Starting phenix.real_space_refine
on Sat May 10 22:00:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgg_44512/05_2025/9bgg_44512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgg_44512/05_2025/9bgg_44512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bgg_44512/05_2025/9bgg_44512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgg_44512/05_2025/9bgg_44512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgg_44512/05_2025/9bgg_44512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgg_44512/05_2025/9bgg_44512.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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      34      5.16       5
     C    4415      2.51       5
     N    1186      2.21       5
     O    1290      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6925
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3417
          Classifications: {'peptide': 416}
          Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 391}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3452
          Classifications: {'peptide': 419}
          Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 394}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.06, per 1000 atoms: 0.73
  Number of scatterers: 6925
  At special positions: 0
  Unit cell: (72.864, 101.016, 112.608, 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      34     16.00
     O    1290      8.00
     N    1186      7.00
     C    4415      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  27 " - pdb=" SG  CYS B  27 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A 286 "
      " NAG A 502 " - " ASN A 406 "
      " NAG B 501 " - " ASN B 286 "
      " NAG B 502 " - " ASN B 406 "
  Time building additional restraints: 1.55
  Conformation dependent library (CDL) restraints added in 944.8 milliseconds
  

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1610

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      51.7% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
      removed outlier: 3.731A  pdb=" N   TYR A  13 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 27
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 90 through 103
      removed outlier: 4.220A  pdb=" N   TYR A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 139 through 143
      removed outlier: 3.691A  pdb=" N   HIS A 142 " --> pdb=" O   ASN A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 154
      removed outlier: 3.696A  pdb=" N   ILE A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   HIS A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 179 through 182
    Processing helix  chain 'A' and resid 198 through 202
    Processing helix  chain 'A' and resid 206 through 223
    Processing helix  chain 'A' and resid 240 through 250
    Processing helix  chain 'A' and resid 250 through 260
      removed outlier: 3.667A  pdb=" N   PHE A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 280
      removed outlier: 3.765A  pdb=" N   SER A 273 " --> pdb=" O   GLN A 269 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   TYR A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.511A  pdb=" N   VAL A 290 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 315
      removed outlier: 3.949A  pdb=" N   ARG A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   THR A 309 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 338
      removed outlier: 3.777A  pdb=" N   LEU A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 371 through 382
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 3.593A  pdb=" N   GLY A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 453
    Processing helix  chain 'B' and resid 7 through 15
      removed outlier: 4.485A  pdb=" N   TYR B  13 " --> pdb=" O   LEU B   9 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ARG B  14 " --> pdb=" O   PHE B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 27
    Processing helix  chain 'B' and resid 42 through 56
    Processing helix  chain 'B' and resid 90 through 103
      removed outlier: 4.034A  pdb=" N   TYR B  94 " --> pdb=" O   GLU B  90 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B  97 " --> pdb=" O   ARG B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 136
    Processing helix  chain 'B' and resid 139 through 143
      removed outlier: 3.992A  pdb=" N   HIS B 142 " --> pdb=" O   ASN B 139 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU B 143 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 139 through 143'
    Processing helix  chain 'B' and resid 147 through 153
      removed outlier: 3.759A  pdb=" N   ILE B 151 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 158
      removed outlier: 3.996A  pdb=" N   ILE B 158 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 182
    Processing helix  chain 'B' and resid 208 through 224
    Processing helix  chain 'B' and resid 240 through 250
    Processing helix  chain 'B' and resid 250 through 260
    Processing helix  chain 'B' and resid 269 through 281
      removed outlier: 3.604A  pdb=" N   SER B 273 " --> pdb=" O   GLN B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 295
      removed outlier: 3.839A  pdb=" N   VAL B 290 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 315
    Processing helix  chain 'B' and resid 320 through 337
      removed outlier: 3.689A  pdb=" N   LEU B 324 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 3.561A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 382
    Processing helix  chain 'B' and resid 406 through 420
    Processing helix  chain 'B' and resid 437 through 453
    Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 132
      removed outlier: 6.272A  pdb=" N   ILE A 109 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   VAL A 131 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   ILE A 111 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 112 " --> pdb=" O   TYR A  36 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASP A  33 " --> pdb=" O   LYS A 164 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173
      removed outlier: 6.376A  pdb=" N   ALA A 399 " --> pdb=" O   CYS A 426 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185
      removed outlier: 4.604A  pdb=" N   TRP A 196 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185
      removed outlier: 3.606A  pdb=" N   MET A 393 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 283
      removed outlier: 4.652A  pdb=" N   LYS A 385 " --> pdb=" O   GLN A 283 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 131
      removed outlier: 6.661A  pdb=" N   ILE B 109 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   VAL B 131 " --> pdb=" O   ILE B 109 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ILE B 111 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL B  34 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   VAL B 112 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TYR B  36 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ASP B  33 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   LEU B 168 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   VAL B  35 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 172 through 174
    Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 185
      removed outlier: 6.954A  pdb=" N   VAL B 230 " --> pdb=" O   THR B 195 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 185

    287 hydrogen bonds defined for protein.
