Starting phenix.real_space_refine
on Thu Jun  5 11:47:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wcn_37444/06_2025/8wcn_37444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wcn_37444/06_2025/8wcn_37444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wcn_37444/06_2025/8wcn_37444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wcn_37444/06_2025/8wcn_37444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wcn_37444/06_2025/8wcn_37444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wcn_37444/06_2025/8wcn_37444.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      2      5.21       5
     S      26      5.16       5
     C    3894      2.51       5
     N    1061      2.21       5
     O    1091      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6086
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2982
          Classifications: {'peptide': 379}
          Link IDs: {'PTRANS': 10, 'TRANS': 368}
    Chain: "B"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 2974
          Classifications: {'peptide': 378}
          Link IDs: {'PTRANS': 10, 'TRANS': 367}
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 65
          Unusual residues: {' MG': 1, 'G2P': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 65
          Unusual residues: {' MG': 1, 'G2P': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.54, per 1000 atoms: 0.75
  Number of scatterers: 6086
  At special positions: 0
  Unit cell: (61.456, 74.148, 124.248, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      26     16.00
     P      12     15.00
     Mg      2     11.99
     O    1091      8.00
     N    1061      7.00
     C    3894      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: 1.63
  Conformation dependent library (CDL) restraints added in 839.2 milliseconds
  

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1386

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      72.9% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 24
    Processing helix  chain 'A' and resid 31 through 46
    Processing helix  chain 'A' and resid 46 through 72
      removed outlier: 3.523A  pdb=" N   ARG A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ARG A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA A  52 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   MET A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 99
      removed outlier: 3.595A  pdb=" N   PHE A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 102
      No H-bonds generated for 'chain 'A' and resid 100 through 102'
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 107 through 112
    Processing helix  chain 'A' and resid 114 through 136
      removed outlier: 3.727A  pdb=" N   ASP A 130 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   PHE A 133 " --> pdb=" O   CYS A 129 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 152
      removed outlier: 3.501A  pdb=" N   GLY A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 150 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 182
    Processing helix  chain 'A' and resid 187 through 232
      removed outlier: 3.611A  pdb=" N   LEU A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 259
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 4.166A  pdb=" N   TYR A 275 " --> pdb=" O   ASP A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 298
      removed outlier: 3.522A  pdb=" N   GLN A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 340
    Processing helix  chain 'A' and resid 367 through 384
      removed outlier: 3.598A  pdb=" N   LEU A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 24
    Processing helix  chain 'B' and resid 31 through 46
    Processing helix  chain 'B' and resid 46 through 72
    Processing helix  chain 'B' and resid 77 through 99
      removed outlier: 3.513A  pdb=" N   PHE B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 104
      removed outlier: 3.795A  pdb=" N   PHE B 103 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 99 through 104'
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 3.558A  pdb=" N   ARG B 108 " --> pdb=" O   PRO B 105 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   LYS B 109 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 105 through 109'
    Processing helix  chain 'B' and resid 110 through 134
      Proline residue:  B 116  - end of helix
      removed outlier: 3.883A  pdb=" N   ILE B 122 " --> pdb=" O   CYS B 118 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASP B 130 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE B 133 " --> pdb=" O   CYS B 129 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLU B 134 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 152
    Processing helix  chain 'B' and resid 160 through 182
      removed outlier: 3.853A  pdb=" N   PHE B 179 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 232
      removed outlier: 3.693A  pdb=" N   ALA B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 259
    Processing helix  chain 'B' and resid 271 through 280
      removed outlier: 4.047A  pdb=" N   TYR B 275 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 287
