Starting phenix.real_space_refine
on Fri Jun 13 13:23:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vsu_43506/06_2025/8vsu_43506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vsu_43506/06_2025/8vsu_43506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vsu_43506/06_2025/8vsu_43506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vsu_43506/06_2025/8vsu_43506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vsu_43506/06_2025/8vsu_43506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vsu_43506/06_2025/8vsu_43506.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.102
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      41      5.16       5
     C    4859      2.51       5
     N    1301      2.21       5
     O    1391      1.98       5
     H    7646      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15240
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 5458
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 9, 'TRANS': 318}
    Chain: "C"
      Number of atoms: 4900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 4900
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 21, 'TRANS': 285}
    Chain: "B"
      Number of atoms: 4855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 4855
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 17, 'TRANS': 288}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.21, per 1000 atoms: 0.54
  Number of scatterers: 15240
  At special positions: 0
  Unit cell: (87.675, 88.51, 106.045, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P       2     15.00
     O    1391      8.00
     N    1301      7.00
     C    4859      6.00
     H    7646      1.00
    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: 4.50
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1782

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      58.7% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 27
    Processing helix  chain 'A' and resid 32 through 56
      removed outlier: 3.654A  pdb=" N   ALA A  36 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   LYS A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 78 through 86
    Processing helix  chain 'A' and resid 87 through 90
    Processing helix  chain 'A' and resid 91 through 107
      removed outlier: 3.744A  pdb=" N   LYS A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN A 104 " --> pdb=" O   GLN A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 121
    Processing helix  chain 'A' and resid 124 through 133
      removed outlier: 3.798A  pdb=" N   PHE A 128 " --> pdb=" O   GLN A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 153 through 162
    Processing helix  chain 'A' and resid 163 through 167
      removed outlier: 3.672A  pdb=" N   TYR A 167 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 177 through 194
      removed outlier: 3.646A  pdb=" N   ASP A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 206 through 219
      removed outlier: 3.612A  pdb=" N   SER A 212 " --> pdb=" O   ASP A 208 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   LYS A 216 " --> pdb=" O   SER A 212 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU A 217 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 218 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 239
      removed outlier: 3.629A  pdb=" N   ASP A 239 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
    Processing helix  chain 'A' and resid 252 through 263
      removed outlier: 3.505A  pdb=" N   LEU A 256 " --> pdb=" O   LYS A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 284
      removed outlier: 3.546A  pdb=" N   VAL A 277 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   VAL A 280 " --> pdb=" O   HIS A 276 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE A 281 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 282 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASN A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 298
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 316 through 332
      removed outlier: 3.886A  pdb=" N   ASN A 320 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 86
      removed outlier: 3.532A  pdb=" N   ARG C  86 " --> pdb=" O   LYS C  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 82 through 86'
    Processing helix  chain 'C' and resid 90 through 103
    Processing helix  chain 'C' and resid 136 through 141
    Processing helix  chain 'C' and resid 149 through 170
      removed outlier: 3.575A  pdb=" N   GLY C 155 " --> pdb=" O   CYS C 151 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLN C 159 " --> pdb=" O   GLY C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 180
      No H-bonds generated for 'chain 'C' and resid 178 through 180'
    Processing helix  chain 'C' and resid 194 through 198
      removed outlier: 4.308A  pdb=" N   VAL C 197 " --> pdb=" O   ASP C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 220
    Processing helix  chain 'C' and resid 221 through 226
    Processing helix  chain 'C' and resid 233 through 251
      removed outlier: 3.585A  pdb=" N   ASP C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TRP C 239 " --> pdb=" O   LYS C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 269
    Processing helix  chain 'C' and resid 279 through 289
    Processing helix  chain 'C' and resid 299 through 306
