Starting phenix.real_space_refine
on Fri Feb 14 14:48:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn2_3237/02_2025/5fn2_3237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn2_3237/02_2025/5fn2_3237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fn2_3237/02_2025/5fn2_3237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn2_3237/02_2025/5fn2_3237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn2_3237/02_2025/5fn2_3237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn2_3237/02_2025/5fn2_3237.cif"
  }
  resolution = 4.2
  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=   0.012
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      40      5.16       5
     C    6733      2.51       5
     N    1674      2.21       5
     O    1829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10276
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5222
          Classifications: {'peptide': 665}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627}
    Chain: "B"
      Number of atoms: 2339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2339
          Classifications: {'peptide': 301}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'CIS': 6, 'PTRANS': 10, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "C"
      Number of atoms: 1868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1868
          Classifications: {'peptide': 243}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 235}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 847
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.53, per 1000 atoms: 0.54
  Number of scatterers: 10276
  At special positions: 0
  Unit cell: (89.6, 144.2, 105, 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      40     16.00
     O    1829      8.00
     N    1674      7.00
     C    6733      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 620 " 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
  Time building additional restraints: 2.76
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2462

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      58.8% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 41
    Processing helix  chain 'A' and resid 78 through 88
      removed outlier: 3.773A  pdb=" N   LEU A  82 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 114
      removed outlier: 3.631A  pdb=" N   ARG A 114 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 198
    Processing helix  chain 'A' and resid 202 through 206
      removed outlier: 3.821A  pdb=" N   GLY A 205 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 240
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 339 through 350
    Processing helix  chain 'A' and resid 381 through 387
    Processing helix  chain 'A' and resid 387 through 407
      removed outlier: 3.825A  pdb=" N   GLY A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 431
    Processing helix  chain 'A' and resid 474 through 478
    Processing helix  chain 'A' and resid 481 through 502
    Processing helix  chain 'A' and resid 514 through 527
      removed outlier: 3.742A  pdb=" N   VAL A 518 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 536
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.776A  pdb=" N   SER A 544 " --> pdb=" O   ASP A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 576
      removed outlier: 3.616A  pdb=" N   TYR A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 665 through 693
    Processing helix  chain 'A' and resid 693 through 698
    Processing helix  chain 'B' and resid 79 through 103
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 124 through 156
      removed outlier: 3.557A  pdb=" N   ILE B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TYR B 154 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR B 156 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 190
      removed outlier: 3.869A  pdb=" N   HIS B 163 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU B 166 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 215
    Processing helix  chain 'B' and resid 218 through 241
    Processing helix  chain 'B' and resid 242 through 263
      removed outlier: 3.535A  pdb=" N   LEU B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   CYS B 263 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 276
    Processing helix  chain 'B' and resid 382 through 399
    Processing helix  chain 'B' and resid 403 through 429
    Processing helix  chain 'B' and resid 434 through 452
      removed outlier: 3.610A  pdb=" N   ALA B 448 " --> pdb=" O   VAL B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 464
      removed outlier: 4.398A  pdb=" N   PHE B 456 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 25
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 28 through 61
    Processing helix  chain 'C' and resid 64 through 105
      removed outlier: 3.810A  pdb=" N   GLU C  99 " --> pdb=" O   LYS C  95 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLY C 100 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU C 104 " --> pdb=" O   GLY C 100 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   SER C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 143
      removed outlier: 4.844A  pdb=" N   ASN C 136 " --> pdb=" O   PHE C 132 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ILE C 137 " --> pdb=" O   SER C 133 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLY C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 185
      removed outlier: 3.523A  pdb=" N   THR C 159 " --> pdb=" O   TYR C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 206
    Processing helix  chain 'C' and resid 213 through 233
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.783A  pdb=" N   ILE C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU C 243 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 23
      removed outlier: 3.710A  pdb=" N   PHE D  23 " --> pdb=" O   TYR D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 37
    Processing helix  chain 'D' and resid 37 through 43
    Processing helix  chain 'D' and resid 49 through 82
    Processing helix  chain 'D' and resid 86 through 92
    Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 44
      removed outlier: 4.654A  pdb=" N   ALA A 658 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   CYS A 213 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   GLU A  99 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   VAL A  96 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   LEU A 121 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU A  98 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   VAL A 123 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
    Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60
      removed outlier: 3.523A  pdb=" N   LEU A  53 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
    Processing sheet with id=AC, first strand: chain 'A' and resid 275 through 278
    Processing sheet with id=AD, first strand: chain 'A' and resid 361 through 366
    Processing sheet with id=AE, first strand: chain 'A' and resid 375 through 377
      removed outlier: 3.950A  pdb=" N   ARG A 414 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing sheet with id=AF, first strand: chain 'A' and resid 577 through 579
      removed outlier: 3.531A  pdb=" N   THR A 577 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 622 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A 579 " --> pdb=" O   CYS A 620 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   CYS A 620 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
    Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194
      removed outlier: 6.604A  pdb=" N   VAL B 193 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)

    610 hydrogen bonds defined for protein.
