Starting phenix.real_space_refine
on Tue Feb 11 15:17:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wcn_37444/02_2025/8wcn_37444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wcn_37444/02_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_37444/02_2025/8wcn_37444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wcn_37444/02_2025/8wcn_37444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wcn_37444/02_2025/8wcn_37444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wcn_37444/02_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-5592/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: 4.95, per 1000 atoms: 0.81
  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: 1.81
  Conformation dependent library (CDL) restraints added in 911.2 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: 0.53
  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: 1.63

  Time building geometry restraints manager: 1.96 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:             6.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     17.060
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.290
-------------------------------------------------------------------------------
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= 0.232
  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 

*********************** 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  : 0.626 
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: 0.2575
  time to fit residues: 38.0478
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  : 0.617 
-------------------------------------------------------------------------------
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 = 0.168483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.143414 restraints weight = 10455.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.60
r_work: 0.3830 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
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= 0.246
  Angle     :  0.670   8.432   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 

*********************** 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  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8203 (p) cc_final: 0.7689 (p)
REVERT: A   85 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6100 (tp)
REVERT: A  185 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6687 (tm-30)
REVERT: A  228 MET cc_start: 0.7960 (ttm) cc_final: 0.7743 (ttm)
REVERT: A  377 ARG cc_start: 0.8089 (tpm-80) cc_final: 0.7644 (tpm-80)
REVERT: B   63 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6925 (tp)
REVERT: B   70 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7970 (ttp)
REVERT: B  209 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7176 (tp)
REVERT: B  278 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6885 (m-70)
  outliers start: 25
  outliers final: 12
  residues processed: 125
  average time/residue: 0.2312
  time to fit residues: 35.9963
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  : 0.669 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.4268 r_free = 0.4268 target = 0.167842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.142749 restraints weight = 10439.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.69
r_work: 0.3816 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6212  Z= 0.250
  Angle     :  0.675  10.197   8455  Z= 0.323
  Chirality :  0.043   0.326    945
  Planarity :  0.003   0.026   1064
  Dihedral  : 10.016  83.785    973
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 18.47 %
    Favored  : 75.37 %
  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:  1.16 (0.31), residues: 753
  helix:  1.60 (0.23), residues: 515
  sheet:  1.61 (0.62), residues: 59
  loop : -2.07 (0.46), residues: 179

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   0.020   0.002   PHE A  81 
 TYR   0.006   0.001   TYR A 319 
 ARG   0.005   0.000   ARG B 391 

*********************** 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
  143 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 106
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7115 (pm20) cc_final: 0.6880 (pm20)
REVERT: A   46 SER cc_start: 0.8264 (p) cc_final: 0.7777 (p)
REVERT: A   85 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6028 (tp)
REVERT: A  185 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6652 (tm-30)
REVERT: A  218 GLU cc_start: 0.7361 (tt0) cc_final: 0.6958 (tt0)
REVERT: A  228 MET cc_start: 0.8022 (ttm) cc_final: 0.7682 (ttm)
REVERT: A  377 ARG cc_start: 0.8124 (tpm-80) cc_final: 0.7717 (tpm-80)
REVERT: B   41 PHE cc_start: 0.7770 (t80) cc_final: 0.7413 (t80)
REVERT: B   63 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6869 (tp)
REVERT: B   70 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8086 (ttp)
REVERT: B  209 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7144 (tp)
REVERT: B  278 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6885 (m-70)
REVERT: B  290 GLN cc_start: 0.7250 (mp10) cc_final: 0.6955 (mp10)
REVERT: B  325 ASN cc_start: 0.8331 (t0) cc_final: 0.8125 (t0)
REVERT: B  327 LEU cc_start: 0.8996 (mm) cc_final: 0.8792 (mm)
REVERT: B  332 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7501 (ptt-90)
  outliers start: 37
  outliers final: 22
  residues processed: 131
  average time/residue: 0.2200
  time to fit residues: 36.1487
Evaluate side-chains
  135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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  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  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
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:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.168177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.142948 restraints weight = 10582.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.73
r_work: 0.3792 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.2855