    Processing helix  chain 'C' and resid 306 through 311
    Processing helix  chain 'C' and resid 337 through 345
    Processing helix  chain 'B' and resid 65 through 67
      No H-bonds generated for 'chain 'B' and resid 65 through 67'
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 125
      removed outlier: 3.859A  pdb=" N   GLU B 118 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B 125 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 160
    Processing helix  chain 'B' and resid 168 through 189
      removed outlier: 3.602A  pdb=" N   TYR B 185 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.748A  pdb=" N   LEU B 241 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      Proline residue:  B 242  - end of helix
    Processing helix  chain 'B' and resid 245 through 250
    Processing helix  chain 'B' and resid 258 through 275
      removed outlier: 4.281A  pdb=" N   ILE B 262 " --> pdb=" O   ALA B 258 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   TYR B 263 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 293
    Processing helix  chain 'B' and resid 349 through 359
    Processing helix  chain 'B' and resid 363 through 367
    Processing helix  chain 'B' and resid 369 through 374
    Processing helix  chain 'B' and resid 375 through 382
      removed outlier: 6.085A  pdb=" N   PHE B 378 " --> pdb=" O   ASN B 375 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLN B 381 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 394
      Proline residue:  B 391  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 46
      removed outlier: 4.987A  pdb=" N   GLU C  65 " --> pdb=" O   GLY C  52 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU C  54 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   VAL C  63 " --> pdb=" O   LEU C  54 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS C  62 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   LYS C 124 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   TYR C 118 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TYR C 126 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   VAL C 116 " --> pdb=" O   TYR C 126 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL C 128 " --> pdb=" O   VAL C 114 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 134 through 135
      removed outlier: 3.781A  pdb=" N   CYS C 134 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 172 through 173
    Processing sheet with id=AA4, first strand: chain 'C' and resid 209 through 210
    Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 78
      removed outlier: 6.809A  pdb=" N   LEU B  87 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   VAL B  74 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   VAL B  85 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   GLY B  76 " --> pdb=" O   MET B  83 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   MET B  83 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B 135 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   SER B 148 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   TYR B 133 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
    Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 203
    Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 222

    363 hydrogen bonds defined for protein.
    1032 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: 5.63

  Time building geometry restraints manager: 5.03 seconds

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

  Histogram of bond lengths:
        0.74 -     0.96: 22
        0.96 -     1.17: 7608
        1.17 -     1.39: 2601
        1.39 -     1.60: 5111
        1.60 -     1.82: 67
  Bond restraints: 15409
  Sorted by residual:
  bond pdb=" N   LYS B  91 "
       pdb=" H   LYS B  91 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" CD2 TYR A 325 "
       pdb=" HD2 TYR A 325 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" NH1 ARG A 113 "
       pdb="HH11 ARG A 113 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CE1 TYR B 152 "
       pdb=" HE1 TYR B 152 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CE1 HIS C 313 "
       pdb=" HE1 HIS C 313 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  ... (remaining 15404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 24822
        2.95 -     5.91: 2384
        5.91 -     8.86: 703
        8.86 -    11.81: 10
       11.81 -    14.77: 13
  Bond angle restraints: 27932
  Sorted by residual:
  angle pdb=" CA  ASP B 301 "
        pdb=" CB  ASP B 301 "
        pdb=" CG  ASP B 301 "
      ideal   model   delta    sigma   weight residual
     112.60  117.73   -5.13 1.00e+00 1.00e+00 2.63e+01
  angle pdb=" CA  PHE C 298 "
        pdb=" CB  PHE C 298 "
        pdb=" CG  PHE C 298 "
      ideal   model   delta    sigma   weight residual
     113.80  118.88   -5.08 1.00e+00 1.00e+00 2.58e+01
  angle pdb=" O1B ADP B2001 "
        pdb=" PB  ADP B2001 "
        pdb=" O2B ADP B2001 "
      ideal   model   delta    sigma   weight residual
     119.90  105.13   14.77 3.00e+00 1.11e-01 2.42e+01
  angle pdb=" CA  PHE B 279 "
        pdb=" CB  PHE B 279 "
        pdb=" CG  PHE B 279 "
      ideal   model   delta    sigma   weight residual
     113.80  118.48   -4.68 1.00e+00 1.00e+00 2.19e+01
  angle pdb=" CA  PHE C 148 "
        pdb=" CB  PHE C 148 "