    822 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.94

  Time building geometry restraints manager: 1.85 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: 2236
        1.34 -     1.46: 1243
        1.46 -     1.58: 3563
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 7102
  Sorted by residual:
  bond pdb=" C   LEU A 143 "
       pdb=" N   PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.21e+00
  bond pdb=" CB  ASP A 170 "
       pdb=" CG  ASP A 170 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.89e-01
  bond pdb=" CG  GLU A  90 "
       pdb=" CD  GLU A  90 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.61e-01
  bond pdb=" N   ARG A 107 "
       pdb=" CA  ARG A 107 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.010 1.22e-02 6.72e+03 6.57e-01
  bond pdb=" C   LEU B 143 "
       pdb=" N   PRO B 144 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 2.34e-02 1.83e+03 6.20e-01
  ... (remaining 7097 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 9479
        1.73 -     3.45: 118
        3.45 -     5.18: 16
        5.18 -     6.90: 4
        6.90 -     8.63: 2
  Bond angle restraints: 9619
  Sorted by residual:
  angle pdb=" N   GLY A 394 "
        pdb=" CA  GLY A 394 "
        pdb=" C   GLY A 394 "
      ideal   model   delta    sigma   weight residual
     110.77  115.68   -4.91 1.59e+00 3.96e-01 9.54e+00
  angle pdb=" C   PHE B 254 "
        pdb=" N   ASP B 255 "
        pdb=" CA  ASP B 255 "
      ideal   model   delta    sigma   weight residual
     120.72  116.22    4.50 1.67e+00 3.59e-01 7.26e+00
  angle pdb=" CA  LEU B 143 "
        pdb=" CB  LEU B 143 "
        pdb=" CG  LEU B 143 "
      ideal   model   delta    sigma   weight residual
     116.30  124.93   -8.63 3.50e+00 8.16e-02 6.08e+00
  angle pdb=" CA  LEU A 143 "
        pdb=" CB  LEU A 143 "
        pdb=" CG  LEU A 143 "
      ideal   model   delta    sigma   weight residual
     116.30  124.88   -8.58 3.50e+00 8.16e-02 6.01e+00
  angle pdb=" C   PHE B 275 "
        pdb=" N   TYR B 276 "
        pdb=" CA  TYR B 276 "
      ideal   model   delta    sigma   weight residual
     121.14  117.31    3.83 1.75e+00 3.27e-01 4.78e+00
  ... (remaining 9614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4007
       17.87 -    35.73: 271
       35.73 -    53.60: 44
       53.60 -    71.46: 11
       71.46 -    89.33: 8
  Dihedral angle restraints: 4341
    sinusoidal: 1869
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CA  ASN B 406 "
           pdb=" C   ASN B 406 "
           pdb=" N   VAL B 407 "
           pdb=" CA  VAL B 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.00  -17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU A 266 "
           pdb=" CG  GLU A 266 "
           pdb=" CD  GLU A 266 "
           pdb=" OE1 GLU A 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.33  -89.33     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 100 "
           pdb=" CG  GLU A 100 "
           pdb=" CD  GLU A 100 "
           pdb=" OE1 GLU A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.97  -88.97     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 4338 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 672
       0.032 -    0.065: 249
       0.065 -    0.097: 82
       0.097 -    0.130: 47
       0.130 -    0.162: 1
  Chirality restraints: 1051
  Sorted by residual:
  chirality pdb=" C2  NAG B 502 "
            pdb=" C1  NAG B 502 "
            pdb=" C3  NAG B 502 "
            pdb=" N2  NAG B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.16 2.00e-01 2.50e+01 6.59e-01
  chirality pdb=" CA  ILE A 431 "
            pdb=" N   ILE A 431 "
            pdb=" C   ILE A 431 "
            pdb=" CB  ILE A 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  VAL A 230 "
            pdb=" N   VAL A 230 "
            pdb=" C   VAL A 230 "
            pdb=" CB  VAL A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 1048 not shown)

  Planarity restraints: 1244
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 408 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.51e+00
        pdb=" C   SER B 408 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   SER B 408 "    0.010 2.00e-02 2.50e+03
        pdb=" N   HIS B 409 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 234 "    0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO A 235 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 234 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO B 235 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 235 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 235 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1241 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 528