      removed outlier: 3.695A  pdb=" N   ASP B 285 " --> pdb=" O   HIS B 281 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 298
      removed outlier: 3.789A  pdb=" N   GLY B 298 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 341
      removed outlier: 4.076A  pdb=" N   GLY B 341 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 4.332A  pdb=" N   ARG B 377 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   ALA B 378 " --> pdb=" O   GLU B 374 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310
      removed outlier: 3.620A  pdb=" N   LEU A 309 " --> pdb=" O   GLU A 313 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   GLU A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ARG A 391 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 305 through 308
      removed outlier: 3.907A  pdb=" N   ARG B 391 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1203
        1.33 -     1.46: 2056
        1.46 -     1.59: 2893
        1.59 -     1.72: 12
        1.72 -     1.85: 48
  Bond restraints: 6212
  Sorted by residual:
  bond pdb=" CA  ASP A 130 "
       pdb=" C   ASP A 130 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.058 9.90e-03 1.02e+04 3.46e+01
  bond pdb=" N   VAL B 390 "
       pdb=" CA  VAL B 390 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.19e-02 7.06e+03 8.72e+00
  bond pdb=" CA  ASP B 130 "
       pdb=" C   ASP B 130 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.038 1.32e-02 5.74e+03 8.39e+00
  bond pdb=" N   ARG B 391 "
       pdb=" CA  ARG B 391 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.031 1.23e-02 6.61e+03 6.48e+00
  bond pdb=" N   ASP B 384 "
       pdb=" CA  ASP B 384 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.27e-02 6.20e+03 6.44e+00
  ... (remaining 6207 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 8252
        1.94 -     3.89: 144
        3.89 -     5.83: 38
        5.83 -     7.77: 14
        7.77 -     9.72: 7
  Bond angle restraints: 8455
  Sorted by residual:
  angle pdb=" N   GLN B 219 "
        pdb=" CA  GLN B 219 "
        pdb=" C   GLN B 219 "
      ideal   model   delta    sigma   weight residual
     112.45  105.11    7.34 1.39e+00 5.18e-01 2.79e+01
  angle pdb=" N   ALA B 286 "
        pdb=" CA  ALA B 286 "
        pdb=" C   ALA B 286 "
      ideal   model   delta    sigma   weight residual
     111.75  106.80    4.95 1.28e+00 6.10e-01 1.49e+01
  angle pdb=" CA  ARG A 377 "
        pdb=" CB  ARG A 377 "
        pdb=" CG  ARG A 377 "
      ideal   model   delta    sigma   weight residual
     114.10  121.70   -7.60 2.00e+00 2.50e-01 1.44e+01
  angle pdb=" CB  MET A  91 "
        pdb=" CG  MET A  91 "
        pdb=" SD  MET A  91 "
      ideal   model   delta    sigma   weight residual
     112.70  122.42   -9.72 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" CA  ALA B 389 "
        pdb=" C   ALA B 389 "
        pdb=" O   ALA B 389 "
      ideal   model   delta    sigma   weight residual
     121.87  118.37    3.50 1.10e+00 8.26e-01 1.01e+01
  ... (remaining 8450 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 3200
       16.86 -    33.71: 347
       33.71 -    50.56: 110
       50.56 -    67.42: 42
       67.42 -    84.27: 8
  Dihedral angle restraints: 3707
    sinusoidal: 1540
      harmonic: 2167
  Sorted by residual:
  dihedral pdb=" CA  MET B 366 "
           pdb=" C   MET B 366 "
           pdb=" N   GLY B 367 "
           pdb=" CA  GLY B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ASP B 130 "
           pdb=" CB  ASP B 130 "
           pdb=" CG  ASP B 130 "
           pdb=" OD1 ASP B 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.90   59.90     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CB  GLU A  35 "
           pdb=" CG  GLU A  35 "
           pdb=" CD  GLU A  35 "
           pdb=" OE1 GLU A  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.27   84.27     1      3.00e+01 1.11e-03 9.60e+00
  ... (remaining 3704 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 714
       0.040 -    0.079: 170
       0.079 -    0.119: 50
       0.119 -    0.159: 6
       0.159 -    0.199: 5
  Chirality restraints: 945
  Sorted by residual:
  chirality pdb=" CB  ILE B 265 "
            pdb=" CA  ILE B 265 "
            pdb=" CG1 ILE B 265 "
            pdb=" CG2 ILE B 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.85e-01
  chirality pdb=" CG  LEU A 192 "
            pdb=" CB  LEU A 192 "
            pdb=" CD1 LEU A 192 "
            pdb=" CD2 LEU A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" CA  LEU B 148 "
            pdb=" N   LEU B 148 "
            pdb=" C   LEU B 148 "
            pdb=" CB  LEU B 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 942 not shown)

  Planarity restraints: 1064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 218 "   -0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   GLU B 218 "    0.059 2.00e-02 2.50e+03
        pdb=" O   GLU B 218 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLN B 219 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 187 "    0.013 2.00e-02 2.50e+03   2.51e-02 6.28e+00
        pdb=" C   ASN B 187 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ASN B 187 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B 188 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 242 "    0.121 9.50e-02 1.11e+02   5.53e-02 3.39e+00
