Starting phenix.real_space_refine
on Fri Jun  6 13:55:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ffy_29070/06_2025/8ffy_29070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ffy_29070/06_2025/8ffy_29070.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/8ffy_29070/06_2025/8ffy_29070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ffy_29070/06_2025/8ffy_29070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ffy_29070/06_2025/8ffy_29070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ffy_29070/06_2025/8ffy_29070.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=   0.000 sd=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     P      61      5.49       5
     S      34      5.16       5
     C    4455      2.51       5
     N    1333      2.21       5
     O    1559      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7442
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2493
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 3590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3590
          Classifications: {'peptide': 452}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 424}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 1301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1301
          Classifications: {'RNA': 61}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 25}
          Link IDs: {'rna2p': 6, 'rna3p': 54}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SSA%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SSA%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 5.18, per 1000 atoms: 0.70
  Number of scatterers: 7442
  At special positions: 0
  Unit cell: (105.8, 80.5, 113.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P      61     15.00
     O    1559      8.00
     N    1333      7.00
     C    4455      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.11
  Conformation dependent library (CDL) restraints added in 737.4 milliseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1422

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      40.9% alpha, 17.3% beta
      20 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 2.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 3.510A  pdb=" N   LEU A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 254
    Processing helix  chain 'A' and resid 266 through 273
    Processing helix  chain 'A' and resid 299 through 307
      removed outlier: 4.054A  pdb=" N   GLY A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 383
    Processing helix  chain 'A' and resid 427 through 434
    Processing helix  chain 'A' and resid 457 through 468
    Processing helix  chain 'A' and resid 481 through 486
    Processing helix  chain 'B' and resid 42 through 51
    Processing helix  chain 'B' and resid 59 through 65
      removed outlier: 4.155A  pdb=" N   PHE B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA B  65 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 78
      removed outlier: 3.536A  pdb=" N   ALA B  70 " --> pdb=" O   CYS B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 121
    Processing helix  chain 'B' and resid 132 through 168
      Proline residue:  B 154  - end of helix
    Processing helix  chain 'B' and resid 204 through 212
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 233 through 252
    Processing helix  chain 'B' and resid 265 through 273
      removed outlier: 3.800A  pdb=" N   PHE B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 309
      removed outlier: 3.780A  pdb=" N   GLY B 303 " --> pdb=" O   THR B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 383
    Processing helix  chain 'B' and resid 427 through 434
    Processing helix  chain 'B' and resid 457 through 468
    Processing helix  chain 'B' and resid 481 through 486
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
      removed outlier: 7.069A  pdb=" N   VAL A 388 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   MET A 191 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   PHE A 386 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ARG A 402 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   SER A 423 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   PHE A 404 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   SER A 421 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 9.974A  pdb=" N   VAL A 419 " --> pdb=" O   CYS A 455 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   CYS A 455 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   SER A 421 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR A 453 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS A 425 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 449 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A 448 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL A 351 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ALA A 456 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 232
      removed outlier: 3.618A  pdb=" N   LEU A 231 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   SER B 325 " --> pdb=" O   MET B 258 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   THR B 349 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   ALA B 456 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL B 351 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR B 357 " --> pdb=" O   HIS B 448 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   HIS B 448 " --> pdb=" O   THR B 357 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   SER B 421 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   CYS B 455 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 9.504A  pdb=" N   VAL B 419 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   PHE B 416 " --> pdb=" O   MET B 410 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   MET B 410 " --> pdb=" O   PHE B 416 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   ALA B 408 " --> pdb=" O   GLU B 418 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 420 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 402 " --> pdb=" O   ASN B 424 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   HIS B 190 " --> pdb=" O   VAL B 388 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASP B 390 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL B 188 " --> pdb=" O   ASP B 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265
    Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 446
      removed outlier: 5.642A  pdb=" N   HIS A 311 " --> pdb=" O   MET A 436 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLN A 438 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 313 " --> pdb=" O   GLN A 438 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 476
      removed outlier: 3.565A  pdb=" N   VAL A 475 " --> pdb=" O   ILE A 490 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264
    Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 438
    Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 476

    288 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 2.59

  Time building geometry restraints manager: 2.46 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: 2124
        1.34 -     1.45: 1565
        1.45 -     1.57: 3860
        1.57 -     1.69: 128
        1.69 -     1.81: 56
  Bond restraints: 7733
  Sorted by residual:
  bond pdb=" C6  SSA A 601 "
       pdb=" N6  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.524 -0.191 2.00e-02 2.50e+03 9.13e+01
  bond pdb=" C6  SSA B 601 "
       pdb=" N6  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.524 -0.191 2.00e-02 2.50e+03 9.09e+01
  bond pdb=" O5' SSA B 601 "
       pdb=" S1  SSA B 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.735 -0.154 2.00e-02 2.50e+03 5.89e+01
  bond pdb=" O5' SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.581  1.733 -0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" O2S SSA A 601 "
       pdb=" S1  SSA A 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.586 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 7728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 10717
        4.04 -     8.08: 40
        8.08 -    12.11: 11
       12.11 -    16.15: 0
       16.15 -    20.19: 2
  Bond angle restraints: 10770
  Sorted by residual:
  angle pdb=" C3'   U C  72 "
        pdb=" O3'   U C  72 "
        pdb=" P     G C  73 "
      ideal   model   delta    sigma   weight residual
     120.20  109.80   10.40 1.50e+00 4.44e-01 4.80e+01
  angle pdb=" O1S SSA B 601 "
        pdb=" S1  SSA B 601 "
        pdb=" O2S SSA B 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.15   20.19 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" O1S SSA A 601 "
        pdb=" S1  SSA A 601 "
        pdb=" O2S SSA A 601 "
      ideal   model   delta    sigma   weight residual
     121.34  101.15   20.19 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" C3'   U C  71 "
        pdb=" O3'   U C  71 "
        pdb=" P     U C  72 "
      ideal   model   delta    sigma   weight residual
     120.20  111.06    9.14 1.50e+00 4.44e-01 3.71e+01
  angle pdb=" C   HIS A 226 "
        pdb=" N   ARG A 227 "
        pdb=" CA  ARG A 227 "
      ideal   model   delta    sigma   weight residual
     122.93  113.99    8.94 1.51e+00 4.39e-01 3.51e+01
  ... (remaining 10765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.51: 4491
       32.51 -    65.02: 269
       65.02 -    97.54: 39
       97.54 -   130.05: 0
      130.05 -   162.56: 1
  Dihedral angle restraints: 4800
    sinusoidal: 2589
      harmonic: 2211
  Sorted by residual:
  dihedral pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
           pdb=" N1    U C   9 "
           pdb=" C2    U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00  162.24   69.76     1      1.70e+01 3.46e-03 2.17e+01
  dihedral pdb=" C5'   U C   9 "
           pdb=" C4'   U C   9 "
           pdb=" C3'   U C   9 "
           pdb=" O3'   U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  116.13   30.87     1      8.00e+00 1.56e-02 2.12e+01
  dihedral pdb=" C3'   U C   9 "
           pdb=" C4'   U C   9 "
           pdb=" O4'   U C   9 "
           pdb=" C1'   U C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   24.84  -26.84     1      8.00e+00 1.56e-02 1.62e+01
  ... (remaining 4797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1187
       0.110 -    0.220: 40
       0.220 -    0.329: 2
       0.329 -    0.439: 3
       0.439 -    0.549: 3
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CA  SSA A 601 "
            pdb=" CB  SSA A 601 "
            pdb=" C9  SSA A 601 "
            pdb=" N10 SSA A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.02    0.55 2.00e-01 2.50e+01 7.53e+00
  chirality pdb=" CA  SSA B 601 "
            pdb=" CB  SSA B 601 "
            pdb=" C9  SSA B 601 "
            pdb=" N10 SSA B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -3.01    0.55 2.00e-01 2.50e+01 7.43e+00
  chirality pdb=" P     U C  71 "
            pdb=" OP1   U C  71 "
            pdb=" OP2   U C  71 "
            pdb=" O5'   U C  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.88   -0.47 2.00e-01 2.50e+01 5.54e+00
  ... (remaining 1232 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 226 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   HIS A 226 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   HIS A 226 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A 227 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  71 "   -0.012 2.00e-02 2.50e+03   1.25e-02 3.50e+00
