Starting phenix.real_space_refine
on Sat May  2 15:16:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w0w_65518/05_2026/9w0w_65518_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w0w_65518/05_2026/9w0w_65518.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w0w_65518/05_2026/9w0w_65518_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w0w_65518/05_2026/9w0w_65518_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w0w_65518/05_2026/9w0w_65518.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w0w_65518/05_2026/9w0w_65518.map"
  }
  resolution = 3.2
  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=   0.088
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      42      5.16       5
     C    4282      2.51       5
     N    1132      2.21       5
     O    1195      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6651
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2141
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 7, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 75
    Chain: "A"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1640
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "B"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2467
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 141
          Unresolved non-hydrogen dihedrals: 93
          Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 95
    Chain: "C"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 378
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'SY9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.39, per 1000 atoms: 0.21
  Number of scatterers: 6651
  At special positions: 0
  Unit cell: (78.183, 100.674, 128.52, 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      42     16.00
     O    1195      8.00
     N    1132      7.00
     C    4282      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: 0.40
  Conformation dependent library (CDL) restraints added in 313.5 milliseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1678

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      49.8% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'R' and resid 8 through 38
      removed outlier: 4.113A  pdb=" N   LEU R  12 " --> pdb=" O   ILE R   8 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 71
    Processing helix  chain 'R' and resid 72 through 76
    Processing helix  chain 'R' and resid 77 through 111
    Processing helix  chain 'R' and resid 115 through 124
      removed outlier: 3.929A  pdb=" N   ARG R 124 " --> pdb=" O   HIS R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 134
      removed outlier: 4.186A  pdb=" N   VAL R 129 " --> pdb=" O   VAL R 125 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU R 130 " --> pdb=" O   LYS R 126 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL R 131 " --> pdb=" O   SER R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 153
    Processing helix  chain 'R' and resid 173 through 211
      removed outlier: 3.732A  pdb=" N   ASN R 184 " --> pdb=" O   THR R 180 " (cutoff:3.500A)
      Proline residue:  R 187  - end of helix
      removed outlier: 3.935A  pdb=" N   LEU R 211 " --> pdb=" O   LYS R 207 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 252
      removed outlier: 4.185A  pdb=" N   VAL R 223 " --> pdb=" O   PRO R 219 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR R 230 " --> pdb=" O   LYS R 226 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL R 231 " --> pdb=" O   ALA R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 284
      Proline residue:  R 272  - end of helix
      Proline residue:  R 276  - end of helix
      removed outlier: 3.563A  pdb=" N   LYS R 284 " --> pdb=" O   ILE R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 301
      removed outlier: 3.775A  pdb=" N   GLN R 288 " --> pdb=" O   LYS R 284 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR R 299 " --> pdb=" O   TRP R 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 33
      removed outlier: 3.816A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.276A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.787A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.078A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 350
      removed outlier: 4.001A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASN A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.571A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.665A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.502A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.637A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.789A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.347A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.583A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.983A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.508A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.743A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.491A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.535A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1167 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: 0.89