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= 0.250
  Angle     :  0.677  12.466   8455  Z= 0.322
  Chirality :  0.044   0.397    945
  Planarity :  0.003   0.031   1064
  Dihedral  :  9.912  85.806    973
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 21.46 %
    Favored  : 73.04 %
  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:  1.18 (0.31), residues: 753
  helix:  1.67 (0.23), residues: 514
  sheet:  1.35 (0.62), residues: 59
  loop : -2.12 (0.45), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.015   0.002   PHE A  81 
 TYR   0.007   0.001   TYR A 244 
 ARG   0.005   0.000   ARG A 391 

*********************** 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
  143 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7263 (pm20) cc_final: 0.7028 (pm20)
REVERT: A   46 SER cc_start: 0.8287 (p) cc_final: 0.7848 (p)
REVERT: A   85 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.5892 (tp)
REVERT: A  185 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6589 (tm-30)
REVERT: A  228 MET cc_start: 0.8040 (ttm) cc_final: 0.7672 (ttm)
REVERT: A  377 ARG cc_start: 0.8085 (tpm-80) cc_final: 0.7785 (tpm-80)
REVERT: B   63 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6908 (tp)
REVERT: B   70 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (ttp)
REVERT: B  209 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7146 (tp)
REVERT: B  278 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6846 (m-70)
REVERT: B  290 GLN cc_start: 0.7328 (mp10) cc_final: 0.7038 (mp10)
REVERT: B  332 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7483 (ptt-90)
  outliers start: 33
  outliers final: 21
  residues processed: 128
  average time/residue: 0.2431
  time to fit residues: 38.6608
Evaluate side-chains
  135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
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  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 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  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  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:    3.9990
   chunk 54 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0070
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 = 0.4290 r_free = 0.4290 target = 0.169649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.145651 restraints weight = 10363.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.67
r_work: 0.3822 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6212  Z= 0.195
  Angle     :  0.694  14.332   8455  Z= 0.319
  Chirality :  0.042   0.382    945
  Planarity :  0.003   0.031   1064
  Dihedral  :  9.686  87.993    973
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 23.63 %
    Favored  : 70.88 %
  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:  1.34 (0.32), residues: 753
  helix:  1.80 (0.23), residues: 515
  sheet:  1.32 (0.63), residues: 59
  loop : -2.07 (0.46), residues: 179

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   0.015   0.001   PHE A  81 
 TYR   0.008   0.001   TYR A 319 
 ARG   0.004   0.000   ARG B 334 

*********************** 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
  140 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7277 (pm20) cc_final: 0.7043 (pm20)
REVERT: A   46 SER cc_start: 0.8253 (p) cc_final: 0.7828 (p)
REVERT: A   85 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.5924 (tp)
REVERT: A  185 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6448 (tm-30)
REVERT: A  228 MET cc_start: 0.8050 (ttm) cc_final: 0.7703 (ttm)
REVERT: A  235 LEU cc_start: 0.8748 (tt) cc_final: 0.8523 (tt)
REVERT: A  366 MET cc_start: 0.7146 (ppp) cc_final: 0.6788 (tmm)
REVERT: A  377 ARG cc_start: 0.8075 (tpm-80) cc_final: 0.7753 (tpm-80)
REVERT: B   63 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6889 (tp)
REVERT: B  209 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7166 (tp)
REVERT: B  278 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6779 (m-70)
REVERT: B  290 GLN cc_start: 0.7282 (mp10) cc_final: 0.6973 (mp10)
REVERT: B  338 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7220 (mt-10)
REVERT: B  366 MET cc_start: 0.7592 (tmm) cc_final: 0.7366 (tmm)
REVERT: B  383 LYS cc_start: 0.8360 (tptp) cc_final: 0.7575 (mmmt)
  outliers start: 33
  outliers final: 19
  residues processed: 127
  average time/residue: 0.2252
  time to fit residues: 36.0975
Evaluate side-chains
  130 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  246 LEU
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   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  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  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:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 14 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0020
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.5388