        pdb=" NE  ARG B 242 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 242 "    0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 242 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 242 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1061 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 38
        2.50 -     3.10: 4380
        3.10 -     3.70: 9763
        3.70 -     4.30: 12907
        4.30 -     4.90: 20597
  Nonbonded interactions: 47685
  Sorted by model distance:
  nonbonded pdb=" O1B G2P A 501 "
            pdb="MG    MG A 503 "
     model   vdw
     1.902 2.170
  nonbonded pdb=" OE2 GLU A 312 "
            pdb="MG    MG A 503 "
     model   vdw
     1.982 2.170
  nonbonded pdb=" O3B G2P B 501 "
            pdb="MG    MG B 503 "
     model   vdw
     2.011 2.170
  nonbonded pdb=" OE1 GLU B 312 "
            pdb="MG    MG B 503 "
     model   vdw
     2.014 2.170
  nonbonded pdb=" O3G G2P A 501 "
            pdb="MG    MG A 503 "
     model   vdw
     2.078 2.170
  ... (remaining 47680 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 15 through 392 or resid 501 through 503))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             61.910
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.260
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   83.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
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      :  0.004   0.058   6212  Z= 0.215
  Angle     :  0.725   9.717   8455  Z= 0.366
  Chirality :  0.040   0.199    945
  Planarity :  0.004   0.055   1064
  Dihedral  : 16.646  84.273   2321
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 19.30 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.30), residues: 753
  helix:  0.95 (0.23), residues: 509
  sheet:  1.85 (0.57), residues: 59
  loop : -1.75 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.002   0.000   HIS B 136 
 PHE   0.008   0.001   PHE B 103 
 TYR   0.016   0.001   TYR A 244 
 ARG   0.022   0.001   ARG B 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24461 (  424)
  hydrogen bonds       : angle       7.25728 ( 1263)
  covalent geometry    : bond        0.00357 ( 6212)
  covalent geometry    : angle       0.72473 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: A  303 LEU cc_start: 0.7989 (mt) cc_final: 0.7634 (tt)
REVERT: B   41 PHE cc_start: 0.7401 (t80) cc_final: 0.7103 (t80)
REVERT: B  313 GLU cc_start: 0.6613 (pp20) cc_final: 0.6280 (pp20)
REVERT: B  338 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8021 (mt-10)
  outliers start: 3
  outliers final: 1
  residues processed: 121
  average time/residue: 0.2990
  time to fit residues: 45.0932
Evaluate side-chains
  110 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  130 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
B 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.168482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.143410 restraints weight = 10455.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.60
r_work: 0.3829 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6212  Z= 0.175
  Angle     :  0.670   8.433   8455  Z= 0.331
  Chirality :  0.045   0.364    945
  Planarity :  0.004   0.027   1064
  Dihedral  : 10.589  82.479    973
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 17.80 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.32), residues: 753
  helix:  1.67 (0.23), residues: 514
  sheet:  1.66 (0.61), residues: 59
  loop : -1.88 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.002   0.001   HIS A 136 
 PHE   0.016   0.002   PHE B 207 
 TYR   0.010   0.001   TYR A 244 
 ARG   0.003   0.001   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05597 (  424)
  hydrogen bonds       : angle       4.70584 ( 1263)
  covalent geometry    : bond        0.00386 ( 6212)
  covalent geometry    : angle       0.66971 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8201 (p) cc_final: 0.7687 (p)
REVERT: A   85 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6100 (tp)
REVERT: A  185 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6686 (tm-30)
REVERT: A  228 MET cc_start: 0.7957 (ttm) cc_final: 0.7740 (ttm)
REVERT: A  377 ARG cc_start: 0.8097 (tpm-80) cc_final: 0.7650 (tpm-80)
REVERT: B   63 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6925 (tp)
REVERT: B   70 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7967 (ttp)
REVERT: B  209 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7177 (tp)
REVERT: B  278 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6889 (m-70)
  outliers start: 25
  outliers final: 12
  residues processed: 125
  average time/residue: 0.2311
  time to fit residues: 35.9309
Evaluate side-chains
  120 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  278 HIS
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0270
   chunk 41 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.6442

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.168750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.143762 restraints weight = 10430.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.68