  Time building geometry restraints manager: 0.56 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: 2013
        1.34 -     1.45: 999
        1.45 -     1.57: 3724
        1.57 -     1.69: 1
        1.69 -     1.81: 57
  Bond restraints: 6794
  Sorted by residual:
  bond pdb=" CAV SY9 R 401 "
       pdb=" NAY SY9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.454  1.501 -0.047 2.00e-02 2.50e+03 5.52e+00
  bond pdb=" CB  PRO B  39 "
       pdb=" CG  PRO B  39 "
    ideal  model  delta    sigma   weight residual
    1.492  1.609 -0.117 5.00e-02 4.00e+02 5.44e+00
  bond pdb=" CAX SY9 R 401 "
       pdb=" NAY SY9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.449  1.482 -0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" CAG SY9 R 401 "
       pdb=" CAV SY9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.578  1.549  0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" CAM SY9 R 401 "
       pdb=" OAO SY9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.411  1.433 -0.022 2.00e-02 2.50e+03 1.25e+00
  ... (remaining 6789 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 9067
        1.39 -     2.79: 144
        2.79 -     4.18: 33
        4.18 -     5.57: 15
        5.57 -     6.96: 4
  Bond angle restraints: 9263
  Sorted by residual:
  angle pdb=" C   GLN R 217 "
        pdb=" N   ASP R 218 "
        pdb=" CA  ASP R 218 "
      ideal   model   delta    sigma   weight residual
     121.62  128.58   -6.96 1.57e+00 4.06e-01 1.97e+01
  angle pdb=" CA  PRO B  39 "
        pdb=" N   PRO B  39 "
        pdb=" CD  PRO B  39 "
      ideal   model   delta    sigma   weight residual
     112.00  105.83    6.17 1.40e+00 5.10e-01 1.94e+01
  angle pdb=" N   GLN R 217 "
        pdb=" CA  GLN R 217 "
        pdb=" C   GLN R 217 "
      ideal   model   delta    sigma   weight residual
     108.19  113.19   -5.00 1.29e+00 6.01e-01 1.50e+01
  angle pdb=" N   GLN B  17 "
        pdb=" CA  GLN B  17 "
        pdb=" CB  GLN B  17 "
      ideal   model   delta    sigma   weight residual
     110.40  115.89   -5.49 1.63e+00 3.76e-01 1.13e+01
  angle pdb=" C   ASN B  16 "
        pdb=" N   GLN B  17 "
        pdb=" CA  GLN B  17 "
      ideal   model   delta    sigma   weight residual
     121.14  115.79    5.35 1.75e+00 3.27e-01 9.34e+00
  ... (remaining 9258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.70: 3922
       33.70 -    67.40: 84
       67.40 -   101.10: 8
      101.10 -   134.80: 3
      134.80 -   168.49: 1
  Dihedral angle restraints: 4018
    sinusoidal: 1445
      harmonic: 2573
  Sorted by residual:
  dihedral pdb=" CAM SY9 R 401 "
           pdb=" CAP SY9 R 401 "
           pdb=" OAO SY9 R 401 "
           pdb=" CAQ SY9 R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.84   83.65 -168.49     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" CAN SY9 R 401 "
           pdb=" CAM SY9 R 401 "
           pdb=" OAO SY9 R 401 "
           pdb=" CAP SY9 R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.91   54.93 -119.84     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" CAL SY9 R 401 "
           pdb=" CAM SY9 R 401 "
           pdb=" OAO SY9 R 401 "
           pdb=" CAP SY9 R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.53  -68.02 -117.45     1      3.00e+01 1.11e-03 1.56e+01
  ... (remaining 4015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 953
       0.058 -    0.115: 151
       0.115 -    0.173: 8
       0.173 -    0.230: 0
       0.230 -    0.288: 2
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" NAY SY9 R 401 "
            pdb=" CAS SY9 R 401 "
            pdb=" CAV SY9 R 401 "
            pdb=" CAX SY9 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.12   -2.41    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CAK SY9 R 401 "
            pdb=" CAG SY9 R 401 "
            pdb=" CAN SY9 R 401 "
            pdb=" NAH SY9 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.81   -0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CB  THR B 181 "
            pdb=" CA  THR B 181 "
            pdb=" OG1 THR B 181 "
            pdb=" CG2 THR B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.30e-01
  ... (remaining 1111 not shown)

  Planarity restraints: 1149
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAA SY9 R 401 "   -0.198 2.00e-02 2.50e+03   1.36e-01 2.77e+02
        pdb=" CAI SY9 R 401 "    0.042 2.00e-02 2.50e+03
        pdb=" CAK SY9 R 401 "    0.077 2.00e-02 2.50e+03
        pdb=" CAL SY9 R 401 "   -0.168 2.00e-02 2.50e+03
        pdb=" NAH SY9 R 401 "    0.175 2.00e-02 2.50e+03