        2.74 -     3.28: 7085
        3.28 -     3.82: 11185
        3.82 -     4.36: 12963
        4.36 -     4.90: 22665
  Nonbonded interactions: 54426
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 302 "
            pdb=" OH  TYR B 355 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" NE1 TRP A 105 "
            pdb=" O   VAL A 178 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" ND2 ASN A 169 "
            pdb=" OD1 ASP A 171 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" O   PRO A 104 "
            pdb=" ND2 ASN B  16 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" NE2 GLN B 190 "
            pdb=" OD1 ASP B 239 "
     model   vdw
     2.242 3.120
  ... (remaining 54421 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 339 or resid 351 through 463 or resid 501 throug \ 
h 502))
  selection = (chain 'B' and (resid 6 through 56 or resid 89 through 463 or resid 501 through  \ 
502))
}

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:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.840
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
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      :  0.003   0.026   7107  Z= 0.117
  Angle     :  0.541   8.627   9633  Z= 0.274
  Chirality :  0.042   0.162   1051
  Planarity :  0.004   0.038   1240
  Dihedral  : 12.808  89.327   2728
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.43 (0.30), residues: 823
  helix:  1.11 (0.28), residues: 344
  sheet:  0.55 (0.58), residues: 97
  loop : -0.50 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 196 
 HIS   0.002   0.001   HIS A 435 
 PHE   0.010   0.001   PHE B 272 
 TYR   0.013   0.001   TYR B 276 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00487 (    4)
  link_NAG-ASN         : angle       2.60275 (   12)
  hydrogen bonds       : bond        0.16513 (  283)
  hydrogen bonds       : angle       6.36731 (  822)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.28745 (    2)
  covalent geometry    : bond        0.00252 ( 7102)
  covalent geometry    : angle       0.53335 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  122 ASN cc_start: 0.7890 (t0) cc_final: 0.7685 (t0)
REVERT: A  292 ASP cc_start: 0.7905 (m-30) cc_final: 0.7188 (m-30)
REVERT: A  330 MET cc_start: 0.7010 (ptp) cc_final: 0.6779 (ptp)
REVERT: A  413 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7658 (mm110)
REVERT: A  452 MET cc_start: 0.7334 (mmm) cc_final: 0.6946 (mmm)
REVERT: B   30 MET cc_start: 0.7611 (mmm) cc_final: 0.7052 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2103
  time to fit residues: 38.5926
Evaluate side-chains
  108 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0060
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
A 428 ASN
B  16 ASN
B  89 ASN
B 190 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.194025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.160691 restraints weight = 9930.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 2.70
r_work: 0.3875 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7107  Z= 0.131
  Angle     :  0.576   7.910   9633  Z= 0.292
  Chirality :  0.044   0.154   1051
  Planarity :  0.004   0.038   1240
  Dihedral  :  4.984  59.852    993
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.26 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.49 (0.30), residues: 823
  helix:  1.14 (0.28), residues: 353
  sheet:  0.55 (0.56), residues: 97
  loop : -0.45 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 179 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.019   0.001   PHE A 270 
 TYR   0.023   0.001   TYR B 276 
 ARG   0.004   0.000   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00516 (    4)
  link_NAG-ASN         : angle       1.52360 (   12)
  hydrogen bonds       : bond        0.03700 (  283)
  hydrogen bonds       : angle       4.79405 (  822)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.96015 (    2)
  covalent geometry    : bond        0.00288 ( 7102)
  covalent geometry    : angle       0.57403 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A   13 TYR cc_start: 0.7314 (m-80) cc_final: 0.7075 (m-10)
REVERT: A  249 MET cc_start: 0.8010 (ttt) cc_final: 0.7463 (mtp)
REVERT: A  292 ASP cc_start: 0.7994 (m-30) cc_final: 0.7302 (m-30)
REVERT: A  429 ASP cc_start: 0.7891 (t0) cc_final: 0.7644 (t70)
REVERT: A  452 MET cc_start: 0.7254 (mmm) cc_final: 0.6981 (mmm)
REVERT: B   30 MET cc_start: 0.7555 (mmm) cc_final: 0.7017 (mmp)
