc_final: 0.8893 (t80)
REVERT: B   72 MET cc_start: 0.9290 (mtt) cc_final: 0.8716 (tpt)
REVERT: B  137 MET cc_start: 0.6507 (ppp) cc_final: 0.6171 (ppp)
REVERT: D  132 LYS cc_start: 0.7092 (mttt) cc_final: 0.6849 (mmmt)
REVERT: D  133 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8122 (mtt180)
REVERT: K 2179 ASP cc_start: 0.9065 (t0) cc_final: 0.8744 (t0)
REVERT: K 2201 LEU cc_start: 0.8996 (mt) cc_final: 0.8708 (mt)
REVERT: K 2324 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7796 (tttt)
REVERT: N  175 CYS cc_start: 0.8918 (m) cc_final: 0.8492 (p)
REVERT: N  269 TRP cc_start: 0.8698 (m100) cc_final: 0.7956 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1328
  time to fit residues: 22.4356
Evaluate side-chains
  105 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 104 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.084798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.070064 restraints weight = 87807.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.071551 restraints weight = 57707.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.072532 restraints weight = 42735.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.073293 restraints weight = 34229.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.073687 restraints weight = 29046.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.9735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9762  Z= 0.150
  Angle     :  0.715  10.474  13171  Z= 0.371
  Chirality :  0.045   0.181   1452
  Planarity :  0.004   0.038   1709
  Dihedral  :  4.932  29.518   1258
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.72 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.25), residues: 1155
  helix:  0.92 (0.18), residues: 744
  sheet: -1.80 (0.53), residues: 85
  loop : -1.17 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 195 
 TYR   0.015   0.001   TYR 4 153 
 PHE   0.027   0.002   PHE A  28 
 TRP   0.016   0.002   TRP K2249 
 HIS   0.008   0.001   HIS N 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9762)
  covalent geometry    : angle       0.71506 (13171)
  hydrogen bonds       : bond        0.03978 (  658)
  hydrogen bonds       : angle       5.08352 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.394 
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: symmetry clash
REVERT: 4  159 MET cc_start: 0.8611 (ppp) cc_final: 0.7227 (ppp)
REVERT: 4  180 LEU cc_start: 0.7801 (tp) cc_final: 0.7562 (tp)
REVERT: 5  131 LEU cc_start: 0.8998 (mt) cc_final: 0.8776 (pp)
REVERT: 5  171 MET cc_start: 0.6355 (mmp) cc_final: 0.5997 (mmm)
REVERT: A    1 MET cc_start: 0.4361 (mmm) cc_final: 0.4088 (mmm)
REVERT: A    6 MET cc_start: 0.5477 (mtt) cc_final: 0.5224 (mtt)
REVERT: A   79 PHE cc_start: 0.9114 (m-80) cc_final: 0.8614 (m-80)
REVERT: A  175 ARG cc_start: 0.8627 (tpt170) cc_final: 0.8142 (tpt90)
REVERT: B   66 TYR cc_start: 0.9218 (t80) cc_final: 0.8876 (t80)
REVERT: B   72 MET cc_start: 0.9326 (mtt) cc_final: 0.8733 (tpt)
REVERT: B  137 MET cc_start: 0.6451 (ppp) cc_final: 0.6123 (ppp)
REVERT: D  132 LYS cc_start: 0.7112 (mttt) cc_final: 0.6713 (mppt)
REVERT: D  133 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8036 (mtt180)
REVERT: D  311 GLN cc_start: 0.9099 (tt0) cc_final: 0.8702 (tm-30)
REVERT: K 2179 ASP cc_start: 0.9168 (t0) cc_final: 0.8908 (t0)
REVERT: K 2181 ASN cc_start: 0.8962 (t0) cc_final: 0.8603 (t0)
REVERT: K 2201 LEU cc_start: 0.8917 (mt) cc_final: 0.8654 (mt)
REVERT: N  175 CYS cc_start: 0.8855 (m) cc_final: 0.8404 (p)
REVERT: N  269 TRP cc_start: 0.8629 (m100) cc_final: 0.7868 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1230
  time to fit residues: 22.2608
Evaluate side-chains
  104 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 75 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 ASN