        pdb=" OAJ SY9 R 401 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.037 5.00e-02 4.00e+02   5.37e-02 4.62e+00
        pdb=" N   PRO B  39 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  59 "   -0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO C  60 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1146 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 669
        2.75 -     3.29: 6584
        3.29 -     3.82: 11301
        3.82 -     4.36: 12598
        4.36 -     4.90: 22472
  Nonbonded interactions: 53624
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.296 3.120
  ... (remaining 53619 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 individual isotropic
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:             1.440
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
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      :  0.002   0.117   6794  Z= 0.115
  Angle     :  0.511   6.964   9263  Z= 0.286
  Chirality :  0.041   0.288   1114
  Planarity :  0.005   0.136   1149
  Dihedral  : 14.930 168.494   2340
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.30), residues: 868
  helix:  2.28 (0.27), residues: 394
  sheet:  0.55 (0.41), residues: 169
  loop : -1.22 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.020   0.001   TYR R  85 
 PHE   0.016   0.001   PHE R 263 
 TRP   0.020   0.001   TRP B 211 
 HIS   0.009   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6794)
  covalent geometry    : angle       0.51126 ( 9263)
  hydrogen bonds       : bond        0.13669 (  404)
  hydrogen bonds       : angle       5.80324 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.186 
Fit side-chains
REVERT: R  124 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6312 (mtt90)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0901
  time to fit residues: 13.6242
Evaluate side-chains
  97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0570
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.137785 restraints weight = 8248.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.63
r_work: 0.3298 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6794  Z= 0.144
  Angle     :  0.514   8.684   9263  Z= 0.272
  Chirality :  0.041   0.227   1114
  Planarity :  0.003   0.037   1149
  Dihedral  :  7.718 138.716    989
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.73 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.30), residues: 868
  helix:  2.85 (0.27), residues: 389
  sheet:  0.21 (0.38), residues: 181
  loop : -1.22 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 208 
 TYR   0.011   0.001   TYR A 320 
 PHE   0.020   0.002   PHE R  26 
 TRP   0.020   0.001   TRP B 211 
 HIS   0.008   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6794)
  covalent geometry    : angle       0.51432 ( 9263)
  hydrogen bonds       : bond        0.03741 (  404)
  hydrogen bonds       : angle       4.11129 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.170 
Fit side-chains
REVERT: R  139 PHE cc_start: 0.7770 (t80) cc_final: 0.7540 (t80)
REVERT: A   28 GLU cc_start: 0.7851 (pp20) cc_final: 0.7271 (tm-30)
REVERT: A   29 LYS cc_start: 0.7844 (tptt) cc_final: 0.7539 (ttmm)
REVERT: A  284 THR cc_start: 0.8940 (m) cc_final: 0.8416 (t)
REVERT: B  321 THR cc_start: 0.8918 (p) cc_final: 0.8593 (p)
  outliers start: 6
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0913
  time to fit residues: 13.5228
Evaluate side-chains
  106 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  177 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 49 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0670
   chunk 26 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0570
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 ASN
R 176 ASN
A 269 ASN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.168620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137984 restraints weight = 8191.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.59
r_work: 0.3310 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6794  Z= 0.105
  Angle     :  0.462   5.474   9263  Z= 0.247
  Chirality :  0.039   0.163   1114
  Planarity :  0.003   0.036   1149
  Dihedral  :  4.077  52.681    989
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.95 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 868
  helix:  2.86 (0.26), residues: 396
  sheet:  0.16 (0.39), residues: 174
  loop : -1.18 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 123 
 TYR   0.010   0.001   TYR A 320 
 PHE   0.015   0.001   PHE R 263 
 TRP   0.019   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6794)
  covalent geometry    : angle       0.46178 ( 9263)
  hydrogen bonds       : bond        0.03306 (  404)
  hydrogen bonds       : angle       3.98744 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7703 (pp20) cc_final: 0.7350 (tm-30)