    1797 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: 3.06

  Time building geometry restraints manager: 3.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1689
        1.32 -     1.45: 2961
        1.45 -     1.58: 5831
        1.58 -     1.70: 2
        1.70 -     1.83: 61
  Bond restraints: 10544
  Sorted by residual:
  bond pdb=" CA  ASP A 458 "
       pdb=" C   ASP A 458 "
    ideal  model  delta    sigma   weight residual
    1.523  1.586 -0.062 1.34e-02 5.57e+03 2.17e+01
  bond pdb=" C   THR B 116 "
       pdb=" N   PRO B 117 "
    ideal  model  delta    sigma   weight residual
    1.332  1.389 -0.057 1.30e-02 5.92e+03 1.93e+01
  bond pdb=" CA  VAL B  87 "
       pdb=" CB  VAL B  87 "
    ideal  model  delta    sigma   weight residual
    1.539  1.563 -0.024 5.40e-03 3.43e+04 1.90e+01
  bond pdb=" N   PRO B 117 "
       pdb=" CD  PRO B 117 "
    ideal  model  delta    sigma   weight residual
    1.473  1.530 -0.057 1.40e-02 5.10e+03 1.66e+01
  bond pdb=" N   PRO B 264 "
       pdb=" CD  PRO B 264 "
    ideal  model  delta    sigma   weight residual
    1.473  1.529 -0.056 1.40e-02 5.10e+03 1.62e+01
  ... (remaining 10539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 13247
        2.93 -     5.87: 1034
        5.87 -     8.80: 86
        8.80 -    11.74: 12
       11.74 -    14.67: 4
  Bond angle restraints: 14383
  Sorted by residual:
  angle pdb=" C   ASN A  91 "
        pdb=" N   PRO A  92 "
        pdb=" CA  PRO A  92 "
      ideal   model   delta    sigma   weight residual
     120.38  132.33  -11.95 1.03e+00 9.43e-01 1.35e+02
  angle pdb=" N   PRO A  92 "
        pdb=" CA  PRO A  92 "
        pdb=" C   PRO A  92 "
      ideal   model   delta    sigma   weight residual
     110.70  122.17  -11.47 1.22e+00 6.72e-01 8.84e+01
  angle pdb=" CA  VAL B  87 "
        pdb=" C   VAL B  87 "
        pdb=" N   PRO B  88 "
      ideal   model   delta    sigma   weight residual
     120.83  115.48    5.35 6.10e-01 2.69e+00 7.69e+01
  angle pdb=" N   ARG B 108 "
        pdb=" CA  ARG B 108 "
        pdb=" C   ARG B 108 "
      ideal   model   delta    sigma   weight residual
     109.52  122.31  -12.79 1.55e+00 4.16e-01 6.81e+01
  angle pdb=" N   ILE B 227 "
        pdb=" CA  ILE B 227 "
        pdb=" CB  ILE B 227 "
      ideal   model   delta    sigma   weight residual
     110.55  119.16   -8.61 1.17e+00 7.31e-01 5.41e+01
  ... (remaining 14378 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 5154
       17.08 -    34.15: 725
       34.15 -    51.22: 207
       51.22 -    68.30: 65
       68.30 -    85.37: 10
  Dihedral angle restraints: 6161
    sinusoidal: 2343
      harmonic: 3818
  Sorted by residual:
  dihedral pdb=" CA  CYS B 263 "
           pdb=" C   CYS B 263 "
           pdb=" N   PRO B 264 "
           pdb=" CA  PRO B 264 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -123.15  -56.85     0      5.00e+00 4.00e-02 1.29e+02
  dihedral pdb=" CB  CYS A 586 "
           pdb=" SG  CYS A 586 "
           pdb=" SG  CYS A 620 "
           pdb=" CB  CYS A 620 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.37   85.37     1      1.00e+01 1.00e-02 8.83e+01
  dihedral pdb=" CB  CYS A 140 "
           pdb=" SG  CYS A 140 "
           pdb=" SG  CYS A 159 "
           pdb=" CB  CYS A 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.64   69.64     1      1.00e+01 1.00e-02 6.26e+01
  ... (remaining 6158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1331
       0.118 -    0.236: 285
       0.236 -    0.353: 43
       0.353 -    0.471: 12
       0.471 -    0.589: 1
  Chirality restraints: 1672
  Sorted by residual:
  chirality pdb=" CA  PHE A 302 "
            pdb=" N   PHE A 302 "
            pdb=" C   PHE A 302 "
            pdb=" CB  PHE A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.67e+00
  chirality pdb=" CA  PHE B 388 "
            pdb=" N   PHE B 388 "
            pdb=" C   PHE B 388 "
            pdb=" CB  PHE B 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.67e+00
  chirality pdb=" CA  PHE A 525 "
            pdb=" N   PHE A 525 "
            pdb=" C   PHE A 525 "
            pdb=" CB  PHE A 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.49e+00
  ... (remaining 1669 not shown)

  Planarity restraints: 1789
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 178 "   -0.058 5.00e-02 4.00e+02   8.80e-02 1.24e+01
        pdb=" N   PRO A 179 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO A 179 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 179 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 215 "   -0.058 5.00e-02 4.00e+02   8.75e-02 1.23e+01
        pdb=" N   PRO C 216 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO C 216 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO C 216 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "   -0.053 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO B 267 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "   -0.043 5.00e-02 4.00e+02
  ... (remaining 1786 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 55
        2.49 -     3.09: 7753
        3.09 -     3.70: 16942
        3.70 -     4.30: 22833
        4.30 -     4.90: 38468
  Nonbonded interactions: 86051
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 263 "
            pdb=" N   GLY B 266 "
     model   vdw
     1.890 3.120
  nonbonded pdb=" CD2 LEU B 113 "
            pdb=" O   TYR B 240 "
     model   vdw
     2.001 3.460
  nonbonded pdb=" O   ILE B 114 "
            pdb=" CD  PRO B 117 "
     model   vdw
     2.060 3.440
  nonbonded pdb=" ND1 HIS B 163 "
            pdb=" OE1 GLU B 280 "
     model   vdw
     2.106 3.120
  nonbonded pdb=" O   CYS B 263 "
            pdb=" CD  PRO B 267 "
     model   vdw
     2.152 3.440
  ... (remaining 86046 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.510
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5693
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      :  0.009   0.066  10544  Z= 0.625
  Angle     :  1.735  14.672  14383  Z= 1.240
  Chirality :  0.101   0.589   1672
  Planarity :  0.008   0.088   1789
  Dihedral  : 17.975  83.353   3684
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  3.93 %
    Allowed  : 11.93 %
    Favored  : 84.14 %
  Rotamer:
    Outliers : 11.69 %
    Allowed  : 14.66 %
    Favored  : 73.65 %