r_work: 0.3827 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6212  Z= 0.157
  Angle     :  0.666  10.335   8455  Z= 0.317
  Chirality :  0.043   0.318    945
  Planarity :  0.003   0.026   1064
  Dihedral  :  9.932  84.107    973
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 18.47 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.31), residues: 753
  helix:  1.67 (0.23), residues: 515
  sheet:  1.63 (0.62), residues: 59
  loop : -2.03 (0.46), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.020   0.002   PHE A  81 
 TYR   0.007   0.001   TYR A 319 
 ARG   0.004   0.000   ARG B 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05156 (  424)
  hydrogen bonds       : angle       4.52690 ( 1263)
  covalent geometry    : bond        0.00347 ( 6212)
  covalent geometry    : angle       0.66591 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7116 (pm20) cc_final: 0.6882 (pm20)
REVERT: A   46 SER cc_start: 0.8251 (p) cc_final: 0.7761 (p)
REVERT: A   85 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6008 (tp)
REVERT: A  185 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: A  218 GLU cc_start: 0.7361 (tt0) cc_final: 0.6996 (tt0)
REVERT: A  228 MET cc_start: 0.8031 (ttm) cc_final: 0.7705 (ttm)
REVERT: A  377 ARG cc_start: 0.8132 (tpm-80) cc_final: 0.7716 (tpm-80)
REVERT: B   41 PHE cc_start: 0.7712 (t80) cc_final: 0.7373 (t80)
REVERT: B   63 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6858 (tp)
REVERT: B   70 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8060 (ttp)
REVERT: B  209 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7145 (tp)
REVERT: B  278 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6914 (m-70)
REVERT: B  290 GLN cc_start: 0.7238 (mp10) cc_final: 0.6937 (mp10)
REVERT: B  325 ASN cc_start: 0.8333 (t0) cc_final: 0.8125 (t0)
REVERT: B  327 LEU cc_start: 0.8978 (mm) cc_final: 0.8685 (mm)
REVERT: B  332 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7502 (ptt-90)
  outliers start: 36
  outliers final: 21
  residues processed: 132
  average time/residue: 0.2345
  time to fit residues: 39.2951
Evaluate side-chains
  138 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  278 HIS
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  332 ARG
Chi-restraints excluded: chain B residue  368 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 63 optimal weight:    0.2980
   chunk 73 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.169718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.145269 restraints weight = 10594.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.71
r_work: 0.3807 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6212  Z= 0.157
  Angle     :  0.667  12.415   8455  Z= 0.316
  Chirality :  0.043   0.366    945
  Planarity :  0.003   0.027   1064
  Dihedral  :  9.759  85.890    973
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 21.13 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.31), residues: 753
  helix:  1.78 (0.23), residues: 514
  sheet:  1.41 (0.62), residues: 59
  loop : -2.05 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.016   0.002   PHE A  81 
 TYR   0.007   0.001   TYR A 244 
 ARG   0.005   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04877 (  424)
  hydrogen bonds       : angle       4.42554 ( 1263)
  covalent geometry    : bond        0.00347 ( 6212)
  covalent geometry    : angle       0.66725 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7218 (pm20) cc_final: 0.7001 (pm20)
REVERT: A   46 SER cc_start: 0.8287 (p) cc_final: 0.7844 (p)
REVERT: A   85 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6113 (tp)
REVERT: A  185 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6529 (tm-30)
REVERT: A  228 MET cc_start: 0.8030 (ttm) cc_final: 0.7678 (ttm)
REVERT: A  377 ARG cc_start: 0.8077 (tpm-80) cc_final: 0.7763 (tpm-80)
REVERT: B   63 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6930 (tp)
REVERT: B   70 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8080 (ttp)
REVERT: B  209 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7163 (tp)
REVERT: B  278 HIS cc_start: 0.7020 (OUTLIER) cc_final: 0.6788 (m-70)
REVERT: B  290 GLN cc_start: 0.7178 (mp10) cc_final: 0.6899 (mp10)
REVERT: B  332 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7434 (ptt-90)
  outliers start: 31
  outliers final: 20
  residues processed: 125
  average time/residue: 0.2412
  time to fit residues: 37.8404
Evaluate side-chains
  131 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  278 HIS
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  332 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 10 optimal weight:    0.1980
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.168539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.144389 restraints weight = 10442.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.67
r_work: 0.3803 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6212  Z= 0.162
  Angle     :  0.696  14.366   8455  Z= 0.322
  Chirality :  0.043   0.386    945
  Planarity :  0.003   0.027   1064
  Dihedral  :  9.780  87.537    973
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 21.80 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.31), residues: 753