REVERT: A   29 LYS cc_start: 0.7964 (tptt) cc_final: 0.7571 (ttmm)
REVERT: A  284 THR cc_start: 0.8953 (m) cc_final: 0.8412 (t)
REVERT: B  234 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8426 (t80)
REVERT: B  321 THR cc_start: 0.8889 (p) cc_final: 0.8551 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0906
  time to fit residues: 13.0858
Evaluate side-chains
  108 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    0.0030
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.9194

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 205 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.163254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130225 restraints weight = 8116.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.66
r_work: 0.3253 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6794  Z= 0.167
  Angle     :  0.507   6.633   9263  Z= 0.275
  Chirality :  0.041   0.133   1114
  Planarity :  0.003   0.036   1149
  Dihedral  :  3.864  17.014    989
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.42 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.29), residues: 868
  helix:  2.74 (0.26), residues: 400
  sheet: -0.07 (0.37), residues: 188
  loop : -1.09 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 123 
 TYR   0.018   0.001   TYR A 320 
 PHE   0.015   0.002   PHE R  17 
 TRP   0.025   0.001   TRP B 211 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6794)
  covalent geometry    : angle       0.50725 ( 9263)
  hydrogen bonds       : bond        0.03808 (  404)
  hydrogen bonds       : angle       4.11544 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.204 
Fit side-chains
REVERT: R  124 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6932 (mtt90)
REVERT: R  139 PHE cc_start: 0.8069 (t80) cc_final: 0.7663 (t80)
REVERT: R  236 LEU cc_start: 0.8163 (mm) cc_final: 0.7825 (tp)
REVERT: A   25 GLU cc_start: 0.8523 (tt0) cc_final: 0.8181 (mt-10)
REVERT: B  105 TYR cc_start: 0.9226 (t80) cc_final: 0.8856 (t80)
REVERT: B  234 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8621 (t80)
REVERT: B  321 THR cc_start: 0.9085 (p) cc_final: 0.8738 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 112
  average time/residue: 0.0797
  time to fit residues: 11.7450
Evaluate side-chains
  104 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0970
   chunk 78 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 ASN
R 176 ASN
B  17 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.164567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132554 restraints weight = 8167.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.81
r_work: 0.3233 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6794  Z= 0.121
  Angle     :  0.472   6.381   9263  Z= 0.253
  Chirality :  0.040   0.172   1114
  Planarity :  0.003   0.039   1149
  Dihedral  :  3.621  15.039    989
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.63 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.29), residues: 868
  helix:  2.77 (0.26), residues: 402
  sheet: -0.07 (0.37), residues: 179
  loop : -1.14 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 123 
 TYR   0.011   0.001   TYR A 320 
 PHE   0.015   0.001   PHE R  17 
 TRP   0.019   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6794)
  covalent geometry    : angle       0.47151 ( 9263)
  hydrogen bonds       : bond        0.03437 (  404)
  hydrogen bonds       : angle       4.01558 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.234 
Fit side-chains
REVERT: R  124 ARG cc_start: 0.7351 (mtm180) cc_final: 0.6938 (mtt90)
REVERT: R  236 LEU cc_start: 0.8190 (mm) cc_final: 0.7874 (tp)
REVERT: A   25 GLU cc_start: 0.8575 (tt0) cc_final: 0.8252 (mt-10)
REVERT: A   28 GLU cc_start: 0.7600 (pp20) cc_final: 0.7052 (pp20)
REVERT: B   17 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7671 (pm20)
REVERT: B  105 TYR cc_start: 0.9259 (t80) cc_final: 0.8922 (t80)
REVERT: B  234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8549 (t80)
REVERT: B  321 THR cc_start: 0.9094 (p) cc_final: 0.8734 (p)
  outliers start: 14
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0853
  time to fit residues: 12.7917
Evaluate side-chains
  106 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  120 HIS
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0020
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.163094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.131509 restraints weight = 8182.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.81
r_work: 0.3217 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6794  Z= 0.136
  Angle     :  0.481   5.826   9263  Z= 0.261
  Chirality :  0.040   0.146   1114
  Planarity :  0.003   0.039   1149
  Dihedral  :  3.633  14.915    989
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.26 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 868