        pdb=" CG  PHE C 148 "
      ideal   model   delta    sigma   weight residual
     113.80  118.43   -4.63 1.00e+00 1.00e+00 2.14e+01
  ... (remaining 27927 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.69: 6808
       21.69 -    43.37: 232
       43.37 -    65.06: 164
       65.06 -    86.74: 22
       86.74 -   108.43: 2
  Dihedral angle restraints: 7228
    sinusoidal: 3975
      harmonic: 3253
  Sorted by residual:
  dihedral pdb=" CA  GLY C 288 "
           pdb=" C   GLY C 288 "
           pdb=" N   MET C 289 "
           pdb=" CA  MET C 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.99   29.01     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" C5' ADP B2001 "
           pdb=" O5' ADP B2001 "
           pdb=" PA  ADP B2001 "
           pdb=" O2A ADP B2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   48.43 -108.43     1      2.00e+01 2.50e-03 3.16e+01
  dihedral pdb=" CA  GLN B 358 "
           pdb=" C   GLN B 358 "
           pdb=" N   CYS B 359 "
           pdb=" CA  CYS B 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.33   26.67     0      5.00e+00 4.00e-02 2.85e+01
  ... (remaining 7225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 661
       0.067 -    0.133: 363
       0.133 -    0.200: 115
       0.200 -    0.267: 19
       0.267 -    0.334: 6
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" C2' ADP B2001 "
            pdb=" C1' ADP B2001 "
            pdb=" C3' ADP B2001 "
            pdb=" O2' ADP B2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.84    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CA  SER C 193 "
            pdb=" N   SER C 193 "
            pdb=" C   SER C 193 "
            pdb=" CB  SER C 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  SER B 195 "
            pdb=" N   SER B 195 "
            pdb=" C   SER B 195 "
            pdb=" CB  SER B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  ... (remaining 1161 not shown)

  Planarity restraints: 2229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 207 "    0.139 2.00e-02 2.50e+03   5.75e-02 9.92e+01
        pdb=" CG  TYR A 207 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 207 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 207 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 207 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 207 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 207 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A 207 "    0.103 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 207 "   -0.049 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 207 "   -0.024 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 207 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 207 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 243 "    0.106 2.00e-02 2.50e+03   4.81e-02 9.25e+01
        pdb=" CG  TRP B 243 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 243 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 243 "   -0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 243 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 243 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 243 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 243 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 243 "   -0.017 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 243 "    0.028 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 243 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 243 "   -0.075 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 243 "   -0.090 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 243 "    0.021 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 243 "   -0.002 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 243 "    0.070 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 227 "    0.198 9.50e-02 1.11e+02   8.72e-02 7.75e+01
        pdb=" NE  ARG A 227 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 227 "    0.023 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 227 "    0.026 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 227 "    0.015 2.00e-02 2.50e+03
        pdb="HH11 ARG A 227 "   -0.117 2.00e-02 2.50e+03
        pdb="HH12 ARG A 227 "    0.095 2.00e-02 2.50e+03
        pdb="HH21 ARG A 227 "   -0.018 2.00e-02 2.50e+03
        pdb="HH22 ARG A 227 "   -0.062 2.00e-02 2.50e+03
  ... (remaining 2226 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 778
        2.18 -     2.79: 26413
        2.79 -     3.39: 41785
        3.39 -     4.00: 55814
        4.00 -     4.60: 81224
  Nonbonded interactions: 206014
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 208 "
            pdb=" HG  SER C 232 "
     model   vdw
     1.577 2.450
  nonbonded pdb=" OD1 ASP B 301 "
            pdb=" HG  SER B 303 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" OD1 ASP C 207 "
            pdb=" HG1 THR C 209 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" OE1 GLU C  65 "
            pdb=" HG1 THR C 336 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" HH  TYR A 223 "
            pdb=" OE1 GLU B 105 "
     model   vdw
     1.618 2.450
  ... (remaining 206009 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:             1.800
  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:             0.290
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     36.710