  Cbeta Deviations :  1.87 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 3.39 %
    Twisted General : 0.40 %

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: -1.77 (0.20), residues: 1299
  helix:  0.96 (0.15), residues: 745
  sheet: -3.87 (0.50), residues: 57
  loop : -4.43 (0.20), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP D  58 
 HIS   0.011   0.003   HIS A 553 
 PHE   0.052   0.004   PHE A 302 
 TYR   0.042   0.004   TYR C 119 
 ARG   0.006   0.001   ARG C 184 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  587 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 130
    poor density    : 457
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7859 (p)
REVERT: A   86 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6137 (mp)
REVERT: A   87 THR cc_start: 0.7955 (t) cc_final: 0.7657 (t)
REVERT: A   95 MET cc_start: 0.7656 (mmt) cc_final: 0.7334 (mmm)
REVERT: A  156 PHE cc_start: 0.7993 (m-80) cc_final: 0.7391 (m-80)
REVERT: A  221 MET cc_start: 0.8672 (mmp) cc_final: 0.8414 (mmp)
REVERT: A  243 ASN cc_start: 0.7305 (m-40) cc_final: 0.7079 (p0)
REVERT: A  326 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6681 (tmm)
REVERT: A  426 SER cc_start: 0.8703 (t) cc_final: 0.8398 (m)
REVERT: A  443 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5693 (t70)
REVERT: A  444 HIS cc_start: 0.8256 (p-80) cc_final: 0.7908 (p90)
REVERT: A  454 GLN cc_start: 0.7887 (pt0) cc_final: 0.7630 (mp10)
REVERT: A  561 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6619 (p)
REVERT: A  575 THR cc_start: 0.8077 (p) cc_final: 0.7794 (p)
REVERT: A  622 ARG cc_start: 0.8137 (ptt90) cc_final: 0.7920 (ptp90)
REVERT: B  174 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (tt)
REVERT: B  203 TRP cc_start: 0.6969 (t-100) cc_final: 0.6732 (t-100)
REVERT: B  222 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (tm-30)
REVERT: C   62 ARG cc_start: 0.6636 (tpt-90) cc_final: 0.6088 (ptp-110)
REVERT: C  174 TRP cc_start: 0.8117 (m-10) cc_final: 0.7534 (m-90)
REVERT: C  206 LEU cc_start: 0.8303 (mp) cc_final: 0.8012 (tp)
REVERT: C  207 ASN cc_start: 0.7250 (t0) cc_final: 0.6270 (t0)
REVERT: C  214 LEU cc_start: 0.8046 (tp) cc_final: 0.7738 (tp)
REVERT: C  218 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (m-80)
REVERT: C  231 THR cc_start: 0.6993 (p) cc_final: 0.6654 (p)
REVERT: C  236 LEU cc_start: 0.7549 (mt) cc_final: 0.7116 (tp)
REVERT: C  243 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5244 (mt)
REVERT: D    6 VAL cc_start: 0.4617 (t) cc_final: 0.3878 (t)
REVERT: D   34 ILE cc_start: 0.8012 (mt) cc_final: 0.7731 (mt)
REVERT: D   40 GLU cc_start: 0.8278 (mp0) cc_final: 0.7769 (mp0)
REVERT: D   64 PHE cc_start: 0.7213 (t80) cc_final: 0.6985 (t80)
REVERT: D   84 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7618 (ttp-170)
REVERT: D   94 PHE cc_start: 0.7342 (t80) cc_final: 0.6925 (t80)
REVERT: D   95 THR cc_start: 0.7508 (m) cc_final: 0.6675 (t)
  outliers start: 130
  outliers final: 49
  residues processed: 525
  average time/residue: 0.2213
  time to fit residues: 166.3057
Evaluate side-chains
  383 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 325
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 GLN
A 199 HIS
A 313 GLN
** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 GLN
B 405 ASN
B 464 GLN
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 HIS
C 171 HIS
D   8 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.095103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.083374 restraints weight = 36542.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.085531 restraints weight = 22306.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.087066 restraints weight = 15315.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  10544  Z= 0.314
  Angle     :  0.941  13.681  14383  Z= 0.492
  Chirality :  0.050   0.217   1672
  Planarity :  0.007   0.064   1789
  Dihedral  :  7.108  43.432   1410
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  9.16 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  5.22 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 1.69 %
    Twisted General : 0.40 %

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: -0.62 (0.24), residues: 1299
  helix:  1.86 (0.19), residues: 751
  sheet: -3.60 (0.38), residues: 98
  loop : -3.86 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 247 
 HIS   0.007   0.002   HIS A 199 
 PHE   0.054   0.003   PHE C 162 
 TYR   0.030   0.002   TYR B 466 
 ARG   0.009   0.001   ARG A 657 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  448 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 439
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 HIS cc_start: 0.6815 (m90) cc_final: 0.6507 (m90)
REVERT: A  175 ASP cc_start: 0.7818 (t0) cc_final: 0.7500 (p0)
REVERT: A  182 LEU cc_start: 0.9155 (tp) cc_final: 0.8947 (tp)
REVERT: A  330 PHE cc_start: 0.8594 (m-80) cc_final: 0.8069 (m-80)
REVERT: A  333 GLU cc_start: 0.8954 (mp0) cc_final: 0.7923 (mp0)
REVERT: A  335 PHE cc_start: 0.9269 (m-80) cc_final: 0.8858 (m-10)
REVERT: A  411 VAL cc_start: 0.9283 (t) cc_final: 0.9076 (t)
REVERT: A  474 GLU cc_start: 0.8206 (mp0) cc_final: 0.7990 (mp0)
REVERT: A  555 ILE cc_start: 0.8776 (mp) cc_final: 0.8482 (mt)
REVERT: A  566 VAL cc_start: 0.9609 (t) cc_final: 0.9370 (p)
REVERT: A  595 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6441 (mm-30)
REVERT: B  203 TRP cc_start: 0.8573 (t-100) cc_final: 0.8344 (t-100)
REVERT: B  204 ASN cc_start: 0.8591 (m-40) cc_final: 0.8073 (m110)
REVERT: B  210 MET cc_start: 0.8797 (mmm) cc_final: 0.8523 (mmt)
REVERT: B  223 GLN cc_start: 0.8907 (mt0) cc_final: 0.7851 (mp10)
REVERT: B  257 ASP cc_start: 0.8967 (m-30) cc_final: 0.8661 (m-30)
REVERT: B  406 THR cc_start: 0.8809 (m) cc_final: 0.8555 (t)
REVERT: B  416 ILE cc_start: 0.8548 (mm) cc_final: 0.8097 (mm)
REVERT: B  423 LEU cc_start: 0.8579 (mt) cc_final: 0.8020 (pp)
REVERT: B  466 TYR cc_start: 0.7557 (m-10) cc_final: 0.7185 (m-10)
REVERT: C   14 PHE cc_start: 0.8524 (m-10) cc_final: 0.8294 (m-80)
REVERT: C   92 LYS cc_start: 0.8132 (mptt) cc_final: 0.7545 (mmtm)
REVERT: C  117 MET cc_start: 0.7550 (mtm) cc_final: 0.7244 (mtm)
REVERT: C  136 ASN cc_start: 0.8665 (p0) cc_final: 0.7259 (m-40)
REVERT: C  137 ILE cc_start: 0.9309 (pt) cc_final: 0.8379 (tt)