  helix:  2.80 (0.26), residues: 401
  sheet: -0.05 (0.37), residues: 177
  loop : -1.12 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.013   0.001   TYR A 320 
 PHE   0.016   0.002   PHE R  17 
 TRP   0.025   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6794)
  covalent geometry    : angle       0.48116 ( 9263)
  hydrogen bonds       : bond        0.03530 (  404)
  hydrogen bonds       : angle       4.06781 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.243 
Fit side-chains
REVERT: R  124 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6881 (mtt90)
REVERT: R  236 LEU cc_start: 0.8148 (mm) cc_final: 0.7838 (tp)
REVERT: A   25 GLU cc_start: 0.8594 (tt0) cc_final: 0.8297 (mt-10)
REVERT: A   28 GLU cc_start: 0.7739 (pp20) cc_final: 0.7135 (pp20)
REVERT: B   17 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7698 (pm20)
REVERT: B  105 TYR cc_start: 0.9266 (t80) cc_final: 0.8911 (t80)
REVERT: B  234 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8608 (t80)
REVERT: B  321 THR cc_start: 0.9112 (p) cc_final: 0.8759 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0747
  time to fit residues: 10.8956
Evaluate side-chains
  107 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0020
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8792

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.162031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.130991 restraints weight = 8108.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.68
r_work: 0.3220 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6794  Z= 0.153
  Angle     :  0.492   6.249   9263  Z= 0.267
  Chirality :  0.040   0.135   1114
  Planarity :  0.003   0.039   1149
  Dihedral  :  3.690  15.782    989
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.40 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 868
  helix:  2.79 (0.26), residues: 401
  sheet: -0.08 (0.37), residues: 177
  loop : -1.08 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.014   0.001   TYR A 320 
 PHE   0.021   0.002   PHE R 290 
 TRP   0.032   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6794)
  covalent geometry    : angle       0.49167 ( 9263)
  hydrogen bonds       : bond        0.03663 (  404)
  hydrogen bonds       : angle       4.06653 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.172 
Fit side-chains
REVERT: R  236 LEU cc_start: 0.8158 (mm) cc_final: 0.7864 (tp)
REVERT: A   25 GLU cc_start: 0.8582 (tt0) cc_final: 0.8314 (mt-10)
REVERT: A   28 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7292 (pp20)
REVERT: A  241 ASN cc_start: 0.7879 (m110) cc_final: 0.7593 (m-40)
REVERT: B   17 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7941 (pm20)
REVERT: B  105 TYR cc_start: 0.9216 (t80) cc_final: 0.8843 (t80)
REVERT: B  234 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8573 (t80)
REVERT: B  321 THR cc_start: 0.9131 (p) cc_final: 0.8786 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0856
  time to fit residues: 12.9593
Evaluate side-chains
  110 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.162802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.130536 restraints weight = 8182.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.79
r_work: 0.3211 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6794  Z= 0.129
  Angle     :  0.480   5.523   9263  Z= 0.260
  Chirality :  0.040   0.133   1114
  Planarity :  0.003   0.038   1149
  Dihedral  :  3.654  15.031    989
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.99 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.29), residues: 868
  helix:  2.84 (0.26), residues: 399
  sheet: -0.11 (0.37), residues: 177
  loop : -1.09 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.012   0.001   TYR A 320 
 PHE   0.019   0.002   PHE R 290 
 TRP   0.035   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6794)
  covalent geometry    : angle       0.48002 ( 9263)
  hydrogen bonds       : bond        0.03531 (  404)
  hydrogen bonds       : angle       4.02946 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.254 
Fit side-chains
REVERT: R  130 LEU cc_start: 0.7806 (mt) cc_final: 0.7571 (mm)
REVERT: R  236 LEU cc_start: 0.8093 (mm) cc_final: 0.7802 (tp)
REVERT: A   25 GLU cc_start: 0.8382 (tt0) cc_final: 0.8113 (mt-10)
REVERT: A   28 GLU cc_start: 0.7735 (pp20) cc_final: 0.7141 (pp20)
REVERT: A  241 ASN cc_start: 0.7778 (m110) cc_final: 0.7513 (m-40)
REVERT: B   17 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7817 (pm20)
REVERT: B  105 TYR cc_start: 0.9143 (t80) cc_final: 0.8755 (t80)
REVERT: B  234 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8481 (t80)
REVERT: B  321 THR cc_start: 0.9043 (p) cc_final: 0.8698 (p)
  outliers start: 14
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0814
  time to fit residues: 11.9105
Evaluate side-chains