  helix:  1.79 (0.23), residues: 514
  sheet:  1.33 (0.63), residues: 59
  loop : -2.09 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.019   0.002   PHE A  81 
 TYR   0.007   0.001   TYR A 244 
 ARG   0.004   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04879 (  424)
  hydrogen bonds       : angle       4.41065 ( 1263)
  covalent geometry    : bond        0.00362 ( 6212)
  covalent geometry    : angle       0.69627 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 107
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7289 (pm20) cc_final: 0.7053 (pm20)
REVERT: A   46 SER cc_start: 0.8262 (p) cc_final: 0.7828 (p)
REVERT: A   85 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.5877 (tp)
REVERT: A  185 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6496 (tm-30)
REVERT: A  228 MET cc_start: 0.8040 (ttm) cc_final: 0.7682 (ttm)
REVERT: A  366 MET cc_start: 0.7166 (ppp) cc_final: 0.6795 (tmm)
REVERT: A  377 ARG cc_start: 0.8088 (tpm-80) cc_final: 0.7762 (tpm-80)
REVERT: B   63 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6896 (tp)
REVERT: B   70 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8108 (ttp)
REVERT: B  209 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7147 (tp)
REVERT: B  278 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6814 (m-70)
REVERT: B  290 GLN cc_start: 0.7327 (mp10) cc_final: 0.7022 (mp10)
REVERT: B  338 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6943 (mt-10)
REVERT: B  383 LYS cc_start: 0.8382 (tptp) cc_final: 0.7617 (mmmt)
  outliers start: 38
  outliers final: 26
  residues processed: 130
  average time/residue: 0.2173
  time to fit residues: 35.7563
Evaluate side-chains
  139 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 107
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 63 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0970
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.169844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.146192 restraints weight = 10304.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.65
r_work: 0.3840 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6212  Z= 0.132
  Angle     :  0.681  15.312   8455  Z= 0.316
  Chirality :  0.042   0.348    945
  Planarity :  0.003   0.024   1064
  Dihedral  :  9.524  89.814    973
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 23.13 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.32), residues: 753
  helix:  1.94 (0.23), residues: 515
  sheet:  1.33 (0.64), residues: 59
  loop : -2.07 (0.46), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.017   0.001   PHE A  81 
 TYR   0.008   0.001   TYR A 244 
 ARG   0.006   0.000   ARG A 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  424)
  hydrogen bonds       : angle       4.27996 ( 1263)
  covalent geometry    : bond        0.00279 ( 6212)
  covalent geometry    : angle       0.68084 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7253 (pm20) cc_final: 0.7010 (pm20)
REVERT: A   46 SER cc_start: 0.8233 (p) cc_final: 0.7819 (p)
REVERT: A   85 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.5971 (tp)
REVERT: A  185 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6333 (tm-30)
REVERT: A  228 MET cc_start: 0.8021 (ttm) cc_final: 0.7677 (ttm)
REVERT: A  235 LEU cc_start: 0.8822 (tt) cc_final: 0.8582 (tt)
REVERT: B   28 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6591 (mp)
REVERT: B   63 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6894 (tp)
REVERT: B  209 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: B  278 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6814 (m-70)
REVERT: B  290 GLN cc_start: 0.7267 (mp10) cc_final: 0.6945 (mp10)
REVERT: B  332 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7399 (ptt-90)
REVERT: B  383 LYS cc_start: 0.8332 (tptp) cc_final: 0.7617 (mmmt)
  outliers start: 30
  outliers final: 17
  residues processed: 125
  average time/residue: 0.2428
  time to fit residues: 38.0130
Evaluate side-chains
  127 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  332 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 66 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.168924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.144168 restraints weight = 10290.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 2.71
r_work: 0.3824 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6212  Z= 0.142
  Angle     :  0.691  14.137   8455  Z= 0.321
  Chirality :  0.043   0.404    945
  Planarity :  0.005   0.107   1064
  Dihedral  :  9.492  88.662    973
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 24.63 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.32), residues: 753
  helix:  2.02 (0.23), residues: 510
  sheet:  1.29 (0.64), residues: 59
  loop : -2.04 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  61 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.015   0.001   PHE A  81 
 TYR   0.008   0.001   TYR A 244 
 ARG   0.007   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  424)
  hydrogen bonds       : angle       4.29795 ( 1263)
  covalent geometry    : bond        0.00310 ( 6212)
  covalent geometry    : angle       0.69124 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8243 (p) cc_final: 0.7837 (p)