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 169 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.085285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.070428 restraints weight = 88218.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.071902 restraints weight = 58200.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.072941 restraints weight = 43333.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.073606 restraints weight = 34681.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.074149 restraints weight = 29429.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.9870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9762  Z= 0.144
  Angle     :  0.720  10.478  13171  Z= 0.378
  Chirality :  0.045   0.199   1452
  Planarity :  0.004   0.046   1709
  Dihedral  :  4.877  32.522   1258
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.46 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.25), residues: 1155
  helix:  1.00 (0.19), residues: 750
  sheet: -1.84 (0.52), residues: 85
  loop : -1.10 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG N  37 
 TYR   0.030   0.001   TYR A  31 
 PHE   0.022   0.002   PHE B  80 
 TRP   0.016   0.002   TRP K2249 
 HIS   0.007   0.001   HIS N 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9762)
  covalent geometry    : angle       0.71983 (13171)
  hydrogen bonds       : bond        0.03870 (  658)
  hydrogen bonds       : angle       5.09928 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.409 
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: 4  159 MET cc_start: 0.8584 (ppp) cc_final: 0.7284 (ppp)
REVERT: 5  131 LEU cc_start: 0.9000 (mt) cc_final: 0.8789 (pp)
REVERT: 5  171 MET cc_start: 0.5932 (mmp) cc_final: 0.5704 (mmp)
REVERT: A    1 MET cc_start: 0.4458 (mmm) cc_final: 0.4256 (mmp)
REVERT: A    6 MET cc_start: 0.5413 (mtt) cc_final: 0.5181 (mtt)
REVERT: A   79 PHE cc_start: 0.9079 (m-80) cc_final: 0.8550 (m-80)
REVERT: A  175 ARG cc_start: 0.8480 (tpt170) cc_final: 0.8255 (tpt170)
REVERT: B   66 TYR cc_start: 0.9195 (t80) cc_final: 0.8839 (t80)
REVERT: B   72 MET cc_start: 0.9323 (mtt) cc_final: 0.8730 (tpt)
REVERT: B  137 MET cc_start: 0.6482 (ppp) cc_final: 0.6187 (ppp)
REVERT: D  133 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8005 (mtt180)
REVERT: D  288 MET cc_start: 0.8624 (ptm) cc_final: 0.8325 (ptt)
REVERT: D  311 GLN cc_start: 0.9073 (tt0) cc_final: 0.8717 (tm-30)
REVERT: K 2179 ASP cc_start: 0.9194 (t0) cc_final: 0.8902 (t0)
REVERT: K 2181 ASN cc_start: 0.8948 (t0) cc_final: 0.8589 (t0)
REVERT: K 2201 LEU cc_start: 0.8879 (mt) cc_final: 0.8609 (mt)
REVERT: K 2227 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8523 (tp30)
REVERT: K 2236 CYS cc_start: 0.9230 (m) cc_final: 0.9003 (p)
REVERT: N  175 CYS cc_start: 0.8854 (m) cc_final: 0.8385 (p)
REVERT: N  269 TRP cc_start: 0.8605 (m100) cc_final: 0.7842 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1208
  time to fit residues: 22.3011
Evaluate side-chains
  104 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 66 optimal weight:    0.1980
   chunk 77 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0040
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  41 GLN
B 155 GLN
B 194 GLN
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K2235 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.086196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.071448 restraints weight = 86829.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.072971 restraints weight = 57565.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.073898 restraints weight = 42444.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.074702 restraints weight = 34266.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.075212 restraints weight = 29015.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          1.0001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9762  Z= 0.135
  Angle     :  0.703  10.513  13171  Z= 0.367
  Chirality :  0.045   0.194   1452
  Planarity :  0.005   0.062   1709
  Dihedral  :  4.791  31.912   1258