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  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:12.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
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      :  0.013   0.141   7763  Z= 0.767
  Angle     :  1.761  14.765  10493  Z= 1.194
  Chirality :  0.086   0.334   1164
  Planarity :  0.013   0.117   1339
  Dihedral  : 12.495 108.425   2943
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 0.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.60 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.25), residues: 933
  helix: -1.20 (0.20), residues: 478
  sheet: -0.48 (0.52), residues: 87
  loop :  0.04 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.013   TRP B 243 
 HIS   0.010   0.002   HIS B 200 
 PHE   0.052   0.010   PHE A 188 
 TYR   0.119   0.016   TYR A 207 
 ARG   0.010   0.001   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22313 (  363)
  hydrogen bonds       : angle       6.73502 ( 1032)
  covalent geometry    : bond        0.01258 ( 7763)
  covalent geometry    : angle       1.76097 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 1.151 
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: A  257 LYS cc_start: 0.8469 (mttt) cc_final: 0.8250 (mtmt)
REVERT: C  104 ARG cc_start: 0.7980 (ptt90) cc_final: 0.7401 (mmt90)
REVERT: B  287 MET cc_start: 0.8750 (tmm) cc_final: 0.8542 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 2.9751
  time to fit residues: 505.8782
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
A 329 GLN
C 220 GLN
B 227 GLN
B 286 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.132728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.101935 restraints weight = 26606.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.05
r_work: 0.2903 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7763  Z= 0.149
  Angle     :  0.605   6.653  10493  Z= 0.324
  Chirality :  0.042   0.144   1164
  Planarity :  0.005   0.045   1339
  Dihedral  :  7.035 120.389   1030
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 0.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  6.21 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 933
  helix:  0.63 (0.24), residues: 479
  sheet: -0.17 (0.55), residues: 75
  loop :  0.20 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 308 
 HIS   0.007   0.001   HIS A 276 
 PHE   0.024   0.002   PHE A 188 
 TYR   0.010   0.001   TYR C 246 
 ARG   0.004   0.001   ARG A 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06208 (  363)
  hydrogen bonds       : angle       4.69415 ( 1032)
  covalent geometry    : bond        0.00327 ( 7763)
  covalent geometry    : angle       0.60524 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.7892 (mt0) cc_final: 0.7627 (mt0)
REVERT: A   72 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7660 (tp-100)
REVERT: A  215 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7259 (pp20)
REVERT: A  257 LYS cc_start: 0.8164 (mttt) cc_final: 0.7640 (mtmt)
REVERT: C   42 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.7068 (tpt170)
REVERT: C  262 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7670 (mttt)
REVERT: C  271 SER cc_start: 0.8884 (t) cc_final: 0.8531 (m)
REVERT: B  247 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7503 (pm20)
REVERT: B  287 MET cc_start: 0.8705 (tmm) cc_final: 0.8464 (tmm)
REVERT: B  362 ARG cc_start: 0.7900 (ttt180) cc_final: 0.7591 (ttm-80)
  outliers start: 15
  outliers final: 5
  residues processed: 124
  average time/residue: 3.0349
  time to fit residues: 396.2002
Evaluate side-chains
  108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain C residue  230 THR
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  247 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 71 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
C 220 GLN
B 225 GLN
B 227 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.133774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.103232 restraints weight = 26285.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.04
r_work: 0.3116 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7763  Z= 0.114
  Angle     :  0.527   5.816  10493  Z= 0.274
  Chirality :  0.040   0.149   1164
  Planarity :  0.004   0.046   1339
  Dihedral  :  6.335 119.707   1030
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.23 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 933
  helix:  1.38 (0.25), residues: 477
  sheet: -0.23 (0.58), residues: 75
  loop :  0.04 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.011   0.001   HIS B 162 
 PHE   0.016   0.001   PHE A 188 
 TYR   0.010   0.001   TYR C 246 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  363)
  hydrogen bonds       : angle       4.15119 ( 1032)
  covalent geometry    : bond        0.00252 ( 7763)
  covalent geometry    : angle       0.52750 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 1.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8006 (tp-100)
REVERT: A  257 LYS cc_start: 0.8354 (mttt) cc_final: 0.7882 (mtmt)
REVERT: C   42 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7281 (tpt90)
REVERT: C  262 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7918 (mttt)
REVERT: C  271 SER cc_start: 0.8935 (t) cc_final: 0.8685 (m)
REVERT: C  336 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.6995 (t)