REVERT: C  140 ASP cc_start: 0.8933 (m-30) cc_final: 0.8168 (m-30)
REVERT: C  173 PHE cc_start: 0.7948 (m-10) cc_final: 0.7579 (m-80)
REVERT: C  198 LEU cc_start: 0.8497 (tt) cc_final: 0.8247 (tp)
REVERT: C  200 THR cc_start: 0.8791 (p) cc_final: 0.8534 (p)
REVERT: C  206 LEU cc_start: 0.8535 (mp) cc_final: 0.7921 (tp)
REVERT: C  214 LEU cc_start: 0.7809 (tp) cc_final: 0.7316 (tp)
REVERT: D   36 TRP cc_start: 0.8792 (t60) cc_final: 0.8517 (t60)
REVERT: D   40 GLU cc_start: 0.8359 (mp0) cc_final: 0.7892 (mp0)
REVERT: D   64 PHE cc_start: 0.7964 (t80) cc_final: 0.7314 (t80)
REVERT: D   92 LEU cc_start: 0.9020 (pp) cc_final: 0.8518 (pp)
  outliers start: 9
  outliers final: 0
  residues processed: 442
  average time/residue: 0.2010
  time to fit residues: 128.1773
Evaluate side-chains
  302 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 302
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 117 optimal weight:    0.5980
   chunk 1 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 85 optimal weight:    9.9990
   chunk 37 optimal weight:    0.1980
   chunk 8 optimal weight:    0.0370
   chunk 36 optimal weight:    0.9990
   chunk 125 optimal weight:    6.9990
   chunk 106 optimal weight:   20.0000
   chunk 73 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.5662

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 GLN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 GLN
B 405 ASN
B 464 GLN
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 116 GLN
C 171 HIS
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.096265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.085957 restraints weight = 36292.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.087647 restraints weight = 23947.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.088897 restraints weight = 17352.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10544  Z= 0.260
  Angle     :  0.882  13.707  14383  Z= 0.455
  Chirality :  0.048   0.235   1672
  Planarity :  0.007   0.102   1789
  Dihedral  :  6.506  38.604   1410
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  8.85 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  3.96 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.78 (0.23), residues: 1299
  helix:  1.45 (0.19), residues: 753
  sheet: -2.96 (0.42), residues: 101
  loop : -3.56 (0.25), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 174 
 HIS   0.011   0.001   HIS C 197 
 PHE   0.040   0.002   PHE B  86 
 TYR   0.041   0.002   TYR B 389 
 ARG   0.012   0.001   ARG A 432 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 388
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 PHE cc_start: 0.7898 (m-80) cc_final: 0.7480 (m-80)
REVERT: A  175 ASP cc_start: 0.8008 (t0) cc_final: 0.7288 (p0)
REVERT: A  305 GLN cc_start: 0.8439 (tp40) cc_final: 0.8106 (tp40)
REVERT: A  327 PHE cc_start: 0.7516 (m-80) cc_final: 0.7209 (m-80)
REVERT: A  474 GLU cc_start: 0.7805 (mp0) cc_final: 0.7594 (mp0)
REVERT: A  555 ILE cc_start: 0.8489 (mp) cc_final: 0.8238 (mt)
REVERT: A  693 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7893 (mttp)
REVERT: B  163 HIS cc_start: 0.5972 (m170) cc_final: 0.5265 (m-70)
REVERT: B  222 GLN cc_start: 0.8086 (tm130) cc_final: 0.7372 (tm-30)
REVERT: B  223 GLN cc_start: 0.8746 (mt0) cc_final: 0.7826 (mp10)
REVERT: B  253 ILE cc_start: 0.8159 (mt) cc_final: 0.7274 (tp)
REVERT: B  267 PRO cc_start: 0.6811 (OUTLIER) cc_final: 0.6499 (Cg_endo)
REVERT: B  387 ILE cc_start: 0.9127 (mt) cc_final: 0.8903 (tt)
REVERT: B  419 CYS cc_start: 0.8138 (p) cc_final: 0.7896 (p)
REVERT: B  423 LEU cc_start: 0.8554 (mt) cc_final: 0.8077 (pp)
REVERT: C   92 LYS cc_start: 0.8355 (mptt) cc_final: 0.7998 (mmtm)
REVERT: C  134 VAL cc_start: 0.8642 (p) cc_final: 0.8327 (p)
REVERT: C  140 ASP cc_start: 0.8862 (m-30) cc_final: 0.8414 (m-30)
REVERT: C  173 PHE cc_start: 0.7763 (m-10) cc_final: 0.7497 (m-80)
REVERT: C  174 TRP cc_start: 0.7312 (m-10) cc_final: 0.7101 (m-10)
REVERT: C  198 LEU cc_start: 0.8207 (tt) cc_final: 0.8006 (tp)
REVERT: C  206 LEU cc_start: 0.8329 (mp) cc_final: 0.7712 (tp)
REVERT: C  224 MET cc_start: 0.7959 (mmp) cc_final: 0.7398 (mmm)
REVERT: D   95 THR cc_start: 0.8289 (t) cc_final: 0.7526 (t)
  outliers start: 7
  outliers final: 1
  residues processed: 391
  average time/residue: 0.1785
  time to fit residues: 104.4016
Evaluate side-chains
  285 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 283
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0670
   chunk 74 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7900

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 562 ASN
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 464 GLN
C  68 GLN
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.097018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.085911 restraints weight = 35996.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.087820 restraints weight = 23087.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.089180 restraints weight = 16344.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10544  Z= 0.237
  Angle     :  0.828  11.653  14383  Z= 0.430
  Chirality :  0.046   0.243   1672
  Planarity :  0.006   0.075   1789
  Dihedral  :  6.136  35.074   1410
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  9.08 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.24 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.89 (0.23), residues: 1299
  helix:  1.20 (0.19), residues: 748
  sheet: -2.57 (0.44), residues: 102
  loop : -3.36 (0.25), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP C 227 
 HIS   0.013   0.001   HIS C 171 
 PHE   0.044   0.003   PHE B  86 
 TYR   0.031   0.002   TYR D  56 
 ARG   0.009   0.001   ARG A 432 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 375
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8312 (pttt)
REVERT: A  118 ILE cc_start: 0.9313 (tp) cc_final: 0.9031 (tp)
REVERT: A  156 PHE cc_start: 0.7977 (m-80) cc_final: 0.7384 (m-80)
REVERT: A  175 ASP cc_start: 0.7844 (t0) cc_final: 0.7551 (p0)
REVERT: A  195 CYS cc_start: 0.5518 (t) cc_final: 0.5048 (t)
REVERT: A  221 MET cc_start: 0.8279 (mmt) cc_final: 0.8023 (mmt)
REVERT: A  291 VAL cc_start: 0.8718 (t) cc_final: 0.8434 (t)
REVERT: A  305 GLN cc_start: 0.8521 (tp40) cc_final: 0.8181 (tp40)