  outliers start: 10
  outliers final: 4
  residues processed: 129
  average time/residue: 0.1917
  time to fit residues: 32.8960
Evaluate side-chains
  112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.0040
   chunk 29 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0070
   chunk 61 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5010

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
A 386 ASN
A 409 HIS
B  89 ASN
B 190 GLN
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.194011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.160050 restraints weight = 10014.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 2.82
r_work: 0.3860 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7107  Z= 0.111
  Angle     :  0.536   8.098   9633  Z= 0.270
  Chirality :  0.044   0.149   1051
  Planarity :  0.004   0.042   1240
  Dihedral  :  4.700  56.596    993
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.82 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.53 (0.30), residues: 823
  helix:  1.22 (0.28), residues: 354
  sheet:  0.41 (0.55), residues: 97
  loop : -0.45 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 179 
 HIS   0.003   0.001   HIS B 329 
 PHE   0.011   0.001   PHE A 270 
 TYR   0.024   0.001   TYR B 276 
 ARG   0.004   0.000   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00392 (    4)
  link_NAG-ASN         : angle       1.32255 (   12)
  hydrogen bonds       : bond        0.03237 (  283)
  hydrogen bonds       : angle       4.54534 (  822)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.53869 (    2)
  covalent geometry    : bond        0.00249 ( 7102)
  covalent geometry    : angle       0.53397 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  212 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6809 (tp)
REVERT: A  429 ASP cc_start: 0.8004 (t0) cc_final: 0.7780 (t70)
REVERT: A  452 MET cc_start: 0.7375 (mmm) cc_final: 0.7100 (mmm)
REVERT: B   30 MET cc_start: 0.7616 (mmm) cc_final: 0.7104 (mmp)
REVERT: B  393 MET cc_start: 0.7163 (pmm) cc_final: 0.6453 (ptp)
REVERT: B  452 MET cc_start: 0.7304 (ttp) cc_final: 0.7011 (ttp)
  outliers start: 10
  outliers final: 7
  residues processed: 128
  average time/residue: 0.1986
  time to fit residues: 33.7104
Evaluate side-chains
  122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Chi-restraints excluded: chain B residue  371 CYS
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 47 optimal weight:    0.2980
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 27 optimal weight:    0.1980
   chunk 65 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.193777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.159686 restraints weight = 10088.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.85
r_work: 0.3862 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7107  Z= 0.109
  Angle     :  0.537   9.031   9633  Z= 0.271
  Chirality :  0.043   0.147   1051
  Planarity :  0.004   0.043   1240
  Dihedral  :  4.588  54.330    993
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.26 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.55 (0.30), residues: 823
  helix:  1.33 (0.28), residues: 354
  sheet:  0.25 (0.54), residues: 97
  loop : -0.48 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 179 
 HIS   0.003   0.001   HIS B 329 
 PHE   0.010   0.001   PHE A 254 
 TYR   0.023   0.001   TYR A 274 
 ARG   0.003   0.000   ARG B 101 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00373 (    4)
  link_NAG-ASN         : angle       1.32870 (   12)
  hydrogen bonds       : bond        0.03021 (  283)
  hydrogen bonds       : angle       4.38845 (  822)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.45479 (    2)
  covalent geometry    : bond        0.00245 ( 7102)
  covalent geometry    : angle       0.53565 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A  212 LEU cc_start: 0.7235 (tp) cc_final: 0.6807 (tp)
REVERT: A  429 ASP cc_start: 0.8100 (t0) cc_final: 0.7899 (t70)
REVERT: A  452 MET cc_start: 0.7361 (mmm) cc_final: 0.7088 (mmm)
REVERT: B   30 MET cc_start: 0.7673 (mmm) cc_final: 0.7142 (mmp)
REVERT: B  393 MET cc_start: 0.7156 (pmm) cc_final: 0.6887 (ptp)
REVERT: B  452 MET cc_start: 0.7268 (ttp) cc_final: 0.7052 (ttp)
  outliers start: 8
  outliers final: 4
  residues processed: 125
  average time/residue: 0.1850
  time to fit residues: 31.1371
Evaluate side-chains
  112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
A 386 ASN