REVERT: B   81 ASP cc_start: 0.8580 (t0) cc_final: 0.7965 (t0)
REVERT: B  287 MET cc_start: 0.8745 (tmm) cc_final: 0.8521 (tmm)
REVERT: B  362 ARG cc_start: 0.7862 (ttt180) cc_final: 0.7629 (ttm-80)
REVERT: B  390 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6509 (tt)
  outliers start: 11
  outliers final: 2
  residues processed: 108
  average time/residue: 2.7186
  time to fit residues: 310.4903
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain C residue  334 SER
Chi-restraints excluded: chain C residue  336 THR
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0970
   chunk 90 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
A 289 GLN
C 345 HIS
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.133226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.102622 restraints weight = 26459.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.04
r_work: 0.3112 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7763  Z= 0.120
  Angle     :  0.503   5.812  10493  Z= 0.259
  Chirality :  0.039   0.148   1164
  Planarity :  0.004   0.045   1339
  Dihedral  :  6.025 110.582   1030
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 0.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.71 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 933
  helix:  1.63 (0.24), residues: 484
  sheet: -0.35 (0.59), residues: 75
  loop : -0.00 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 239 
 HIS   0.004   0.001   HIS B 193 
 PHE   0.018   0.001   PHE A 188 
 TYR   0.009   0.001   TYR C 246 
 ARG   0.002   0.000   ARG C 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  363)
  hydrogen bonds       : angle       3.98712 ( 1032)
  covalent geometry    : bond        0.00286 ( 7763)
  covalent geometry    : angle       0.50274 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8048 (tp-100)
REVERT: A  141 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7730 (tp)
REVERT: A  215 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7279 (pp20)
REVERT: A  257 LYS cc_start: 0.8354 (mttt) cc_final: 0.7885 (mtmt)
REVERT: C   42 ARG cc_start: 0.7574 (ttp-110) cc_final: 0.7278 (tpt90)
REVERT: C  262 LYS cc_start: 0.8265 (mmmm) cc_final: 0.7933 (mttt)
REVERT: C  271 SER cc_start: 0.8945 (t) cc_final: 0.8699 (m)
REVERT: B   81 ASP cc_start: 0.8571 (t0) cc_final: 0.7936 (t0)
REVERT: B  362 ARG cc_start: 0.7935 (ttt180) cc_final: 0.7707 (ttm-80)
REVERT: B  390 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6478 (tt)
  outliers start: 9
  outliers final: 2
  residues processed: 102
  average time/residue: 2.8495
  time to fit residues: 306.7289
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
C 345 HIS
B 141 ASN
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.133782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.103114 restraints weight = 26567.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.04
r_work: 0.2917 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7763  Z= 0.107
  Angle     :  0.486   5.902  10493  Z= 0.248
  Chirality :  0.039   0.145   1164
  Planarity :  0.004   0.044   1339
  Dihedral  :  5.732 103.467   1030
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  9.43 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.28), residues: 933
  helix:  1.85 (0.25), residues: 485
  sheet: -0.54 (0.58), residues: 77
  loop : -0.07 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 239 
 HIS   0.003   0.001   HIS A 276 
 PHE   0.016   0.001   PHE A 188 
 TYR   0.009   0.001   TYR C 246 
 ARG   0.004   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  363)
  hydrogen bonds       : angle       3.84425 ( 1032)
  covalent geometry    : bond        0.00249 ( 7763)
  covalent geometry    : angle       0.48564 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 LYS cc_start: 0.8087 (mttt) cc_final: 0.7574 (mtmt)
REVERT: A  293 ASP cc_start: 0.7745 (m-30) cc_final: 0.7471 (m-30)
REVERT: C   42 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7140 (tpt90)
REVERT: C  262 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7743 (mttt)
REVERT: C  271 SER cc_start: 0.8938 (t) cc_final: 0.8617 (m)
REVERT: B   81 ASP cc_start: 0.8602 (t0) cc_final: 0.7969 (t0)
REVERT: B  362 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7678 (ttm-80)
REVERT: B  380 LYS cc_start: 0.7773 (mttm) cc_final: 0.7286 (mtmp)
REVERT: B  390 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6241 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 104
  average time/residue: 2.8287
  time to fit residues: 310.4034
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.131335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.100648 restraints weight = 26585.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.04
r_work: 0.3024 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7763  Z= 0.140
  Angle     :  0.511   6.272  10493  Z= 0.262
  Chirality :  0.040   0.145   1164
  Planarity :  0.004   0.045   1339
  Dihedral  :  5.688  93.942   1030
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  9.79 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.28), residues: 933
  helix:  1.82 (0.25), residues: 485
  sheet: -0.48 (0.59), residues: 77
  loop : -0.09 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 239 
 HIS   0.005   0.001   HIS B 193 
 PHE   0.021   0.001   PHE A 188 
