Starting phenix.real_space_refine
on Tue Mar 11 14:31:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oix_12935/03_2025/7oix_12935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oix_12935/03_2025/7oix_12935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2025/7oix_12935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2025/7oix_12935.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2025/7oix_12935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2025/7oix_12935.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    3814      2.51       5
     N     937      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5869
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 21, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 3558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3558
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 21, 'TRANS': 429}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 4.43, per 1000 atoms: 0.75
  Number of scatterers: 5869
  At special positions: 0
  Unit cell: (68.376, 74.888, 135.124, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1084      8.00
     N     937      7.00
     C    3814      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 301 " - pdb=" SG  CYS A 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 460 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-2
      " MAN D   4 " - " MAN D   5 "
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA D   3 " - " MAN D   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
      " BMA D   3 " - " MAN D   6 "
      " MAN D   6 " - " MAN D   7 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A 601 " - " ASN A 146 "
      " NAG A 602 " - " ASN A 133 "
      " NAG A 603 " - " ASN A 220 "
      " NAG A 604 " - " ASN A 247 "
      " NAG A 605 " - " ASN A 241 "
      " NAG C   1 " - " ASN A 177 "
      " NAG D   1 " - " ASN A 312 "
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 695.5 milliseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      57.4% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 68
      removed outlier: 3.624A  pdb=" N   THR A  66 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 98
    Processing helix  chain 'A' and resid 153 through 156
    Processing helix  chain 'A' and resid 192 through 196
      removed outlier: 4.225A  pdb=" N   ARG A 196 " --> pdb=" O   CYS A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
      removed outlier: 3.693A  pdb=" N   ALA A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 51
    Processing helix  chain 'B' and resid 52 through 73
      removed outlier: 4.436A  pdb=" N   TYR B  56 " --> pdb=" O   GLY B  52 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   GLN B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   ILE B  69 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 107
      Proline residue:  B  98  - end of helix
    Processing helix  chain 'B' and resid 115 through 135
      removed outlier: 3.855A  pdb=" N   ILE B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      Proline residue:  B 124  - end of helix
      removed outlier: 3.927A  pdb=" N   TRP B 134 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 173
      removed outlier: 4.240A  pdb=" N   TRP B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   TYR B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU B 148 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
      Proline residue:  B 164  - end of helix
      removed outlier: 4.393A  pdb=" N   THR B 169 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   MET B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   PHE B 171 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   SER B 173 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 206
    Processing helix  chain 'B' and resid 234 through 264
      removed outlier: 3.957A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 291
    Processing helix  chain 'B' and resid 292 through 322
      removed outlier: 3.917A  pdb=" N   PHE B 303 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA B 316 " --> pdb=" O   GLU B 312 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   LEU B 317 " --> pdb=" O   GLY B 313 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   THR B 320 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 353
      Proline residue:  B 345  - end of helix
    Processing helix  chain 'B' and resid 357 through 373
      removed outlier: 4.134A  pdb=" N   ALA B 367 " --> pdb=" O   GLY B 363 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL B 368 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      Proline residue:  B 369  - end of helix
    Processing helix  chain 'B' and resid 374 through 376
      No H-bonds generated for 'chain 'B' and resid 374 through 376'