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.191662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.157609 restraints weight = 9936.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.82
r_work: 0.3840 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7107  Z= 0.123
  Angle     :  0.559   9.140   9633  Z= 0.282
  Chirality :  0.044   0.155   1051
  Planarity :  0.004   0.043   1240
  Dihedral  :  4.616  53.892    993
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.00 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.54 (0.30), residues: 823
  helix:  1.37 (0.28), residues: 354
  sheet:  0.21 (0.54), residues: 94
  loop : -0.53 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 179 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.012   0.001   PHE A 254 
 TYR   0.024   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00319 (    4)
  link_NAG-ASN         : angle       1.25457 (   12)
  hydrogen bonds       : bond        0.03083 (  283)
  hydrogen bonds       : angle       4.33758 (  822)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       0.41691 (    2)
  covalent geometry    : bond        0.00286 ( 7102)
  covalent geometry    : angle       0.55762 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  212 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7020 (tp)
REVERT: A  279 MET cc_start: 0.8557 (mmm) cc_final: 0.8337 (mmm)
REVERT: A  452 MET cc_start: 0.7419 (mmm) cc_final: 0.7185 (mmm)
REVERT: B   30 MET cc_start: 0.7652 (mmm) cc_final: 0.7109 (mmt)
REVERT: B  393 MET cc_start: 0.7264 (pmm) cc_final: 0.7059 (ptp)
  outliers start: 12
  outliers final: 8
  residues processed: 124
  average time/residue: 0.1951
  time to fit residues: 32.1876
Evaluate side-chains
  113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  433 HIS
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
A 247 GLN
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 GLN
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 GLN
B 322 GLN
B 435 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.189707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.155964 restraints weight = 9985.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.78
r_work: 0.3816 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7107  Z= 0.141
  Angle     :  0.572   9.066   9633  Z= 0.290
  Chirality :  0.045   0.181   1051
  Planarity :  0.004   0.044   1240
  Dihedral  :  4.695  53.439    993
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.54 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.48 (0.30), residues: 823
  helix:  1.36 (0.28), residues: 353
  sheet:  0.00 (0.53), residues: 94
  loop : -0.56 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 196 
 HIS   0.006   0.001   HIS B 329 
 PHE   0.026   0.002   PHE B 453 
 TYR   0.026   0.001   TYR A 274 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00289 (    4)
  link_NAG-ASN         : angle       1.21269 (   12)
  hydrogen bonds       : bond        0.03209 (  283)
  hydrogen bonds       : angle       4.30763 (  822)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       0.42516 (    2)
  covalent geometry    : bond        0.00334 ( 7102)
  covalent geometry    : angle       0.57055 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  212 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7180 (tp)
REVERT: A  452 MET cc_start: 0.7417 (mmm) cc_final: 0.7182 (mmm)
REVERT: B   30 MET cc_start: 0.7772 (mmm) cc_final: 0.7177 (mmt)
  outliers start: 12
  outliers final: 8
  residues processed: 115
  average time/residue: 0.1766
  time to fit residues: 27.6111
Evaluate side-chains
  111 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  433 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0270
   chunk 34 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8842

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.188829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.155356 restraints weight = 9828.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.68
r_work: 0.3814 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7107  Z= 0.141
  Angle     :  0.571   9.256   9633  Z= 0.291
  Chirality :  0.045   0.163   1051
  Planarity :  0.004   0.042   1240
  Dihedral  :  4.706  52.860    993
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.79 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.39 (0.30), residues: 823
  helix:  1.31 (0.28), residues: 355
  sheet: -0.05 (0.53), residues: 94
  loop : -0.64 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 196 
 HIS   0.005   0.001   HIS B 329 
 PHE   0.036   0.002   PHE B 453 
 TYR   0.027   0.001   TYR A 274 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    4)