REVERT: A  326 MET cc_start: 0.8696 (tmm) cc_final: 0.8105 (tmm)
REVERT: A  327 PHE cc_start: 0.8105 (m-80) cc_final: 0.7530 (m-80)
REVERT: A  333 GLU cc_start: 0.8837 (mp0) cc_final: 0.7884 (mp0)
REVERT: A  335 PHE cc_start: 0.8799 (m-80) cc_final: 0.8377 (m-10)
REVERT: A  347 MET cc_start: 0.8295 (mmm) cc_final: 0.7428 (tpp)
REVERT: A  427 LEU cc_start: 0.8968 (tp) cc_final: 0.8615 (tp)
REVERT: A  462 ASN cc_start: 0.7558 (t0) cc_final: 0.7130 (t0)
REVERT: A  538 LEU cc_start: 0.8467 (tp) cc_final: 0.8171 (tp)
REVERT: A  555 ILE cc_start: 0.8557 (mp) cc_final: 0.8190 (mp)
REVERT: A  693 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7990 (mttp)
REVERT: B  103 VAL cc_start: 0.8640 (t) cc_final: 0.7730 (t)
REVERT: B  130 LEU cc_start: 0.7923 (mt) cc_final: 0.7717 (mt)
REVERT: B  163 HIS cc_start: 0.6240 (m170) cc_final: 0.5810 (m-70)
REVERT: B  200 LEU cc_start: 0.9066 (tp) cc_final: 0.8713 (tp)
REVERT: B  222 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: B  223 GLN cc_start: 0.8969 (mt0) cc_final: 0.7968 (mp10)
REVERT: B  257 ASP cc_start: 0.8121 (m-30) cc_final: 0.7895 (m-30)
REVERT: B  397 SER cc_start: 0.8884 (t) cc_final: 0.8649 (p)
REVERT: B  419 CYS cc_start: 0.8404 (p) cc_final: 0.8183 (p)
REVERT: B  423 LEU cc_start: 0.8564 (mt) cc_final: 0.8133 (pp)
REVERT: B  466 TYR cc_start: 0.7511 (m-10) cc_final: 0.7302 (m-10)
REVERT: C   18 PHE cc_start: 0.8091 (t80) cc_final: 0.7871 (t80)
REVERT: C   67 LEU cc_start: 0.8738 (mt) cc_final: 0.8345 (mt)
REVERT: C   87 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8507 (mtp180)
REVERT: C   92 LYS cc_start: 0.8329 (mptt) cc_final: 0.7900 (mmtm)
REVERT: C  133 SER cc_start: 0.9106 (p) cc_final: 0.8891 (p)
REVERT: C  140 ASP cc_start: 0.9005 (m-30) cc_final: 0.8479 (m-30)
REVERT: C  171 HIS cc_start: 0.8263 (m-70) cc_final: 0.7800 (m-70)
REVERT: C  173 PHE cc_start: 0.7774 (m-10) cc_final: 0.7409 (m-80)
REVERT: C  198 LEU cc_start: 0.8220 (tt) cc_final: 0.8007 (tp)
REVERT: C  206 LEU cc_start: 0.8439 (mp) cc_final: 0.7701 (tp)
REVERT: C  218 TYR cc_start: 0.8298 (m-10) cc_final: 0.8075 (m-10)
REVERT: C  224 MET cc_start: 0.8157 (mmp) cc_final: 0.7784 (mmm)
REVERT: D   25 PHE cc_start: 0.7356 (m-80) cc_final: 0.7055 (m-80)
REVERT: D   26 LEU cc_start: 0.8845 (mp) cc_final: 0.8395 (mp)
REVERT: D   64 PHE cc_start: 0.7665 (t80) cc_final: 0.7056 (t80)
REVERT: D   90 ASP cc_start: 0.8872 (m-30) cc_final: 0.8581 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 377
  average time/residue: 0.1754
  time to fit residues: 99.2590
Evaluate side-chains
  290 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 120 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 48 optimal weight:    0.2980
   chunk 78 optimal weight:    7.9990
   chunk 118 optimal weight:    6.9990
   chunk 123 optimal weight:    0.4980
   chunk 105 optimal weight:    8.9990
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 169 ASN
A 428 GLN
A 449 HIS
** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 ASN
A 587 GLN
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 ASN
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.093433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.082542 restraints weight = 36823.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.084431 restraints weight = 23475.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.085560 restraints weight = 16543.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.6259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  10544  Z= 0.336
  Angle     :  0.831  13.362  14383  Z= 0.439
  Chirality :  0.047   0.191   1672
  Planarity :  0.006   0.068   1789
  Dihedral  :  6.087  32.027   1410
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  8.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.78 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.97 (0.23), residues: 1299
  helix:  0.98 (0.19), residues: 754
  sheet: -2.39 (0.51), residues: 84
  loop : -3.19 (0.25), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  36 
 HIS   0.015   0.002   HIS C 197 
 PHE   0.038   0.003   PHE B  86 
 TYR   0.023   0.002   TYR C  90 
 ARG   0.009   0.001   ARG A 432 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 334
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 THR cc_start: 0.8147 (p) cc_final: 0.7765 (p)
REVERT: A  118 ILE cc_start: 0.9342 (tp) cc_final: 0.9050 (tp)
REVERT: A  175 ASP cc_start: 0.8265 (t0) cc_final: 0.7394 (p0)
REVERT: A  195 CYS cc_start: 0.5634 (t) cc_final: 0.5243 (t)
REVERT: A  221 MET cc_start: 0.8263 (mmt) cc_final: 0.7873 (mmt)
REVERT: A  326 MET cc_start: 0.8446 (tmm) cc_final: 0.7856 (tmm)
REVERT: A  327 PHE cc_start: 0.8278 (m-80) cc_final: 0.7479 (m-80)
REVERT: A  335 PHE cc_start: 0.8700 (m-80) cc_final: 0.8421 (m-10)
REVERT: A  381 ASP cc_start: 0.8776 (t0) cc_final: 0.8541 (t0)
REVERT: A  427 LEU cc_start: 0.9001 (tp) cc_final: 0.8691 (tp)
REVERT: A  462 ASN cc_start: 0.7749 (t0) cc_final: 0.7262 (t0)
REVERT: A  693 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7870 (mttp)
REVERT: B  103 VAL cc_start: 0.9079 (t) cc_final: 0.8601 (t)
REVERT: B  163 HIS cc_start: 0.6242 (m170) cc_final: 0.5878 (m-70)
REVERT: B  219 LEU cc_start: 0.8403 (mm) cc_final: 0.7954 (mm)
REVERT: B  222 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B  223 GLN cc_start: 0.9005 (mt0) cc_final: 0.7987 (mp10)
REVERT: B  226 LEU cc_start: 0.9540 (mt) cc_final: 0.9188 (mt)
REVERT: B  257 ASP cc_start: 0.8357 (m-30) cc_final: 0.8045 (m-30)
REVERT: B  397 SER cc_start: 0.9101 (t) cc_final: 0.8851 (p)
REVERT: B  411 PHE cc_start: 0.8694 (t80) cc_final: 0.8481 (t80)
REVERT: B  416 ILE cc_start: 0.8699 (mm) cc_final: 0.8381 (mm)
REVERT: B  466 TYR cc_start: 0.8121 (m-10) cc_final: 0.7711 (m-10)
REVERT: C   72 LEU cc_start: 0.9182 (mt) cc_final: 0.8956 (mt)
REVERT: C   92 LYS cc_start: 0.8388 (mptt) cc_final: 0.8161 (mmtm)
REVERT: C  127 ILE cc_start: 0.8447 (mm) cc_final: 0.8225 (mm)
REVERT: C  140 ASP cc_start: 0.9005 (m-30) cc_final: 0.8681 (m-30)
REVERT: C  169 LEU cc_start: 0.9331 (mt) cc_final: 0.8659 (mt)
REVERT: C  171 HIS cc_start: 0.8245 (m-70) cc_final: 0.7872 (m170)
REVERT: C  173 PHE cc_start: 0.8091 (m-10) cc_final: 0.7723 (m-80)
REVERT: C  180 ASP cc_start: 0.8180 (t0) cc_final: 0.7714 (t0)
REVERT: C  206 LEU cc_start: 0.8457 (mp) cc_final: 0.7873 (tp)