    Processing helix  chain 'B' and resid 380 through 417
      Proline residue:  B 402  - end of helix
      removed outlier: 3.842A  pdb=" N   LEU B 406 " --> pdb=" O   PRO B 402 " (cutoff:3.500A)
      Proline residue:  B 407  - end of helix
    Processing helix  chain 'B' and resid 423 through 453
      removed outlier: 4.114A  pdb=" N   PHE B 427 " --> pdb=" O   THR B 423 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE B 428 " --> pdb=" O   GLU B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 489
      removed outlier: 3.951A  pdb=" N   LYS B 467 " --> pdb=" O   PRO B 463 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA B 477 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      Proline residue:  B 478  - end of helix
    Processing helix  chain 'B' and resid 494 through 509
      removed outlier: 3.621A  pdb=" N   LYS B 504 " --> pdb=" O   ARG B 500 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   LEU B 509 " --> pdb=" O   ALA B 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 78
      removed outlier: 6.999A  pdb=" N   GLY A 268 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   HIS A 285 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   TYR A 266 " --> pdb=" O   HIS A 285 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78
      removed outlier: 3.682A  pdb=" N   THR A 290 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 136
      removed outlier: 6.453A  pdb=" N   THR A 135 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 8.531A  pdb=" N   THR A 316 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   ILE A 319 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   ILE A 125 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ALA A 123 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   THR A 148 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 8.573A  pdb=" N   ILE A 125 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 10.203A  pdb=" N   THR A 150 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   VAL A 127 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 10.240A  pdb=" N   ASP A 152 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 10.085A  pdb=" N   ALA A 129 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASN A 177 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 136
      removed outlier: 6.453A  pdb=" N   THR A 135 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 8.531A  pdb=" N   THR A 316 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 160
    Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 217

    318 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1743
        1.34 -     1.46: 1525
        1.46 -     1.58: 2713
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 6029
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.497 -0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" C1  MAN D   5 "
       pdb=" C2  MAN D   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.581 -0.055 2.00e-02 2.50e+03 7.49e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.66e+00
  bond pdb=" C1  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.49e+00
  bond pdb=" C2  BMA D   3 "
       pdb=" C3  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.544  1.502  0.042 2.00e-02 2.50e+03 4.35e+00
  ... (remaining 6024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 7737
        2.02 -     4.05: 378
        4.05 -     6.07: 73
        6.07 -     8.09: 20
        8.09 -    10.11: 12
  Bond angle restraints: 8220
  Sorted by residual:
  angle pdb=" C   LEU B 376 "
        pdb=" N   MET B 377 "
        pdb=" CA  MET B 377 "
      ideal   model   delta    sigma   weight residual
     121.54  130.13   -8.59 1.91e+00 2.74e-01 2.02e+01
  angle pdb=" C   ALA A 246 "
        pdb=" N   ASN A 247 "
        pdb=" CA  ASN A 247 "
      ideal   model   delta    sigma   weight residual
     121.85  129.21   -7.36 1.77e+00 3.19e-01 1.73e+01
  angle pdb=" CG  ARG B 111 "
        pdb=" CD  ARG B 111 "
        pdb=" NE  ARG B 111 "
      ideal   model   delta    sigma   weight residual
     112.00  121.12   -9.12 2.20e+00 2.07e-01 1.72e+01
  angle pdb=" N   GLY B 263 "
        pdb=" CA  GLY B 263 "
        pdb=" C   GLY B 263 "
      ideal   model   delta    sigma   weight residual
     113.18  122.79   -9.61 2.37e+00 1.78e-01 1.64e+01
  angle pdb=" CB  ARG B 353 "
        pdb=" CG  ARG B 353 "
        pdb=" CD  ARG B 353 "
      ideal   model   delta    sigma   weight residual
     111.30  119.90   -8.60 2.30e+00 1.89e-01 1.40e+01
  ... (remaining 8215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.55: 3470
       24.55 -    49.10: 223
       49.10 -    73.65: 31
       73.65 -    98.20: 22
       98.20 -   122.75: 6
  Dihedral angle restraints: 3752
    sinusoidal: 1668
      harmonic: 2084
  Sorted by residual:
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.48  -87.52     1      1.00e+01 1.00e-02 9.18e+01
  dihedral pdb=" CB  CYS A 126 "
           pdb=" SG  CYS A 126 "
           pdb=" SG  CYS A 145 "
           pdb=" CB  CYS A 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.80   59.20     1      1.00e+01 1.00e-02 4.68e+01
  dihedral pdb=" CA  VAL B  74 "
           pdb=" C   VAL B  74 "
           pdb=" N   ALA B  75 "
           pdb=" CA  ALA B  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 3749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 880
       0.092 -    0.183: 102
       0.183 -    0.275: 4
       0.275 -    0.366: 1
       0.366 -    0.457: 2
  Chirality restraints: 989
  Sorted by residual:
  chirality pdb=" C1  NAG A 605 "
            pdb=" ND2 ASN A 241 "
            pdb=" C2  NAG A 605 "
            pdb=" O5  NAG A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.23e+00
  chirality pdb=" C1  NAG A 603 "
            pdb=" ND2 ASN A 220 "
            pdb=" C2  NAG A 603 "
            pdb=" O5  NAG A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" CA  ASN B 380 "
            pdb=" N   ASN B 380 "
            pdb=" C   ASN B 380 "
            pdb=" CB  ASN B 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 986 not shown)

  Planarity restraints: 1011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 477 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO B 478 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 478 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 478 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 299 "   -0.016 2.00e-02 2.50e+03   1.52e-02 4.65e+00
        pdb=" CG  TYR A 299 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 299 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 299 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 299 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 299 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 299 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 299 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 118 "    0.017 2.00e-02 2.50e+03   1.26e-02 4.00e+00
        pdb=" CG  TRP B 118 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 118 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 118 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 118 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 118 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 118 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 118 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1008 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 167
        2.69 -     3.24: 6183
        3.24 -     3.79: 9472
        3.79 -     4.35: 11177
        4.35 -     4.90: 19019
  Nonbonded interactions: 46018
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  70 "
            pdb=" O   TRP B 134 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OH  TYR B  49 "
            pdb=" OG1 THR B 169 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER A 198 "
            pdb=" OE1 GLN A 250 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   GLN B 462 "
            pdb=" NZ  LYS B 467 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O4  NAG C   2 "
            pdb=" O5  BMA C   3 "
     model   vdw
     2.312 3.040
  ... (remaining 46013 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:             3.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.510
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
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      :  0.007   0.096   6029  Z= 0.479
  Angle     :  1.081  10.113   8220  Z= 0.547
  Chirality :  0.060   0.457    989
  Planarity :  0.007   0.057   1004
  Dihedral  : 17.878 122.750   2393
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.86 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.28), residues: 710
  helix:  0.08 (0.24), residues: 368
  sheet:  0.41 (0.56), residues: 80
  loop : -2.45 (0.31), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B 118 
 HIS   0.012   0.002   HIS B 414 
 PHE   0.023   0.003   PHE B 135 
 TYR   0.036   0.003   TYR A 299 
 ARG   0.007   0.001   ARG B 111 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8983 (mttt)
REVERT: A   99 ASP cc_start: 0.8802 (t0) cc_final: 0.8572 (t0)
REVERT: A  120 MET cc_start: 0.6624 (ptm) cc_final: 0.6161 (ptp)
REVERT: A  226 GLU cc_start: 0.7434 (pt0) cc_final: 0.7086 (mt-10)
REVERT: A  227 TRP cc_start: 0.8124 (p90) cc_final: 0.7557 (p90)
REVERT: A  262 ILE cc_start: 0.8559 (tt) cc_final: 0.8323 (tt)
REVERT: A  293 LYS cc_start: 0.8707 (tttt) cc_final: 0.8488 (ttpp)
REVERT: B   69 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (mt)
REVERT: B  111 ARG cc_start: 0.4986 (ttm170) cc_final: 0.2973 (ttp-170)