        pdb=" N1    U C  71 "    0.018 2.00e-02 2.50e+03
        pdb=" C2    U C  71 "    0.020 2.00e-02 2.50e+03
        pdb=" O2    U C  71 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    U C  71 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4    U C  71 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U C  71 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    U C  71 "    0.012 2.00e-02 2.50e+03
        pdb=" C6    U C  71 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 457 "   -0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO B 458 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 458 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 458 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 207
        2.68 -     3.24: 6870
        3.24 -     3.79: 12206
        3.79 -     4.35: 15896
        4.35 -     4.90: 25105
  Nonbonded interactions: 60284
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" OP2   G C   1 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OE2 GLU A 352 "
            pdb=" OG  SSA A 601 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OE2 GLU B 352 "
            pdb=" OG  SSA B 601 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OE2 GLU A 352 "
            pdb=" N10 SSA A 601 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   GLU B 418 "
            pdb=" NH1 ARG B 459 "
     model   vdw
     2.246 3.120
  ... (remaining 60279 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.240
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6029
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      :  0.008   0.191   7733  Z= 0.394
  Angle     :  0.732  20.191  10770  Z= 0.369
  Chirality :  0.051   0.549   1235
  Planarity :  0.003   0.036   1178
  Dihedral  : 19.198 162.558   3378
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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: -0.66 (0.29), residues: 760
  helix:  1.87 (0.30), residues: 285
  sheet: -1.42 (0.46), residues: 105
  loop : -2.11 (0.27), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 409 
 HIS   0.002   0.000   HIS A 347 
 PHE   0.007   0.000   PHE A 348 
 TYR   0.006   0.000   TYR B 230 
 ARG   0.005   0.000   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11885 (  338)
  hydrogen bonds       : angle       6.40850 (  926)
  covalent geometry    : bond        0.00775 ( 7733)
  covalent geometry    : angle       0.73188 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7135 (mtm-85)
REVERT: A  218 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7629 (mmmt)
REVERT: A  244 ASN cc_start: 0.7760 (m-40) cc_final: 0.7385 (m110)
REVERT: A  366 GLN cc_start: 0.7153 (pt0) cc_final: 0.6864 (tm-30)
REVERT: A  438 GLN cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0)
REVERT: A  451 ASN cc_start: 0.7540 (p0) cc_final: 0.6953 (p0)
REVERT: A  460 LEU cc_start: 0.7512 (mm) cc_final: 0.7277 (mm)
REVERT: A  466 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6031 (mt-10)
REVERT: B  143 ARG cc_start: 0.6815 (mmm-85) cc_final: 0.5986 (ttm170)
REVERT: B  203 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7094 (mtm-85)
REVERT: B  313 VAL cc_start: 0.8292 (t) cc_final: 0.8066 (m)
REVERT: B  332 GLU cc_start: 0.7442 (tp30) cc_final: 0.7221 (mm-30)
REVERT: B  451 ASN cc_start: 0.8027 (p0) cc_final: 0.7425 (p0)
REVERT: B  499 GLN cc_start: 0.7939 (tp40) cc_final: 0.7269 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2991
  time to fit residues: 79.2974
Evaluate side-chains
  113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 217 GLN
A 346 HIS
A 495 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.172825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139940 restraints weight = 8795.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142778 restraints weight = 5025.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.144646 restraints weight = 3459.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   7733  Z= 0.266
  Angle     :  0.718   7.400  10770  Z= 0.357
  Chirality :  0.045   0.229   1235
  Planarity :  0.005   0.045   1178
  Dihedral  : 18.451 169.060   1891
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 17.87 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.30), residues: 760
  helix:  1.55 (0.30), residues: 289
  sheet: -0.70 (0.47), residues: 100
  loop : -1.92 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B  93 
 HIS   0.007   0.002   HIS A 222 
 PHE   0.017   0.002   PHE A 245 
 TYR   0.022   0.002   TYR B 401 
 ARG   0.008   0.001   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05305 (  338)
  hydrogen bonds       : angle       5.04827 (  926)
  covalent geometry    : bond        0.00628 ( 7733)
  covalent geometry    : angle       0.71826 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8539 (m-40) cc_final: 0.8130 (m110)
REVERT: A  322 MET cc_start: 0.7725 (mpp) cc_final: 0.7386 (mtt)
REVERT: B  143 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7061 (ttm170)
REVERT: B  309 MET cc_start: 0.8838 (ttt) cc_final: 0.8556 (ttt)
  outliers start: 33
  outliers final: 24
  residues processed: 133
  average time/residue: 0.2611
  time to fit residues: 44.6288
Evaluate side-chains
  111 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 244 ASN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 GLN
B 244 ASN
** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.177477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.145594 restraints weight = 8779.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.148312 restraints weight = 4902.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.149967 restraints weight = 3370.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7733  Z= 0.114
  Angle     :  0.514   6.704  10770  Z= 0.255
  Chirality :  0.037   0.161   1235
  Planarity :  0.004   0.031   1178
  Dihedral  : 18.070 168.371   1891
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.26 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  0.04 (0.30), residues: 760
  helix:  2.07 (0.31), residues: 291
  sheet: -0.36 (0.47), residues: 100
  loop : -1.64 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 409 
 HIS   0.005   0.001   HIS A 190 
 PHE   0.011   0.001   PHE A 371 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.013   0.001   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03591 (  338)
  hydrogen bonds       : angle       4.52346 (  926)
  covalent geometry    : bond        0.00259 ( 7733)
  covalent geometry    : angle       0.51401 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8081 (m110) cc_final: 0.7778 (m110)
REVERT: A  307 TYR cc_start: 0.8794 (t80) cc_final: 0.8436 (t80)
REVERT: A  322 MET cc_start: 0.7446 (mpp) cc_final: 0.6973 (mtt)
REVERT: B   64 CYS cc_start: 0.5945 (t) cc_final: 0.5744 (t)
REVERT: B  143 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.6993 (ttm170)
REVERT: B  451 ASN cc_start: 0.8470 (p0) cc_final: 0.8063 (p0)
REVERT: B  498 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8565 (mt)
  outliers start: 23
  outliers final: 14
  residues processed: 111
  average time/residue: 0.3262
  time to fit residues: 47.9415
Evaluate side-chains
  103 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 2.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  498 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 ASN
B 277 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.172540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.140599 restraints weight = 8695.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.143256 restraints weight = 4953.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144970 restraints weight = 3425.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7733  Z= 0.181
  Angle     :  0.584   6.904  10770  Z= 0.291
  Chirality :  0.040   0.166   1235
  Planarity :  0.004   0.035   1178
  Dihedral  : 17.891 168.417   1891
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 19.26 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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 (0.29), residues: 760
  helix:  1.79 (0.30), residues: 296
  sheet: -0.67 (0.46), residues: 109
  loop : -1.70 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 409 
 HIS   0.004   0.001   HIS A 385 
 PHE   0.019   0.002   PHE A 291 
 TYR   0.017   0.002   TYR B  45 
 ARG   0.006   0.001   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  338)
  hydrogen bonds       : angle       4.58565 (  926)
  covalent geometry    : bond        0.00427 ( 7733)
  covalent geometry    : angle       0.58366 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 87
  time to evaluate  : 2.043 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8196 (m-40) cc_final: 0.7694 (m110)
REVERT: A  282 GLN cc_start: 0.8025 (mp10) cc_final: 0.7567 (mt0)
REVERT: B  143 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7061 (ttm170)
  outliers start: 39
  outliers final: 26
  residues processed: 113
  average time/residue: 0.2984
  time to fit residues: 43.3362
Evaluate side-chains
  104 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 80 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 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 = 0.4024 r_free = 0.4024 target = 0.173375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.141204 restraints weight = 8640.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.143982 restraints weight = 4836.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.145756 restraints weight = 3322.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7733  Z= 0.138
  Angle     :  0.547   6.991  10770  Z= 0.273
  Chirality :  0.038   0.162   1235
  Planarity :  0.004   0.035   1178
  Dihedral  : 17.672 168.222   1891
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 19.57 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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: -0.07 (0.30), residues: 760
  helix:  1.89 (0.31), residues: 296
  sheet: -0.63 (0.46), residues: 110
  loop : -1.61 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 409 
 HIS   0.003   0.001   HIS A 385 
 PHE   0.016   0.001   PHE A 291 
 TYR   0.013   0.001   TYR B  45 
 ARG   0.010   0.001   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  338)
  hydrogen bonds       : angle       4.50888 (  926)
  covalent geometry    : bond        0.00321 ( 7733)
  covalent geometry    : angle       0.54701 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 85
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  244 ASN cc_start: 0.7995 (m-40) cc_final: 0.7445 (m110)
REVERT: A  282 GLN cc_start: 0.8043 (mp10) cc_final: 0.7670 (mt0)
REVERT: B   64 CYS cc_start: 0.6169 (t) cc_final: 0.5923 (t)
REVERT: B  143 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7030 (ttm170)
REVERT: B  258 MET cc_start: 0.8128 (mtp) cc_final: 0.7904 (ttm)
REVERT: B  322 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7514 (mtp)
REVERT: B  432 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7127 (mtt-85)
  outliers start: 35
  outliers final: 25
  residues processed: 109
  average time/residue: 0.2537
  time to fit residues: 35.4068
Evaluate side-chains