  link_NAG-ASN         : angle       1.21054 (   12)
  hydrogen bonds       : bond        0.03215 (  283)
  hydrogen bonds       : angle       4.32357 (  822)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.31838 (    2)
  covalent geometry    : bond        0.00331 ( 7102)
  covalent geometry    : angle       0.56952 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  145 THR cc_start: 0.7846 (p) cc_final: 0.7586 (m)
REVERT: A  212 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7230 (tp)
REVERT: A  330 MET cc_start: 0.7093 (ptp) cc_final: 0.6890 (ptp)
REVERT: A  452 MET cc_start: 0.7369 (mmm) cc_final: 0.7149 (mmm)
REVERT: B   30 MET cc_start: 0.7751 (mmm) cc_final: 0.7071 (mmt)
  outliers start: 14
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1874
  time to fit residues: 30.8587
Evaluate side-chains
  113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  433 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0050
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    0.1980
   chunk 16 optimal weight:    4.9990
   chunk 65 optimal weight:    0.3980
   chunk 41 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 HIS
B 435 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.191754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.157805 restraints weight = 9870.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.79
r_work: 0.3830 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7107  Z= 0.114
  Angle     :  0.571   9.311   9633  Z= 0.288
  Chirality :  0.044   0.151   1051
  Planarity :  0.004   0.042   1240
  Dihedral  :  4.594  52.823    993
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.69 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.50 (0.31), residues: 823
  helix:  1.44 (0.28), residues: 355
  sheet: -0.19 (0.53), residues: 97
  loop : -0.57 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 196 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.030   0.001   PHE B 453 
 TYR   0.026   0.001   TYR A 274 
 ARG   0.007   0.000   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    4)
  link_NAG-ASN         : angle       1.23906 (   12)
  hydrogen bonds       : bond        0.02942 (  283)
  hydrogen bonds       : angle       4.26239 (  822)
  SS BOND              : bond        0.00277 (    1)
  SS BOND              : angle       0.63863 (    2)
  covalent geometry    : bond        0.00256 ( 7102)
  covalent geometry    : angle       0.56948 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A  145 THR cc_start: 0.7904 (p) cc_final: 0.7629 (m)
REVERT: A  212 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7072 (tp)
REVERT: A  452 MET cc_start: 0.7352 (mmm) cc_final: 0.6942 (mmt)
REVERT: B   30 MET cc_start: 0.7812 (mmm) cc_final: 0.7222 (mmt)
REVERT: B  337 MET cc_start: 0.7941 (ppp) cc_final: 0.5282 (mtt)
REVERT: B  355 TYR cc_start: 0.6868 (m-80) cc_final: 0.6561 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1830
  time to fit residues: 29.8921
Evaluate side-chains
  112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  433 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    0.3980
   chunk 79 optimal weight:    0.4980
   chunk 58 optimal weight:    0.0980
   chunk 74 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 154 HIS
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.192053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.158781 restraints weight = 10020.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 2.73
r_work: 0.3845 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7107  Z= 0.114
  Angle     :  0.574   9.329   9633  Z= 0.291
  Chirality :  0.044   0.184   1051
  Planarity :  0.004   0.042   1240
  Dihedral  :  4.531  52.848    993
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.69 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.52 (0.31), residues: 823
  helix:  1.44 (0.28), residues: 356
  sheet: -0.07 (0.54), residues: 94
  loop : -0.59 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 196 
 HIS   0.004   0.001   HIS B 409 
 PHE   0.027   0.001   PHE B 453 
 TYR   0.030   0.001   TYR B 277 
 ARG   0.007   0.000   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    4)
  link_NAG-ASN         : angle       1.20962 (   12)
  hydrogen bonds       : bond        0.02941 (  283)
  hydrogen bonds       : angle       4.22724 (  822)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.61241 (    2)
  covalent geometry    : bond        0.00260 ( 7102)