REVERT: B  155 GLU cc_start: 0.8912 (tp30) cc_final: 0.8376 (mm-30)
REVERT: B  176 GLN cc_start: 0.7802 (mt0) cc_final: 0.7116 (tm-30)
REVERT: B  239 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: B  289 MET cc_start: 0.3366 (tpt) cc_final: 0.2588 (tpt)
REVERT: B  309 MET cc_start: 0.7070 (ptp) cc_final: 0.6702 (ptp)
REVERT: B  370 PHE cc_start: 0.7494 (m-80) cc_final: 0.7280 (m-10)
REVERT: B  377 MET cc_start: 0.1822 (ptt) cc_final: 0.1492 (ptt)
REVERT: B  458 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7013 (ttm-80)
  outliers start: 6
  outliers final: 1
  residues processed: 150
  average time/residue: 0.2119
  time to fit residues: 39.6440
Evaluate side-chains
  105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  317 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 105 GLN
A 287 HIS
B  57 GLN
B  68 GLN
B 235 HIS
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
B 421 HIS
** B 501 GLN ** 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 = 0.3912 r_free = 0.3912 target = 0.145932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134126 restraints weight = 11886.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.136742 restraints weight = 6204.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138433 restraints weight = 3799.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6029  Z= 0.242
  Angle     :  0.749   7.620   8220  Z= 0.367
  Chirality :  0.045   0.288    989
  Planarity :  0.005   0.044   1004
  Dihedral  : 12.457 107.985   1114
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 16.75 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.29), residues: 710
  helix:  0.91 (0.26), residues: 366
  sheet:  0.31 (0.57), residues: 80
  loop : -2.17 (0.31), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 146 
 HIS   0.006   0.001   HIS A 287 
 PHE   0.021   0.002   PHE B 468 
 TYR   0.021   0.002   TYR A 299 
 ARG   0.006   0.001   ARG A  77 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6988 (m-80)
REVERT: A  120 MET cc_start: 0.7144 (ptm) cc_final: 0.6888 (ptp)
REVERT: A  262 ILE cc_start: 0.9079 (tt) cc_final: 0.8814 (tt)
REVERT: B  111 ARG cc_start: 0.5537 (ttm170) cc_final: 0.2552 (ttp-170)
REVERT: B  239 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: B  289 MET cc_start: 0.3029 (tpt) cc_final: 0.2137 (tpt)
REVERT: B  309 MET cc_start: 0.7330 (ptp) cc_final: 0.7057 (ptp)
REVERT: B  458 ARG cc_start: 0.7106 (mtp-110) cc_final: 0.6873 (ttm-80)
  outliers start: 20
  outliers final: 12
  residues processed: 133
  average time/residue: 0.2010
  time to fit residues: 33.7871
Evaluate side-chains
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 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 = 0.3897 r_free = 0.3897 target = 0.144919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.133217 restraints weight = 11938.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135823 restraints weight = 6209.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137528 restraints weight = 3807.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6029  Z= 0.239
  Angle     :  0.726   7.942   8220  Z= 0.352
  Chirality :  0.046   0.303    989
  Planarity :  0.005   0.077   1004
  Dihedral  : 10.545 100.442   1110
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.93 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.30), residues: 710
  helix:  1.03 (0.26), residues: 365
  sheet:  0.24 (0.58), residues: 80
  loop : -2.10 (0.32), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 118 
 HIS   0.004   0.001   HIS B 291 
 PHE   0.022   0.001   PHE B 350 
 TYR   0.018   0.001   TYR A 299 
 ARG   0.004   0.000   ARG A  63 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6918 (m-80)
REVERT: B   69 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9025 (mt)
REVERT: B  111 ARG cc_start: 0.5618 (ttm170) cc_final: 0.1824 (ttp80)
REVERT: B  187 MET cc_start: 0.8227 (mmm) cc_final: 0.7996 (mmm)
REVERT: B  239 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: B  289 MET cc_start: 0.2974 (tpt) cc_final: 0.2057 (tpt)
REVERT: B  414 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7229 (t-90)
REVERT: B  431 TYR cc_start: 0.7972 (t80) cc_final: 0.7671 (t80)
REVERT: B  458 ARG cc_start: 0.7169 (mtp-110) cc_final: 0.6884 (ttm-80)
  outliers start: 22
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1862
  time to fit residues: 29.6419
Evaluate side-chains
  121 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0470
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 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 = 0.3900 r_free = 0.3900 target = 0.144940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.133090 restraints weight = 12185.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135710 restraints weight = 6323.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137434 restraints weight = 3866.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6029  Z= 0.222