  102 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  432 ARG
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 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 = 0.4022 r_free = 0.4022 target = 0.172684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.140169 restraints weight = 8685.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142908 restraints weight = 4918.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144679 restraints weight = 3404.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7733  Z= 0.118
  Angle     :  0.527   7.148  10770  Z= 0.264
  Chirality :  0.037   0.160   1235
  Planarity :  0.004   0.030   1178
  Dihedral  : 17.499 167.983   1891
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 20.65 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  0.13 (0.30), residues: 760
  helix:  1.98 (0.31), residues: 296
  sheet: -0.33 (0.46), residues: 110
  loop : -1.49 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 409 
 HIS   0.002   0.001   HIS A 385 
 PHE   0.015   0.001   PHE A 371 
 TYR   0.011   0.001   TYR B  45 
 ARG   0.007   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  338)
  hydrogen bonds       : angle       4.43633 (  926)
  covalent geometry    : bond        0.00275 ( 7733)
  covalent geometry    : angle       0.52744 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7990 (m-40) cc_final: 0.7479 (m110)
REVERT: A  282 GLN cc_start: 0.8129 (mp10) cc_final: 0.7790 (mt0)
REVERT: A  338 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7717 (pp20)
REVERT: B   64 CYS cc_start: 0.6143 (t) cc_final: 0.5901 (t)
REVERT: B  143 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7028 (ttm170)
REVERT: B  168 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7108 (mp)
REVERT: B  432 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7177 (mtt-85)
  outliers start: 31
  outliers final: 26
  residues processed: 105
  average time/residue: 0.2269
  time to fit residues: 31.5124
Evaluate side-chains
  102 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 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 = 0.3951 r_free = 0.3951 target = 0.165746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133072 restraints weight = 8681.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.135638 restraints weight = 5010.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.137295 restraints weight = 3513.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.5136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   7733  Z= 0.246
  Angle     :  0.661   7.293  10770  Z= 0.331
  Chirality :  0.042   0.165   1235
  Planarity :  0.005   0.030   1178
  Dihedral  : 17.668 167.800   1891
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 19.57 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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: -0.22 (0.30), residues: 760
  helix:  1.70 (0.30), residues: 291
  sheet: -0.37 (0.48), residues: 108
  loop : -1.70 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 409 
 HIS   0.005   0.001   HIS A 385 
 PHE   0.024   0.002   PHE A 291 
 TYR   0.020   0.002   TYR B  45 
 ARG   0.006   0.001   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  338)
  hydrogen bonds       : angle       4.78713 (  926)
  covalent geometry    : bond        0.00580 ( 7733)
  covalent geometry    : angle       0.66122 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 81
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.8175 (m-40) cc_final: 0.7947 (m110)
REVERT: A  282 GLN cc_start: 0.8085 (mp10) cc_final: 0.7760 (mt0)
REVERT: A  338 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7922 (pp20)
REVERT: B  203 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7571 (mtm-85)
REVERT: B  432 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7252 (mtt-85)
  outliers start: 40
  outliers final: 32
  residues processed: 111
  average time/residue: 0.2203
  time to fit residues: 33.4874
Evaluate side-chains
  110 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 77
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 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 = 0.3997 r_free = 0.3997 target = 0.170372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.138302 restraints weight = 8724.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.140920 restraints weight = 4995.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142624 restraints weight = 3458.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7733  Z= 0.128
  Angle     :  0.545   7.494  10770  Z= 0.275
  Chirality :  0.037   0.160   1235
  Planarity :  0.004   0.033   1178
  Dihedral  : 17.546 167.556   1891
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 20.49 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  0.01 (0.30), residues: 760
  helix:  2.01 (0.31), residues: 290
  sheet: -0.38 (0.47), residues: 110
  loop : -1.63 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 409 
 HIS   0.003   0.001   HIS A 385 
 PHE   0.014   0.001   PHE A 371 
 TYR   0.012   0.001   TYR B 230 
 ARG   0.006   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  338)
  hydrogen bonds       : angle       4.55691 (  926)
  covalent geometry    : bond        0.00298 ( 7733)
  covalent geometry    : angle       0.54451 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 73
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7991 (m-40) cc_final: 0.7395 (m110)
REVERT: A  282 GLN cc_start: 0.8023 (mp10) cc_final: 0.7781 (mt0)
REVERT: A  338 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7998 (pp20)
REVERT: B  203 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7516 (mtm-85)