REVERT: A   85 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6128 (tp)
REVERT: A  185 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6355 (tm-30)
REVERT: A  288 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7848 (mm)
REVERT: A  377 ARG cc_start: 0.8011 (tpm-80) cc_final: 0.7718 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6664 (mp)
REVERT: B   63 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6900 (tp)
REVERT: B  209 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7166 (tp)
REVERT: B  218 GLU cc_start: 0.7332 (tt0) cc_final: 0.6955 (tt0)
REVERT: B  278 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6803 (m-70)
REVERT: B  290 GLN cc_start: 0.7291 (mp10) cc_final: 0.6963 (mp10)
REVERT: B  332 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7311 (ptt-90)
REVERT: B  383 LYS cc_start: 0.8288 (tptp) cc_final: 0.7586 (mmmt)
  outliers start: 30
  outliers final: 20
  residues processed: 126
  average time/residue: 0.2545
  time to fit residues: 40.0864
Evaluate side-chains
  134 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  332 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.168069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.143423 restraints weight = 10409.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 2.73
r_work: 0.3815 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6212  Z= 0.148
  Angle     :  0.692  12.581   8455  Z= 0.326
  Chirality :  0.043   0.400    945
  Planarity :  0.004   0.074   1064
  Dihedral  :  9.442  87.073    973
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 24.63 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.32), residues: 753
  helix:  2.03 (0.23), residues: 510
  sheet:  1.25 (0.65), residues: 59
  loop : -2.05 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  61 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.014   0.001   PHE A  81 
 TYR   0.008   0.001   TYR A 244 
 ARG   0.011   0.001   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04543 (  424)
  hydrogen bonds       : angle       4.32028 ( 1263)
  covalent geometry    : bond        0.00327 ( 6212)
  covalent geometry    : angle       0.69176 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7077 (pm20) cc_final: 0.6813 (pm20)
REVERT: A   46 SER cc_start: 0.8242 (p) cc_final: 0.7838 (p)
REVERT: A   85 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.5919 (tp)
REVERT: A  185 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6363 (tm-30)
REVERT: A  288 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7868 (mm)
REVERT: A  377 ARG cc_start: 0.8021 (tpm-80) cc_final: 0.7690 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6703 (mp)
REVERT: B   63 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6869 (tp)
REVERT: B   85 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6128 (tp)
REVERT: B  209 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7114 (tp)
REVERT: B  218 GLU cc_start: 0.7335 (tt0) cc_final: 0.6976 (tt0)
REVERT: B  278 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6842 (m-70)
REVERT: B  290 GLN cc_start: 0.7366 (mp10) cc_final: 0.7011 (mp10)
REVERT: B  308 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6777 (ptm160)
REVERT: B  332 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7367 (ptt-90)
REVERT: B  383 LYS cc_start: 0.8274 (tptp) cc_final: 0.7549 (mmmt)
  outliers start: 33
  outliers final: 21
  residues processed: 126
  average time/residue: 0.2957
  time to fit residues: 46.1917
Evaluate side-chains
  135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  273 LYS
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  308 ARG
Chi-restraints excluded: chain B residue  332 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0870
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
** B 388 ASN ** 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 = 0.4249 r_free = 0.4249 target = 0.166666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.141793 restraints weight = 10364.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.72
r_work: 0.3795 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6212  Z= 0.163
  Angle     :  0.700  11.691   8455  Z= 0.331
  Chirality :  0.044   0.399    945
  Planarity :  0.004   0.070   1064
  Dihedral  :  9.462  85.537    973
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 23.79 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.31), residues: 753
  helix:  1.95 (0.23), residues: 516
  sheet:  0.82 (0.63), residues: 63
  loop : -2.22 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.013   0.002   PHE A  81 
 TYR   0.008   0.001   TYR A 244 
 ARG   0.007   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04768 (  424)
  hydrogen bonds       : angle       4.37937 ( 1263)
  covalent geometry    : bond        0.00367 ( 6212)
  covalent geometry    : angle       0.69978 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8272 (p) cc_final: 0.7864 (p)
REVERT: A   85 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.5939 (tp)
REVERT: A  185 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6527 (tm-30)
REVERT: A  278 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.7150 (m-70)