REVERT: C  224 MET cc_start: 0.8320 (mmp) cc_final: 0.8054 (mmm)
REVERT: C  230 ILE cc_start: 0.9329 (tp) cc_final: 0.9098 (pt)
REVERT: C  231 THR cc_start: 0.8989 (p) cc_final: 0.8737 (p)
REVERT: D   79 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: D   90 ASP cc_start: 0.8878 (m-30) cc_final: 0.8641 (m-30)
  outliers start: 6
  outliers final: 0
  residues processed: 338
  average time/residue: 0.1824
  time to fit residues: 92.4933
Evaluate side-chains
  270 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 110 optimal weight:    0.7980
   chunk 116 optimal weight:    6.9990
   chunk 106 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 115 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 428 GLN
A 462 ASN
A 573 ASN
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.096858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.086067 restraints weight = 36871.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.087911 restraints weight = 23659.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.089327 restraints weight = 16815.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.6628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10544  Z= 0.243
  Angle     :  0.805  12.506  14383  Z= 0.415
  Chirality :  0.046   0.216   1672
  Planarity :  0.006   0.068   1789
  Dihedral  :  5.931  31.319   1410
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  8.85 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.15 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.87 (0.23), residues: 1299
  helix:  1.11 (0.19), residues: 745
  sheet: -2.07 (0.53), residues: 82
  loop : -3.21 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 653 
 HIS   0.010   0.001   HIS C 197 
 PHE   0.044   0.002   PHE B  86 
 TYR   0.032   0.002   TYR D  56 
 ARG   0.008   0.001   ARG A 432 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 347
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 THR cc_start: 0.8115 (p) cc_final: 0.7896 (p)
REVERT: A  118 ILE cc_start: 0.9200 (tp) cc_final: 0.8866 (tp)
REVERT: A  175 ASP cc_start: 0.8098 (t0) cc_final: 0.7277 (p0)
REVERT: A  327 PHE cc_start: 0.7881 (m-80) cc_final: 0.7189 (m-80)
REVERT: A  331 GLN cc_start: 0.7276 (tp-100) cc_final: 0.6878 (tp-100)
REVERT: A  335 PHE cc_start: 0.8540 (m-80) cc_final: 0.8171 (m-10)
REVERT: A  427 LEU cc_start: 0.8667 (tp) cc_final: 0.8307 (tp)
REVERT: A  462 ASN cc_start: 0.7527 (t0) cc_final: 0.7202 (t0)
REVERT: A  571 LEU cc_start: 0.8874 (tt) cc_final: 0.8663 (tt)
REVERT: A  662 LEU cc_start: 0.8885 (mm) cc_final: 0.8643 (mm)
REVERT: B   97 VAL cc_start: 0.8953 (t) cc_final: 0.8726 (t)
REVERT: B  186 PHE cc_start: 0.8324 (m-80) cc_final: 0.8117 (m-80)
REVERT: B  222 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: B  223 GLN cc_start: 0.8821 (mt0) cc_final: 0.7869 (mp10)
REVERT: B  226 LEU cc_start: 0.9390 (mt) cc_final: 0.9055 (mt)
REVERT: B  257 ASP cc_start: 0.8346 (m-30) cc_final: 0.8051 (m-30)
REVERT: B  423 LEU cc_start: 0.8265 (mm) cc_final: 0.8054 (pp)
REVERT: C  133 SER cc_start: 0.9137 (p) cc_final: 0.8810 (p)
REVERT: C  140 ASP cc_start: 0.8804 (m-30) cc_final: 0.8429 (m-30)
REVERT: C  173 PHE cc_start: 0.7990 (m-10) cc_final: 0.7744 (m-80)
REVERT: C  180 ASP cc_start: 0.8004 (t0) cc_final: 0.7763 (t0)
REVERT: C  206 LEU cc_start: 0.8230 (mp) cc_final: 0.7671 (tp)
REVERT: C  224 MET cc_start: 0.7956 (mmp) cc_final: 0.7681 (mmm)
REVERT: C  231 THR cc_start: 0.8781 (p) cc_final: 0.8451 (p)
REVERT: D   26 LEU cc_start: 0.8621 (mp) cc_final: 0.8332 (mp)
REVERT: D   74 TRP cc_start: 0.8416 (t-100) cc_final: 0.8009 (t-100)
REVERT: D   79 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7621 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 348
  average time/residue: 0.1927
  time to fit residues: 99.9045
Evaluate side-chains
  269 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 74 optimal weight:    0.2980
   chunk 51 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    3.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 ASN
A 587 GLN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 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 = 0.3583 r_free = 0.3583 target = 0.095228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.085365 restraints weight = 36648.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.087116 restraints weight = 23375.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.088291 restraints weight = 16388.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.6854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  10544  Z= 0.315
  Angle     :  0.824  13.212  14383  Z= 0.431
  Chirality :  0.046   0.256   1672
  Planarity :  0.006   0.069   1789
  Dihedral  :  5.924  35.790   1410
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 19.91
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  8.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.06 (0.23), residues: 1299
  helix:  0.92 (0.19), residues: 745
  sheet: -1.96 (0.50), residues: 98
  loop : -3.27 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 653 
 HIS   0.011   0.002   HIS C 197 
 PHE   0.038   0.003   PHE B  86 
 TYR   0.022   0.002   TYR C 156 
 ARG   0.008   0.001   ARG A 432 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 324
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 ASP cc_start: 0.8340 (t0) cc_final: 0.7406 (p0)
REVERT: A  234 SER cc_start: 0.8998 (t) cc_final: 0.8618 (p)
REVERT: A  285 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8316 (ttt180)
REVERT: A  305 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: A  327 PHE cc_start: 0.7552 (m-80) cc_final: 0.7344 (m-80)
REVERT: A  347 MET cc_start: 0.7899 (mmm) cc_final: 0.7191 (tpp)
REVERT: A  427 LEU cc_start: 0.8728 (tp) cc_final: 0.8426 (tp)
REVERT: A  662 LEU cc_start: 0.8871 (mm) cc_final: 0.8628 (mm)
REVERT: B  219 LEU cc_start: 0.7981 (mm) cc_final: 0.7710 (mm)
REVERT: B  222 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: B  223 GLN cc_start: 0.8674 (mt0) cc_final: 0.7927 (mp10)
REVERT: B  226 LEU cc_start: 0.9363 (mt) cc_final: 0.9081 (mt)
REVERT: B  236 VAL cc_start: 0.9478 (t) cc_final: 0.9201 (t)
REVERT: B  257 ASP cc_start: 0.8151 (m-30) cc_final: 0.7873 (m-30)
REVERT: B  390 SER cc_start: 0.9118 (m) cc_final: 0.8767 (t)