  Angle     :  0.703  13.000   8220  Z= 0.336
  Chirality :  0.044   0.276    989
  Planarity :  0.005   0.080   1004
  Dihedral  :  9.365  91.695   1110
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 21.10 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.30), residues: 710
  helix:  1.07 (0.26), residues: 365
  sheet:  0.16 (0.58), residues: 80
  loop : -2.10 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 118 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.017   0.001   PHE B 468 
 TYR   0.015   0.001   TYR A 299 
 ARG   0.005   0.000   ARG A  63 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6889 (m-80)
REVERT: B  111 ARG cc_start: 0.5720 (ttm170) cc_final: 0.1922 (ttp-110)
REVERT: B  187 MET cc_start: 0.8254 (mmm) cc_final: 0.8048 (mmm)
REVERT: B  207 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8174 (tp40)
REVERT: B  239 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: B  289 MET cc_start: 0.2944 (tpt) cc_final: 0.2026 (tpt)
REVERT: B  370 PHE cc_start: 0.6666 (m-10) cc_final: 0.6439 (m-10)
REVERT: B  431 TYR cc_start: 0.8034 (t80) cc_final: 0.7724 (t80)
REVERT: B  437 PHE cc_start: 0.8613 (t80) cc_final: 0.8409 (t80)
REVERT: B  458 ARG cc_start: 0.7188 (mtp-110) cc_final: 0.6829 (ttm-80)
  outliers start: 30
  outliers final: 20
  residues processed: 129
  average time/residue: 0.1733
  time to fit residues: 29.2903
Evaluate side-chains
  120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.145391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.133738 restraints weight = 11981.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.136301 restraints weight = 6176.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.137957 restraints weight = 3784.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6029  Z= 0.219
  Angle     :  0.697   9.917   8220  Z= 0.335
  Chirality :  0.044   0.351    989
  Planarity :  0.005   0.083   1004
  Dihedral  :  8.755  80.175   1110
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.03 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.30), residues: 710
  helix:  1.09 (0.26), residues: 365
  sheet:  0.06 (0.58), residues: 80
  loop : -2.13 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 118 
 HIS   0.004   0.001   HIS B 414 
 PHE   0.016   0.001   PHE B 468 
 TYR   0.014   0.001   TYR A 299 
 ARG   0.005   0.000   ARG A  63 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6882 (m-80)
REVERT: B  111 ARG cc_start: 0.5711 (ttm170) cc_final: 0.2771 (ttp-170)
REVERT: B  239 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8093 (tm-30)
REVERT: B  289 MET cc_start: 0.2936 (tpt) cc_final: 0.2017 (tpt)
REVERT: B  309 MET cc_start: 0.7666 (ptp) cc_final: 0.7205 (ptp)
REVERT: B  370 PHE cc_start: 0.6647 (m-10) cc_final: 0.6419 (m-10)
REVERT: B  431 TYR cc_start: 0.8061 (t80) cc_final: 0.7726 (t80)
REVERT: B  437 PHE cc_start: 0.8596 (t80) cc_final: 0.8388 (t80)
REVERT: B  458 ARG cc_start: 0.7146 (mtp-110) cc_final: 0.6793 (ttm-80)
  outliers start: 28
  outliers final: 20
  residues processed: 126
  average time/residue: 0.1826
  time to fit residues: 29.8792
Evaluate side-chains
  125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 66 optimal weight:    0.0030
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0370
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.5272

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 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 = 0.3921 r_free = 0.3921 target = 0.145948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.134207 restraints weight = 11923.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.136805 restraints weight = 6099.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.138519 restraints weight = 3712.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6029  Z= 0.187
  Angle     :  0.668   8.702   8220  Z= 0.321
  Chirality :  0.043   0.261    989
  Planarity :  0.005   0.073   1004
  Dihedral  :  7.891  59.604   1110
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 25.12 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.30), residues: 710
  helix:  1.11 (0.26), residues: 365
  sheet: -0.02 (0.58), residues: 80
  loop : -2.15 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 118 
 HIS   0.007   0.001   HIS B 414 
 PHE   0.018   0.001   PHE B 318 
 TYR   0.013   0.001   TYR A 299 
 ARG   0.001   0.000   ARG B 111 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6760 (m-80)
REVERT: B  111 ARG cc_start: 0.5757 (ttm170) cc_final: 0.2524 (ttp-170)
REVERT: B  239 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: B  289 MET cc_start: 0.2870 (tpt) cc_final: 0.1932 (tpt)
REVERT: B  309 MET cc_start: 0.7540 (ptp) cc_final: 0.7196 (ptp)