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.81 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.19 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.25), residues: 1155
  helix:  1.05 (0.18), residues: 751
  sheet: -1.83 (0.51), residues: 85
  loop : -1.06 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG N  37 
 TYR   0.011   0.001   TYR A  25 
 PHE   0.028   0.002   PHE B  80 
 TRP   0.017   0.002   TRP K2249 
 HIS   0.006   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9762)
  covalent geometry    : angle       0.70313 (13171)
  hydrogen bonds       : bond        0.03727 (  658)
  hydrogen bonds       : angle       4.98490 ( 1956)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.401 
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: 4  159 MET cc_start: 0.8587 (ppp) cc_final: 0.7312 (ppp)
REVERT: 5  131 LEU cc_start: 0.8972 (mt) cc_final: 0.8752 (pp)
REVERT: A    6 MET cc_start: 0.5313 (mtt) cc_final: 0.5082 (mtt)
REVERT: A   79 PHE cc_start: 0.9009 (m-80) cc_final: 0.8481 (m-80)
REVERT: B   66 TYR cc_start: 0.9173 (t80) cc_final: 0.8833 (t80)
REVERT: B   72 MET cc_start: 0.9390 (mtt) cc_final: 0.8766 (tpt)
REVERT: B  137 MET cc_start: 0.6611 (ppp) cc_final: 0.6336 (ppp)
REVERT: D  133 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8040 (mtt180)
REVERT: D  288 MET cc_start: 0.8668 (ptm) cc_final: 0.8339 (ptt)
REVERT: D  311 GLN cc_start: 0.9050 (tt0) cc_final: 0.8786 (tm-30)
REVERT: K 2179 ASP cc_start: 0.9234 (t0) cc_final: 0.8992 (t0)
REVERT: K 2181 ASN cc_start: 0.8895 (t0) cc_final: 0.8537 (t0)
REVERT: K 2201 LEU cc_start: 0.8866 (mt) cc_final: 0.8583 (mt)
REVERT: K 2227 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8514 (tp30)
REVERT: N  175 CYS cc_start: 0.8810 (m) cc_final: 0.8347 (p)
REVERT: N  269 TRP cc_start: 0.8589 (m100) cc_final: 0.7836 (m100)
  outliers start: 1
  outliers final: 1
  residues processed: 136
  average time/residue: 0.1178
  time to fit residues: 21.9071
Evaluate side-chains
  106 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0870
   chunk 99 optimal weight:   10.0000
   chunk 108 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 76 optimal weight:    0.4980
   chunk 111 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    1.1160

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

Flipped N/Q/H residues before XYZ refinement:
** 4 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K2332 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.085181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.070427 restraints weight = 87650.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.071821 restraints weight = 59065.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.072818 restraints weight = 43934.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.073538 restraints weight = 35374.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.074070 restraints weight = 29866.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          1.0248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9762  Z= 0.141
  Angle     :  0.698  10.334  13171  Z= 0.367
  Chirality :  0.045   0.190   1452
  Planarity :  0.005   0.055   1709
  Dihedral  :  4.841  30.982   1258
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.07 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.25), residues: 1155
  helix:  1.09 (0.18), residues: 752
  sheet: -1.81 (0.52), residues: 85
  loop : -1.09 (0.38), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG N  37 
 TYR   0.015   0.001   TYR 4 153 
 PHE   0.023   0.002   PHE A  28 
 TRP   0.018   0.002   TRP K2249 
 HIS   0.012   0.001   HIS K2235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9762)
  covalent geometry    : angle       0.69847 (13171)
  hydrogen bonds       : bond        0.03739 (  658)
  hydrogen bonds       : angle       4.99177 ( 1956)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2724.33 seconds
wall clock time: 47 minutes 35.04 seconds (2855.04 seconds total)