REVERT: B  406 THR cc_start: 0.8569 (m) cc_final: 0.8201 (t)
REVERT: B  423 LEU cc_start: 0.8319 (mm) cc_final: 0.8117 (pp)
REVERT: B  466 TYR cc_start: 0.8153 (m-10) cc_final: 0.7663 (m-10)
REVERT: C   81 LEU cc_start: 0.8366 (pp) cc_final: 0.7794 (mm)
REVERT: C  133 SER cc_start: 0.9133 (p) cc_final: 0.8905 (p)
REVERT: C  136 ASN cc_start: 0.8152 (p0) cc_final: 0.7448 (m-40)
REVERT: C  140 ASP cc_start: 0.8765 (m-30) cc_final: 0.8496 (m-30)
REVERT: C  157 PHE cc_start: 0.8433 (m-80) cc_final: 0.8122 (m-10)
REVERT: C  171 HIS cc_start: 0.7753 (m-70) cc_final: 0.7489 (m-70)
REVERT: C  180 ASP cc_start: 0.7833 (t0) cc_final: 0.7626 (t0)
REVERT: C  206 LEU cc_start: 0.8301 (mp) cc_final: 0.7779 (tp)
REVERT: C  224 MET cc_start: 0.7891 (mmp) cc_final: 0.7622 (mmm)
REVERT: D   78 PHE cc_start: 0.7926 (t80) cc_final: 0.7638 (t80)
REVERT: D   79 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7651 (tm-30)
REVERT: D   94 PHE cc_start: 0.7946 (t80) cc_final: 0.7733 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 324
  average time/residue: 0.1847
  time to fit residues: 90.3988
Evaluate side-chains
  253 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0470
   chunk 32 optimal weight:    7.9990
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 ASN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.099173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.088227 restraints weight = 35326.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.090344 restraints weight = 21200.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.091859 restraints weight = 14265.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.7166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10544  Z= 0.239
  Angle     :  0.823  13.080  14383  Z= 0.424
  Chirality :  0.047   0.398   1672
  Planarity :  0.006   0.068   1789
  Dihedral  :  5.752  33.446   1410
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  8.93 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.95 (0.23), residues: 1299
  helix:  0.96 (0.19), residues: 746
  sheet: -1.99 (0.47), residues: 107
  loop : -3.13 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 247 
 HIS   0.011   0.001   HIS C 197 
 PHE   0.042   0.002   PHE B  86 
 TYR   0.024   0.002   TYR D  56 
 ARG   0.006   0.001   ARG A 432 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 343
  time to evaluate  : 1.260 
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  175 ASP cc_start: 0.8053 (t0) cc_final: 0.7336 (p0)
REVERT: A  195 CYS cc_start: 0.5779 (t) cc_final: 0.5373 (t)
REVERT: A  234 SER cc_start: 0.8817 (t) cc_final: 0.8416 (p)
REVERT: A  285 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8466 (ttt-90)
REVERT: A  305 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8509 (tm-30)
REVERT: A  347 MET cc_start: 0.8113 (mmm) cc_final: 0.7118 (tpp)
REVERT: A  427 LEU cc_start: 0.8861 (tp) cc_final: 0.8545 (tp)
REVERT: A  565 TYR cc_start: 0.8117 (m-80) cc_final: 0.7908 (m-10)
REVERT: A  662 LEU cc_start: 0.8955 (mm) cc_final: 0.8675 (mm)
REVERT: B  204 ASN cc_start: 0.7454 (m-40) cc_final: 0.6814 (t0)
REVERT: B  219 LEU cc_start: 0.8360 (mm) cc_final: 0.7959 (mm)
REVERT: B  222 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: B  223 GLN cc_start: 0.8975 (mt0) cc_final: 0.8055 (mp10)
REVERT: B  226 LEU cc_start: 0.9521 (mt) cc_final: 0.9038 (mt)
REVERT: B  257 ASP cc_start: 0.8249 (m-30) cc_final: 0.7926 (m-30)
REVERT: B  387 ILE cc_start: 0.9271 (mt) cc_final: 0.8892 (mt)
REVERT: B  390 SER cc_start: 0.9236 (m) cc_final: 0.8902 (t)
REVERT: B  397 SER cc_start: 0.8995 (p) cc_final: 0.8761 (p)
REVERT: B  466 TYR cc_start: 0.8015 (m-10) cc_final: 0.7587 (m-10)
REVERT: C  133 SER cc_start: 0.8842 (p) cc_final: 0.8545 (p)
REVERT: C  136 ASN cc_start: 0.8313 (p0) cc_final: 0.7540 (m-40)
REVERT: C  137 ILE cc_start: 0.8583 (tt) cc_final: 0.8190 (tt)
REVERT: C  140 ASP cc_start: 0.8952 (m-30) cc_final: 0.8424 (m-30)
REVERT: C  206 LEU cc_start: 0.8402 (mp) cc_final: 0.7889 (tp)
REVERT: C  224 MET cc_start: 0.8156 (mmp) cc_final: 0.7834 (mmm)
REVERT: D   25 PHE cc_start: 0.6908 (m-80) cc_final: 0.6501 (m-80)
REVERT: D   26 LEU cc_start: 0.8703 (mp) cc_final: 0.8306 (mp)
REVERT: D   47 TYR cc_start: 0.5538 (m-80) cc_final: 0.4862 (m-80)
REVERT: D   78 PHE cc_start: 0.8060 (t80) cc_final: 0.7649 (t80)
REVERT: D   90 ASP cc_start: 0.8793 (m-30) cc_final: 0.8585 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 343
  average time/residue: 0.1771
  time to fit residues: 91.5545
Evaluate side-chains
  259 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 113 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 HIS
A 573 ASN
B 163 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 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 = 0.3620 r_free = 0.3620 target = 0.097390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.086023 restraints weight = 35810.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.088170 restraints weight = 21089.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.089723 restraints weight = 14116.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.7259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10544  Z= 0.295
  Angle     :  0.816  11.455  14383  Z= 0.426
  Chirality :  0.047   0.295   1672
  Planarity :  0.006   0.072   1789
  Dihedral  :  5.727  30.560   1410
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  8.85 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.98 (0.23), residues: 1299
  helix:  0.86 (0.18), residues: 746
  sheet: -1.98 (0.50), residues: 101
  loop : -3.00 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP D  36 
 HIS   0.011   0.002   HIS C 197 
 PHE   0.043   0.003   PHE B  86 
 TYR   0.050   0.002   TYR B 389 
 ARG   0.012   0.001   ARG A  52 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ILE cc_start: 0.9327 (tp) cc_final: 0.9089 (tp)
REVERT: A  175 ASP cc_start: 0.8123 (t0) cc_final: 0.7154 (p0)
REVERT: A  195 CYS cc_start: 0.6527 (t) cc_final: 0.5993 (t)
REVERT: A  347 MET cc_start: 0.8239 (mmm) cc_final: 0.7074 (tpp)
REVERT: A  381 ASP cc_start: 0.8828 (t0) cc_final: 0.8584 (t0)
REVERT: A  427 LEU cc_start: 0.8981 (tp) cc_final: 0.8708 (tp)
REVERT: A  565 TYR cc_start: 0.8291 (m-80) cc_final: 0.8060 (m-80)
REVERT: A  662 LEU cc_start: 0.9058 (mm) cc_final: 0.8758 (mm)