REVERT: B  370 PHE cc_start: 0.6519 (m-10) cc_final: 0.6299 (m-10)
REVERT: B  431 TYR cc_start: 0.7949 (t80) cc_final: 0.7607 (t80)
REVERT: B  437 PHE cc_start: 0.8537 (t80) cc_final: 0.8315 (t80)
REVERT: B  458 ARG cc_start: 0.7073 (mtp-110) cc_final: 0.6742 (ttm-80)
  outliers start: 24
  outliers final: 19
  residues processed: 128
  average time/residue: 0.1964
  time to fit residues: 32.1307
Evaluate side-chains
  127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0870
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.146522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.135004 restraints weight = 12130.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.137573 restraints weight = 6223.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.139228 restraints weight = 3798.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6029  Z= 0.180
  Angle     :  0.673   8.806   8220  Z= 0.320
  Chirality :  0.042   0.237    989
  Planarity :  0.004   0.064   1004
  Dihedral  :  6.922  46.470   1110
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.96 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.30), residues: 710
  helix:  1.19 (0.26), residues: 365
  sheet:  0.02 (0.58), residues: 80
  loop : -2.07 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 118 
 HIS   0.005   0.001   HIS B 414 
 PHE   0.015   0.001   PHE B 318 
 TYR   0.013   0.001   TYR A 299 
 ARG   0.007   0.000   ARG A  77 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6763 (m-80)
REVERT: B  111 ARG cc_start: 0.5670 (ttm170) cc_final: 0.3534 (ttm110)
REVERT: B  237 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6884 (mt-10)
REVERT: B  239 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: B  285 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4277 (tt)
REVERT: B  289 MET cc_start: 0.2905 (tpt) cc_final: 0.1984 (tpt)
REVERT: B  309 MET cc_start: 0.7462 (ptp) cc_final: 0.7228 (ptp)
REVERT: B  370 PHE cc_start: 0.6539 (m-10) cc_final: 0.6241 (m-10)
REVERT: B  431 TYR cc_start: 0.7965 (t80) cc_final: 0.7590 (t80)
REVERT: B  437 PHE cc_start: 0.8543 (t80) cc_final: 0.8334 (t80)
REVERT: B  458 ARG cc_start: 0.7135 (mtp-110) cc_final: 0.6778 (ttm-80)
  outliers start: 28
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1719
  time to fit residues: 29.8693
Evaluate side-chains
  125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 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 = 0.3913 r_free = 0.3913 target = 0.145620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.134001 restraints weight = 11914.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.136503 restraints weight = 6233.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.138152 restraints weight = 3846.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6029  Z= 0.213
  Angle     :  0.692   8.664   8220  Z= 0.331
  Chirality :  0.043   0.287    989
  Planarity :  0.005   0.092   1004
  Dihedral  :  6.665  44.741   1110
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.15 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.30), residues: 710
  helix:  1.23 (0.26), residues: 365
  sheet: -0.02 (0.59), residues: 80
  loop : -2.12 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 118 
 HIS   0.007   0.001   HIS B 414 
 PHE   0.013   0.001   PHE B 318 
 TYR   0.013   0.001   TYR A 299 
 ARG   0.006   0.000   ARG A  77 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6859 (m-80)
REVERT: B  111 ARG cc_start: 0.5669 (ttm170) cc_final: 0.2321 (ttp-170)
REVERT: B  237 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6905 (mt-10)
REVERT: B  239 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: B  285 LEU cc_start: 0.5020 (OUTLIER) cc_final: 0.4316 (tt)
REVERT: B  289 MET cc_start: 0.2938 (tpt) cc_final: 0.2011 (tpt)
REVERT: B  370 PHE cc_start: 0.6567 (m-80) cc_final: 0.6268 (m-10)
REVERT: B  431 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7580 (t80)
REVERT: B  458 ARG cc_start: 0.7157 (mtp-110) cc_final: 0.6775 (ttm-80)
  outliers start: 28
  outliers final: 22
  residues processed: 122
  average time/residue: 0.1775
  time to fit residues: 28.2843
Evaluate side-chains
  129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  431 TYR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.145107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133513 restraints weight = 12057.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.136038 restraints weight = 6235.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.137690 restraints weight = 3827.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6029  Z= 0.229
  Angle     :  0.703   8.436   8220  Z= 0.339
  Chirality :  0.044   0.279    989
  Planarity :  0.005   0.087   1004
  Dihedral  :  6.574  46.506   1110