REVERT: A  288 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7858 (mm)
REVERT: A  334 ARG cc_start: 0.7747 (ttm170) cc_final: 0.7456 (ttm-80)
REVERT: A  377 ARG cc_start: 0.8052 (tpm-80) cc_final: 0.7717 (tpm-80)
REVERT: B   28 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6763 (mp)
REVERT: B   63 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6919 (tp)
REVERT: B   85 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6182 (tp)
REVERT: B  209 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7144 (tp)
REVERT: B  218 GLU cc_start: 0.7338 (tt0) cc_final: 0.6808 (tt0)
REVERT: B  278 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6888 (m-70)
REVERT: B  290 GLN cc_start: 0.7394 (mp10) cc_final: 0.7057 (mp10)
REVERT: B  308 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6801 (ptm160)
REVERT: B  332 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7370 (ptt-90)
  outliers start: 36
  outliers final: 21
  residues processed: 131
  average time/residue: 0.2700
  time to fit residues: 43.9738
Evaluate side-chains
  137 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  278 HIS
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  273 LYS
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  308 ARG
Chi-restraints excluded: chain B residue  332 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.168311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.143906 restraints weight = 10268.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.67
r_work: 0.3818 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6212  Z= 0.145
  Angle     :  0.723  11.407   8455  Z= 0.338
  Chirality :  0.043   0.392    945
  Planarity :  0.004   0.062   1064
  Dihedral  :  9.340  85.583    973
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 25.79 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.32), residues: 753
  helix:  1.93 (0.23), residues: 520
  sheet:  0.72 (0.63), residues: 63
  loop : -2.32 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.014   0.001   PHE A  81 
 TYR   0.009   0.001   TYR A 244 
 ARG   0.008   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  424)
  hydrogen bonds       : angle       4.33745 ( 1263)
  covalent geometry    : bond        0.00317 ( 6212)
  covalent geometry    : angle       0.72316 ( 8455)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7094 (pm20) cc_final: 0.6841 (pm20)
REVERT: A   46 SER cc_start: 0.8246 (p) cc_final: 0.7856 (p)
REVERT: A   71 MET cc_start: 0.7209 (ppp) cc_final: 0.6981 (ppp)
REVERT: A   85 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6003 (tp)
REVERT: A  185 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6394 (tm-30)
REVERT: A  288 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7845 (mm)
REVERT: A  377 ARG cc_start: 0.8055 (tpm-80) cc_final: 0.7709 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6683 (mp)
REVERT: B   85 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6146 (tp)
REVERT: B  209 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7119 (tp)
REVERT: B  218 GLU cc_start: 0.7314 (tt0) cc_final: 0.6891 (tt0)
REVERT: B  278 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6918 (m-70)
REVERT: B  290 GLN cc_start: 0.7382 (mp10) cc_final: 0.7035 (mp10)
REVERT: B  308 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6728 (ptm160)
REVERT: B  332 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7335 (ptt-90)
REVERT: B  366 MET cc_start: 0.7650 (tmm) cc_final: 0.7379 (tmm)
  outliers start: 29
  outliers final: 19
  residues processed: 123
  average time/residue: 0.2673
  time to fit residues: 40.6057
Evaluate side-chains
  127 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  273 LYS
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  308 ARG
Chi-restraints excluded: chain B residue  332 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0070
   chunk 47 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0370
   chunk 40 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
** B 388 ASN ** 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 = 0.4281 r_free = 0.4281 target = 0.169271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.144907 restraints weight = 10474.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.72
r_work: 0.3836 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6212  Z= 0.133
  Angle     :  0.705  11.232   8455  Z= 0.331
  Chirality :  0.043   0.383    945
  Planarity :  0.003   0.024   1064
  Dihedral  :  9.185  87.464    973
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 25.79 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.32), residues: 753
  helix:  2.03 (0.23), residues: 520
  sheet:  0.70 (0.63), residues: 63
  loop : -2.36 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.014   0.001   PHE A  81 
 TYR   0.009   0.001   TYR A 244 
 ARG   0.006   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  424)
  hydrogen bonds       : angle       4.25550 ( 1263)
  covalent geometry    : bond        0.00286 ( 6212)
  covalent geometry    : angle       0.70517 ( 8455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3189.46 seconds
wall clock time: 56 minutes 55.35 seconds (3415.35 seconds total)