 TYR   0.011   0.001   TYR C 246 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  363)
  hydrogen bonds       : angle       3.87147 ( 1032)
  covalent geometry    : bond        0.00343 ( 7763)
  covalent geometry    : angle       0.51067 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7326 (pp20)
REVERT: A  257 LYS cc_start: 0.8264 (mttt) cc_final: 0.7782 (mtmt)
REVERT: C   42 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7215 (tpt90)
REVERT: C  262 LYS cc_start: 0.8286 (mmmm) cc_final: 0.7926 (mttt)
REVERT: C  271 SER cc_start: 0.8963 (t) cc_final: 0.8693 (m)
REVERT: B   81 ASP cc_start: 0.8592 (t0) cc_final: 0.7956 (t0)
REVERT: B  362 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7723 (ttm-80)
REVERT: B  380 LYS cc_start: 0.7919 (mttm) cc_final: 0.7407 (mtmp)
REVERT: B  390 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6375 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 106
  average time/residue: 2.7772
  time to fit residues: 310.8878
Evaluate side-chains
  102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 90 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 89 optimal weight:    0.2980
   chunk 57 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.133420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.102628 restraints weight = 26603.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.07
r_work: 0.2910 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7763  Z= 0.103
  Angle     :  0.481   6.189  10493  Z= 0.244
  Chirality :  0.039   0.145   1164
  Planarity :  0.004   0.047   1339
  Dihedral  :  5.493  92.293   1030
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.26 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.28), residues: 933
  helix:  2.02 (0.25), residues: 485
  sheet: -0.32 (0.60), residues: 75
  loop : -0.05 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 144 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.015   0.001   PHE A 188 
 TYR   0.008   0.001   TYR C 246 
 ARG   0.005   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  363)
  hydrogen bonds       : angle       3.75109 ( 1032)
  covalent geometry    : bond        0.00244 ( 7763)
  covalent geometry    : angle       0.48099 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7119 (tm-30)
REVERT: A  257 LYS cc_start: 0.8057 (mttt) cc_final: 0.7550 (mtmt)
REVERT: C   42 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7073 (tpt90)
REVERT: C  262 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7770 (mttt)
REVERT: C  271 SER cc_start: 0.8959 (t) cc_final: 0.8624 (m)
REVERT: B  140 ASP cc_start: 0.7718 (t70) cc_final: 0.7286 (t70)
REVERT: B  141 ASN cc_start: 0.8298 (m-40) cc_final: 0.8088 (m110)
REVERT: B  362 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7699 (ttm-80)
REVERT: B  380 LYS cc_start: 0.7753 (mttm) cc_final: 0.7230 (mtmp)
REVERT: B  390 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6229 (tt)
  outliers start: 11
  outliers final: 4
  residues processed: 112
  average time/residue: 2.6391
  time to fit residues: 312.6752
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.132878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.102311 restraints weight = 26394.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.03
r_work: 0.3110 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7763  Z= 0.102
  Angle     :  0.481   6.363  10493  Z= 0.242
  Chirality :  0.038   0.145   1164
  Planarity :  0.004   0.042   1339
  Dihedral  :  5.353  82.460   1030
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 0.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 11.10 %
    Favored  : 88.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 933
  helix:  2.24 (0.25), residues: 478
  sheet: -0.54 (0.55), residues: 85
  loop :  0.09 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 239 
 HIS   0.006   0.001   HIS B 162 
 PHE   0.015   0.001   PHE A 188 
 TYR   0.008   0.001   TYR C 246 
 ARG   0.007   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (  363)
  hydrogen bonds       : angle       3.69023 ( 1032)
  covalent geometry    : bond        0.00243 ( 7763)
  covalent geometry    : angle       0.48054 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 LYS cc_start: 0.8308 (mttt) cc_final: 0.7853 (mtmt)
REVERT: A  288 THR cc_start: 0.8408 (p) cc_final: 0.8182 (p)
REVERT: C   42 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.7223 (tpt90)
REVERT: C  162 ASP cc_start: 0.8291 (m-30) cc_final: 0.7962 (m-30)
REVERT: C  262 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7965 (mttt)
REVERT: C  271 SER cc_start: 0.8945 (t) cc_final: 0.8695 (m)
REVERT: B  140 ASP cc_start: 0.7720 (t70) cc_final: 0.7363 (t70)
REVERT: B  362 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7748 (ttm-80)
REVERT: B  380 LYS cc_start: 0.7910 (mttm) cc_final: 0.7417 (mtmp)
REVERT: B  390 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6483 (tt)
  outliers start: 6
  outliers final: 4
  residues processed: 108
  average time/residue: 2.7238
  time to fit residues: 311.0528
Evaluate side-chains
  104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain C residue  336 THR
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 227 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.133575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.102992 restraints weight = 26461.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.04