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.15 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.31), residues: 710
  helix:  1.26 (0.26), residues: 365
  sheet:  0.01 (0.59), residues: 80
  loop : -2.14 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 118 
 HIS   0.002   0.001   HIS A 285 
 PHE   0.012   0.001   PHE B 318 
 TYR   0.014   0.001   TYR A 299 
 ARG   0.006   0.000   ARG A  77 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6919 (m-80)
REVERT: B  111 ARG cc_start: 0.5669 (ttm170) cc_final: 0.2326 (ttp-170)
REVERT: B  237 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6969 (mt-10)
REVERT: B  239 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: B  285 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4330 (tt)
REVERT: B  289 MET cc_start: 0.2960 (tpt) cc_final: 0.2043 (tpt)
REVERT: B  309 MET cc_start: 0.7446 (ptp) cc_final: 0.7093 (ptp)
REVERT: B  370 PHE cc_start: 0.6604 (m-80) cc_final: 0.6301 (m-10)
REVERT: B  378 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.1359 (mt-10)
REVERT: B  431 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7581 (t80)
REVERT: B  458 ARG cc_start: 0.7051 (mtp-110) cc_final: 0.6730 (ttm-80)
  outliers start: 28
  outliers final: 23
  residues processed: 127
  average time/residue: 0.1778
  time to fit residues: 29.5487
Evaluate side-chains
  133 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  378 GLU
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  431 TYR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 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 = 0.3914 r_free = 0.3914 target = 0.145712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.134160 restraints weight = 12084.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.136623 restraints weight = 6364.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.138322 restraints weight = 3918.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6029  Z= 0.205
  Angle     :  0.689   8.396   8220  Z= 0.332
  Chirality :  0.044   0.407    989
  Planarity :  0.005   0.087   1004
  Dihedral  :  6.395  47.486   1110
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 23.99 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.31), residues: 710
  helix:  1.28 (0.26), residues: 365
  sheet:  0.07 (0.60), residues: 80
  loop : -2.16 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 118 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.013   0.001   PHE B 318 
 TYR   0.014   0.001   TYR A 299 
 ARG   0.005   0.000   ARG A  77 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6958 (m-80)
REVERT: A  295 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6973 (mp10)
REVERT: B  111 ARG cc_start: 0.5696 (ttm170) cc_final: 0.2332 (ttp-170)
REVERT: B  237 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6941 (mt-10)
REVERT: B  239 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: B  285 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4301 (tt)
REVERT: B  289 MET cc_start: 0.2922 (tpt) cc_final: 0.2007 (tpt)
REVERT: B  309 MET cc_start: 0.7471 (ptp) cc_final: 0.7248 (ptp)
REVERT: B  370 PHE cc_start: 0.6567 (m-80) cc_final: 0.6243 (m-10)
REVERT: B  378 GLU cc_start: 0.4538 (OUTLIER) cc_final: 0.1152 (mt-10)
REVERT: B  431 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7557 (t80)
REVERT: B  458 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6761 (ttm-80)
  outliers start: 29
  outliers final: 25
  residues processed: 125
  average time/residue: 0.1677
  time to fit residues: 27.8286
Evaluate side-chains
  134 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  378 GLU
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  431 TYR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 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 = 0.3922 r_free = 0.3922 target = 0.146166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.134478 restraints weight = 12059.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.137064 restraints weight = 6180.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.138780 restraints weight = 3774.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6029  Z= 0.209
  Angle     :  0.690   8.322   8220  Z= 0.333
  Chirality :  0.044   0.372    989
  Planarity :  0.005   0.085   1004
  Dihedral  :  6.335  47.488   1110
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 24.32 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.30), residues: 710
  helix:  1.23 (0.26), residues: 364
  sheet:  0.06 (0.60), residues: 80
  loop : -2.20 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 118 
 HIS   0.007   0.001   HIS B 414 
 PHE   0.012   0.001   PHE B 318 
 TYR   0.014   0.001   TYR A 299 
 ARG   0.005   0.000   ARG A  77 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2170.71 seconds
wall clock time: 38 minutes 20.68 seconds (2300.68 seconds total)