REVERT: B  130 LEU cc_start: 0.8264 (mt) cc_final: 0.8043 (mt)
REVERT: B  200 LEU cc_start: 0.9129 (tp) cc_final: 0.8846 (tp)
REVERT: B  222 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7622 (tm-30)
REVERT: B  223 GLN cc_start: 0.9117 (mt0) cc_final: 0.8079 (mp10)
REVERT: B  226 LEU cc_start: 0.9615 (mt) cc_final: 0.9114 (mt)
REVERT: B  236 VAL cc_start: 0.9511 (t) cc_final: 0.9210 (t)
REVERT: B  257 ASP cc_start: 0.8368 (m-30) cc_final: 0.7982 (m-30)
REVERT: B  390 SER cc_start: 0.9381 (m) cc_final: 0.9057 (t)
REVERT: B  397 SER cc_start: 0.9099 (p) cc_final: 0.8895 (p)
REVERT: B  406 THR cc_start: 0.8832 (m) cc_final: 0.8516 (t)
REVERT: B  466 TYR cc_start: 0.8188 (m-10) cc_final: 0.7762 (m-10)
REVERT: C   72 LEU cc_start: 0.9219 (mt) cc_final: 0.9014 (mt)
REVERT: C  128 ILE cc_start: 0.9187 (tp) cc_final: 0.8534 (tp)
REVERT: C  136 ASN cc_start: 0.8449 (p0) cc_final: 0.7586 (m-40)
REVERT: C  140 ASP cc_start: 0.9050 (m-30) cc_final: 0.8653 (m-30)
REVERT: C  180 ASP cc_start: 0.8534 (t70) cc_final: 0.8056 (t0)
REVERT: C  206 LEU cc_start: 0.8558 (mp) cc_final: 0.8016 (tp)
REVERT: C  224 MET cc_start: 0.8414 (mmp) cc_final: 0.8082 (mmm)
REVERT: D   26 LEU cc_start: 0.8994 (mp) cc_final: 0.8579 (mp)
REVERT: D   78 PHE cc_start: 0.8290 (t80) cc_final: 0.7933 (t80)
REVERT: D   90 ASP cc_start: 0.8769 (m-30) cc_final: 0.8566 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 317
  average time/residue: 0.1722
  time to fit residues: 83.1383
Evaluate side-chains
  253 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 85 optimal weight:    9.9990
   chunk 119 optimal weight:   30.0000
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 120 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 98 optimal weight:    0.4980
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 HIS
A 573 ASN
B 163 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 HIS
B 405 ASN
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.096620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.085779 restraints weight = 36209.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.087820 restraints weight = 21682.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.089258 restraints weight = 14669.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.7382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10544  Z= 0.296
  Angle     :  0.820  11.390  14383  Z= 0.427
  Chirality :  0.047   0.265   1672
  Planarity :  0.006   0.071   1789
  Dihedral  :  5.795  28.960   1410
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 20.35
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  9.24 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    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: -1.08 (0.23), residues: 1299
  helix:  0.70 (0.18), residues: 749
  sheet: -1.96 (0.50), residues: 101
  loop : -2.93 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP D  36 
 HIS   0.013   0.002   HIS C 171 
 PHE   0.043   0.003   PHE B  86 
 TYR   0.020   0.002   TYR B 389 
 ARG   0.011   0.001   ARG A  52 

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

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

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2598 Ramachandran restraints generated.
    1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 ASP cc_start: 0.8106 (t0) cc_final: 0.7091 (p0)
REVERT: A  195 CYS cc_start: 0.6059 (t) cc_final: 0.5466 (t)
REVERT: A  427 LEU cc_start: 0.8847 (tp) cc_final: 0.8638 (tp)
REVERT: A  662 LEU cc_start: 0.8926 (mm) cc_final: 0.8635 (mm)
REVERT: B  222 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: B  223 GLN cc_start: 0.9012 (mt0) cc_final: 0.8032 (mp10)
REVERT: B  226 LEU cc_start: 0.9538 (mt) cc_final: 0.9050 (mt)
REVERT: B  236 VAL cc_start: 0.9516 (t) cc_final: 0.9173 (t)
REVERT: B  257 ASP cc_start: 0.8380 (m-30) cc_final: 0.8006 (m-30)
REVERT: B  390 SER cc_start: 0.9336 (m) cc_final: 0.9000 (t)
REVERT: B  406 THR cc_start: 0.8740 (m) cc_final: 0.8413 (t)
REVERT: B  466 TYR cc_start: 0.7971 (m-10) cc_final: 0.7466 (m-10)
REVERT: C   72 LEU cc_start: 0.9148 (mt) cc_final: 0.8943 (mt)
REVERT: C  133 SER cc_start: 0.8897 (p) cc_final: 0.8631 (p)
REVERT: C  136 ASN cc_start: 0.8329 (p0) cc_final: 0.7526 (m-40)
REVERT: C  140 ASP cc_start: 0.8958 (m-30) cc_final: 0.8644 (m-30)
REVERT: C  171 HIS cc_start: 0.7984 (m-70) cc_final: 0.7732 (m90)
REVERT: C  172 THR cc_start: 0.9453 (p) cc_final: 0.9149 (p)
REVERT: C  180 ASP cc_start: 0.8345 (t70) cc_final: 0.7490 (t0)
REVERT: C  206 LEU cc_start: 0.8547 (mp) cc_final: 0.8013 (tp)
REVERT: C  224 MET cc_start: 0.8429 (mmp) cc_final: 0.7885 (mmm)
REVERT: D   94 PHE cc_start: 0.8082 (t80) cc_final: 0.7847 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 319
  average time/residue: 0.1711
  time to fit residues: 82.9803
Evaluate side-chains
  254 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 122 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 123 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 110 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
A 573 ASN
B 163 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.096809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.085597 restraints weight = 35813.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.087738 restraints weight = 21121.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.089309 restraints weight = 14084.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.7494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10544  Z= 0.290
  Angle     :  0.819  11.037  14383  Z= 0.428
  Chirality :  0.047   0.247   1672
  Planarity :  0.006   0.068   1789
  Dihedral  :  5.770  28.218   1410
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  9.47 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.48 %
    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 (0.23), residues: 1299
  helix:  0.75 (0.18), residues: 746
  sheet: -1.91 (0.50), residues: 101
  loop : -2.80 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP C 174 
 HIS   0.012   0.002   HIS C 171 
 PHE   0.043   0.003   PHE B  86 
 TYR   0.042   0.002   TYR B 389 
 ARG   0.007   0.001   ARG B 157 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3014.32 seconds
wall clock time: 55 minutes 15.53 seconds (3315.53 seconds total)