r_work: 0.3120 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7763  Z= 0.096
  Angle     :  0.481   6.404  10493  Z= 0.242
  Chirality :  0.038   0.147   1164
  Planarity :  0.004   0.046   1339
  Dihedral  :  5.201  75.210   1030
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.93 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.28), residues: 933
  helix:  2.31 (0.25), residues: 480
  sheet: -0.23 (0.60), residues: 75
  loop :  0.07 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 239 
 HIS   0.006   0.001   HIS B 162 
 PHE   0.014   0.001   PHE A 188 
 TYR   0.007   0.001   TYR C 246 
 ARG   0.008   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03600 (  363)
  hydrogen bonds       : angle       3.63024 ( 1032)
  covalent geometry    : bond        0.00229 ( 7763)
  covalent geometry    : angle       0.48081 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 1.593 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 LYS cc_start: 0.8310 (mttt) cc_final: 0.7858 (mtmt)
REVERT: A  288 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8077 (p)
REVERT: A  293 ASP cc_start: 0.7672 (m-30) cc_final: 0.7453 (m-30)
REVERT: C   42 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7215 (tpt90)
REVERT: C  262 LYS cc_start: 0.8308 (mmmm) cc_final: 0.7944 (mttt)
REVERT: C  271 SER cc_start: 0.8962 (t) cc_final: 0.8705 (m)
REVERT: B  362 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7784 (ttm-80)
REVERT: B  380 LYS cc_start: 0.7882 (mttm) cc_final: 0.7387 (mtmp)
REVERT: B  390 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6451 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 104
  average time/residue: 2.8172
  time to fit residues: 310.2909
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0670
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6922

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

Flipped N/Q/H residues before XYZ refinement:
** B 162 HIS ** 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 = 0.3476 r_free = 0.3476 target = 0.133302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.101826 restraints weight = 26534.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.16
r_work: 0.2918 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7763  Z= 0.094
  Angle     :  0.475   6.463  10493  Z= 0.238
  Chirality :  0.038   0.146   1164
  Planarity :  0.004   0.046   1339
  Dihedral  :  4.864  64.407   1030
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 1.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.93 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.28), residues: 933
  helix:  2.37 (0.25), residues: 480
  sheet: -0.40 (0.55), residues: 80
  loop :  0.09 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP C 239 
 HIS   0.007   0.001   HIS B 162 
 PHE   0.014   0.001   PHE A 188 
 TYR   0.007   0.001   TYR C 246 
 ARG   0.008   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  363)
  hydrogen bonds       : angle       3.58401 ( 1032)
  covalent geometry    : bond        0.00223 ( 7763)
  covalent geometry    : angle       0.47531 (10493)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 LYS cc_start: 0.8031 (mttt) cc_final: 0.7531 (mtmt)
REVERT: A  288 THR cc_start: 0.8245 (p) cc_final: 0.7992 (p)
REVERT: A  293 ASP cc_start: 0.7611 (m-30) cc_final: 0.7339 (m-30)
REVERT: C   42 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7032 (tpt90)
REVERT: C  262 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7694 (mttt)
REVERT: C  271 SER cc_start: 0.8988 (t) cc_final: 0.8630 (m)
REVERT: B  362 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7764 (ttm-80)
REVERT: B  380 LYS cc_start: 0.7676 (mttm) cc_final: 0.7164 (mtmp)
REVERT: B  390 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6182 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 99
  average time/residue: 2.6189
  time to fit residues: 274.5570
Evaluate side-chains
  99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  336 THR
Chi-restraints excluded: chain B residue  390 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0040
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.134158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.103578 restraints weight = 26348.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.04
r_work: 0.3129 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.4041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7763  Z= 0.094
  Angle     :  0.471   6.522  10493  Z= 0.236
  Chirality :  0.038   0.146   1164
  Planarity :  0.004   0.041   1339
  Dihedral  :  4.525  46.424   1030
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 11.81 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.28), residues: 933
  helix:  2.46 (0.25), residues: 480
  sheet: -0.39 (0.56), residues: 80
  loop :  0.13 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 239 
 HIS   0.008   0.001   HIS B 162 
 PHE   0.014   0.001   PHE A 188 
 TYR   0.007   0.001   TYR C 246 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  363)
  hydrogen bonds       : angle       3.53277 ( 1032)
  covalent geometry    : bond        0.00224 ( 7763)
  covalent geometry    : angle       0.47061 (10493)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10702.00 seconds
wall clock time: 181 minutes 48.59 seconds (10908.59 seconds total)