  109 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.130148 restraints weight = 8228.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.01
r_work: 0.3187 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6794  Z= 0.149
  Angle     :  0.496   6.049   9263  Z= 0.268
  Chirality :  0.040   0.135   1114
  Planarity :  0.003   0.038   1149
  Dihedral  :  3.696  15.758    989
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.85 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.29), residues: 868
  helix:  2.74 (0.26), residues: 404
  sheet: -0.17 (0.37), residues: 177
  loop : -1.12 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.014   0.001   TYR A 320 
 PHE   0.018   0.002   PHE R 290 
 TRP   0.035   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6794)
  covalent geometry    : angle       0.49586 ( 9263)
  hydrogen bonds       : bond        0.03628 (  404)
  hydrogen bonds       : angle       4.05222 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.215 
Fit side-chains
REVERT: R  130 LEU cc_start: 0.7764 (mt) cc_final: 0.7517 (mm)
REVERT: R  236 LEU cc_start: 0.8182 (mm) cc_final: 0.7867 (tp)
REVERT: A   25 GLU cc_start: 0.8511 (tt0) cc_final: 0.8218 (mt-10)
REVERT: A   28 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7194 (pp20)
REVERT: A  241 ASN cc_start: 0.7943 (m110) cc_final: 0.7644 (m-40)
REVERT: B   17 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7872 (pm20)
REVERT: B  105 TYR cc_start: 0.9276 (t80) cc_final: 0.8943 (t80)
REVERT: B  234 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8570 (t80)
REVERT: B  321 THR cc_start: 0.9129 (p) cc_final: 0.8767 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0797
  time to fit residues: 11.9157
Evaluate side-chains
  113 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
R 143 HIS
B  17 GLN
B 156 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.159347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126694 restraints weight = 8226.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.84
r_work: 0.3158 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6794  Z= 0.201
  Angle     :  0.538   6.834   9263  Z= 0.291
  Chirality :  0.042   0.136   1114
  Planarity :  0.004   0.039   1149
  Dihedral  :  3.869  18.426    989
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.99 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.29), residues: 868
  helix:  2.62 (0.26), residues: 406
  sheet: -0.50 (0.36), residues: 188
  loop : -1.03 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.018   0.001   TYR A 320 
 PHE   0.019   0.002   PHE R 290 
 TRP   0.043   0.002   TRP B 211 
 HIS   0.004   0.001   HIS R 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 6794)
  covalent geometry    : angle       0.53766 ( 9263)
  hydrogen bonds       : bond        0.04010 (  404)
  hydrogen bonds       : angle       4.16134 ( 1167)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.201 
Fit side-chains
REVERT: R  130 LEU cc_start: 0.7752 (mt) cc_final: 0.7495 (mm)
REVERT: R  236 LEU cc_start: 0.8135 (mm) cc_final: 0.7869 (tp)
REVERT: A   25 GLU cc_start: 0.8468 (tt0) cc_final: 0.8171 (mt-10)
REVERT: A   28 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7271 (pp20)
REVERT: A  241 ASN cc_start: 0.8010 (m110) cc_final: 0.7695 (m-40)
REVERT: B   17 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7775 (pm20)
REVERT: B  105 TYR cc_start: 0.9318 (t80) cc_final: 0.8977 (t80)
REVERT: B  234 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8516 (t80)
REVERT: B  321 THR cc_start: 0.9132 (p) cc_final: 0.8763 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0835
  time to fit residues: 12.4678
Evaluate side-chains
  110 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  288 GLN
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.161418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.128289 restraints weight = 8114.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.10
r_work: 0.3193 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6794  Z= 0.131
  Angle     :  0.489   5.640   9263  Z= 0.265
  Chirality :  0.040   0.131   1114
  Planarity :  0.003   0.038   1149
  Dihedral  :  3.738  16.755    989
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.88 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.29), residues: 868
  helix:  2.71 (0.26), residues: 405
  sheet: -0.34 (0.37), residues: 179
  loop : -1.06 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.012   0.001   TYR A 320 
 PHE   0.018   0.002   PHE R 290 
 TRP   0.038   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6794)
  covalent geometry    : angle       0.48926 ( 9263)
  hydrogen bonds       : bond        0.03640 (  404)
  hydrogen bonds       : angle       4.09547 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1830.42 seconds
wall clock time: 32 minutes 7.73 seconds (1927.73 seconds total)