REVERT: B  432 ARG cc_start: 0.7674 (mtt90) cc_final: 0.7149 (mtt-85)
  outliers start: 33
  outliers final: 26
  residues processed: 98
  average time/residue: 0.2034
  time to fit residues: 27.5874
Evaluate side-chains
  100 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 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 = 0.3987 r_free = 0.3987 target = 0.169314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.136829 restraints weight = 8808.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139521 restraints weight = 5006.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.141273 restraints weight = 3470.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.5183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7733  Z= 0.143
  Angle     :  0.555   7.605  10770  Z= 0.279
  Chirality :  0.038   0.159   1235
  Planarity :  0.004   0.031   1178
  Dihedral  : 17.507 167.357   1891
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 21.11 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  0.05 (0.30), residues: 760
  helix:  2.01 (0.31), residues: 291
  sheet: -0.36 (0.48), residues: 110
  loop : -1.58 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 409 
 HIS   0.003   0.001   HIS A 385 
 PHE   0.015   0.001   PHE A 371 
 TYR   0.016   0.001   TYR B 153 
 ARG   0.006   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  338)
  hydrogen bonds       : angle       4.53790 (  926)
  covalent geometry    : bond        0.00337 ( 7733)
  covalent geometry    : angle       0.55526 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7999 (m-40) cc_final: 0.7425 (m110)
REVERT: A  282 GLN cc_start: 0.7976 (mp10) cc_final: 0.7758 (mt0)
REVERT: A  338 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8029 (pp20)
REVERT: B  203 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7509 (mtm-85)
REVERT: B  432 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7140 (mtt-85)
  outliers start: 31
  outliers final: 26
  residues processed: 98
  average time/residue: 0.2068
  time to fit residues: 28.5372
Evaluate side-chains
  99 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 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 = 0.3997 r_free = 0.3997 target = 0.170227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.137788 restraints weight = 8810.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.140512 restraints weight = 4998.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142288 restraints weight = 3457.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7733  Z= 0.131
  Angle     :  0.543   7.705  10770  Z= 0.273
  Chirality :  0.037   0.159   1235
  Planarity :  0.004   0.031   1178
  Dihedral  : 17.475 167.301   1891
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.73 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  0.14 (0.30), residues: 760
  helix:  2.08 (0.30), residues: 291
  sheet: -0.36 (0.47), residues: 112
  loop : -1.51 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 409 
 HIS   0.004   0.001   HIS A 385 
 PHE   0.014   0.001   PHE A 371 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.006   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03522 (  338)
  hydrogen bonds       : angle       4.47967 (  926)
  covalent geometry    : bond        0.00309 ( 7733)
  covalent geometry    : angle       0.54329 (10770)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 ASN cc_start: 0.7940 (m-40) cc_final: 0.7449 (m110)
REVERT: A  282 GLN cc_start: 0.7982 (mp10) cc_final: 0.7775 (mt0)
REVERT: A  338 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8020 (pp20)
REVERT: B  203 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7497 (mtm-85)
REVERT: B  432 ARG cc_start: 0.7585 (mtt90) cc_final: 0.7136 (mtt-85)
  outliers start: 27
  outliers final: 26
  residues processed: 97
  average time/residue: 0.2031
  time to fit residues: 26.6859
Evaluate side-chains
  101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  430 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  499 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   80 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  496 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 78 optimal weight:   20.0000
   chunk 62 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 375 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 = 0.4016 r_free = 0.4016 target = 0.172210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.139862 restraints weight = 8736.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.142609 restraints weight = 4951.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.144322 restraints weight = 3428.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7733  Z= 0.109
  Angle     :  0.528   7.651  10770  Z= 0.266
  Chirality :  0.037   0.158   1235
  Planarity :  0.004   0.032   1178
  Dihedral  : 17.433 167.210   1891
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 22.03 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    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:  0.33 (0.30), residues: 760
  helix:  2.24 (0.31), residues: 291
  sheet: -0.24 (0.48), residues: 110
  loop : -1.41 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 409 
 HIS   0.002   0.001   HIS A 385 
 PHE   0.013   0.001   PHE A 371 
 TYR   0.040   0.001   TYR B 153 
 ARG   0.011   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03225 (  338)
  hydrogen bonds       : angle       4.45688 (  926)
  covalent geometry    : bond        0.00251 ( 7733)
  covalent geometry    : angle       0.52766 (10770)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2867.76 seconds
wall clock time: 52 minutes 33.61 seconds (3153.61 seconds total)