  covalent geometry    : angle       0.57237 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A  145 THR cc_start: 0.7913 (p) cc_final: 0.7649 (m)
REVERT: A  206 ASP cc_start: 0.7564 (m-30) cc_final: 0.7192 (m-30)
REVERT: A  212 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7078 (tp)
REVERT: A  452 MET cc_start: 0.7308 (mmm) cc_final: 0.6895 (mmt)
REVERT: B   30 MET cc_start: 0.7877 (mmm) cc_final: 0.7284 (mmt)
REVERT: B  337 MET cc_start: 0.7926 (ppp) cc_final: 0.5329 (mtt)
REVERT: B  355 TYR cc_start: 0.6880 (m-80) cc_final: 0.6580 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1983
  time to fit residues: 33.1664
Evaluate side-chains
  118 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  433 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.189793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.156312 restraints weight = 10162.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.75
r_work: 0.3820 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7107  Z= 0.133
  Angle     :  0.587   9.348   9633  Z= 0.298
  Chirality :  0.044   0.177   1051
  Planarity :  0.004   0.043   1240
  Dihedral  :  4.577  52.492    993
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.46 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.50 (0.30), residues: 823
  helix:  1.44 (0.28), residues: 355
  sheet: -0.09 (0.54), residues: 94
  loop : -0.60 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 196 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.026   0.002   PHE B 453 
 TYR   0.033   0.002   TYR B 277 
 ARG   0.007   0.000   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    4)
  link_NAG-ASN         : angle       1.20930 (   12)
  hydrogen bonds       : bond        0.03074 (  283)
  hydrogen bonds       : angle       4.23783 (  822)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.63316 (    2)
  covalent geometry    : bond        0.00310 ( 7102)
  covalent geometry    : angle       0.58533 ( 9619)

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

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

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1646 Ramachandran restraints generated.
    823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  145 THR cc_start: 0.7951 (p) cc_final: 0.7657 (m)
REVERT: A  206 ASP cc_start: 0.7569 (m-30) cc_final: 0.7203 (m-30)
REVERT: A  212 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7209 (tp)
REVERT: A  330 MET cc_start: 0.7053 (ptp) cc_final: 0.6817 (ptp)
REVERT: A  452 MET cc_start: 0.7339 (mmm) cc_final: 0.6940 (mmt)
REVERT: B   30 MET cc_start: 0.7887 (mmm) cc_final: 0.7316 (mmt)
REVERT: B  337 MET cc_start: 0.7941 (ppp) cc_final: 0.5361 (mtt)
REVERT: B  393 MET cc_start: 0.7060 (pmm) cc_final: 0.6687 (ptp)
  outliers start: 10
  outliers final: 9
  residues processed: 119
  average time/residue: 0.1852
  time to fit residues: 30.0265
Evaluate side-chains
  116 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  433 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  364 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 61 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 186 HIS
** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 GLN
** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.190335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.156960 restraints weight = 10022.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.73
r_work: 0.3830 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7107  Z= 0.122
  Angle     :  0.584   9.363   9633  Z= 0.296
  Chirality :  0.044   0.172   1051
  Planarity :  0.004   0.042   1240
  Dihedral  :  4.541  52.451    993
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.72 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.51 %
    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:  0.50 (0.31), residues: 823
  helix:  1.44 (0.28), residues: 357
  sheet: -0.07 (0.54), residues: 94
  loop : -0.60 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 196 
 HIS   0.003   0.001   HIS B 409 
 PHE   0.025   0.001   PHE B 453 
 TYR   0.033   0.002   TYR B 277 
 ARG   0.007   0.000   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    4)
  link_NAG-ASN         : angle       1.22656 (   12)
  hydrogen bonds       : bond        0.02991 (  283)
  hydrogen bonds       : angle       4.21606 (  822)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.59953 (    2)
  covalent geometry    : bond        0.00279 ( 7102)
  covalent geometry    : angle       0.58244 ( 9619)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3321.02 seconds
wall clock time: 58 minutes 45.16 seconds (3525.16 seconds total)