-------------------------------------------------------------------------------
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 = 0.4271 r_free = 0.4271 target = 0.168578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.143563 restraints weight = 10337.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.71
r_work: 0.3815 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.3254

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= 0.206
  Angle     :  0.681  15.423   8455  Z= 0.318
  Chirality :  0.043   0.368    945
  Planarity :  0.003   0.046   1064
  Dihedral  :  9.609  89.502    973
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 22.96 %
    Favored  : 71.05 %
  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 (0.31), residues: 753
  helix:  1.87 (0.23), residues: 510
  sheet:  1.33 (0.64), residues: 59
  loop : -2.06 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.019   0.002   PHE A  81 
 TYR   0.008   0.001   TYR A 244 
 ARG   0.005   0.000   ARG A 334 

*********************** 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
  139 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8257 (p) cc_final: 0.7838 (p)
REVERT: A   85 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6121 (tp)
REVERT: A  185 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6408 (tm-30)
REVERT: A  228 MET cc_start: 0.8038 (ttm) cc_final: 0.7703 (ttm)
REVERT: A  235 LEU cc_start: 0.8825 (tt) cc_final: 0.8584 (tt)
REVERT: A  288 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7857 (mm)
REVERT: A  377 ARG cc_start: 0.8060 (tpm-80) cc_final: 0.7740 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6715 (mp)
REVERT: B   63 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6890 (tp)
REVERT: B  209 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7186 (tp)
REVERT: B  278 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6829 (m-70)
REVERT: B  290 GLN cc_start: 0.7319 (mp10) cc_final: 0.6990 (mp10)
REVERT: B  308 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6750 (ptm160)
REVERT: B  332 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7379 (ptt-90)
REVERT: B  383 LYS cc_start: 0.8357 (tptp) cc_final: 0.7614 (mmmt)
  outliers start: 36
  outliers final: 23
  residues processed: 125
  average time/residue: 0.2440
  time to fit residues: 38.2930
Evaluate side-chains
  134 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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  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   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  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  265 ILE
Chi-restraints excluded: chain B residue  278 HIS
Chi-restraints excluded: chain B residue  308 ARG
Chi-restraints excluded: chain B residue  329 ILE
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:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0270
   chunk 64 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4238

-------------------------------------------------------------------------------
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 = 0.4276 r_free = 0.4276 target = 0.168768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.144382 restraints weight = 10281.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.69
r_work: 0.3826 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.3397

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= 0.185
  Angle     :  0.680  14.307   8455  Z= 0.315
  Chirality :  0.042   0.395    945
  Planarity :  0.004   0.060   1064
  Dihedral  :  9.469  88.399    973
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 24.29 %
    Favored  : 70.88 %
  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:  1.54 (0.32), residues: 753
  helix:  2.00 (0.23), residues: 516
  sheet:  1.32 (0.64), residues: 59
  loop : -2.17 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.017   0.001   PHE A  81 
 TYR   0.008   0.001   TYR A 319 
 ARG   0.006   0.000   ARG B 242 

*********************** 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
  132 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8242 (p) cc_final: 0.7835 (p)
REVERT: A   85 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.5969 (tp)
REVERT: A  185 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6376 (tm-30)
REVERT: A  377 ARG cc_start: 0.8050 (tpm-80) cc_final: 0.7762 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6652 (mp)
REVERT: B   63 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6888 (tp)
REVERT: B  209 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7167 (tp)
REVERT: B  223 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7358 (ttm110)
REVERT: B  278 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6845 (m-70)
REVERT: B  290 GLN cc_start: 0.7330 (mp10) cc_final: 0.6991 (mp10)
REVERT: B  332 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7320 (ptt-90)
REVERT: B  338 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7041 (mt-10)
REVERT: B  383 LYS cc_start: 0.8330 (tptp) cc_final: 0.7566 (mmmt)
  outliers start: 29
  outliers final: 19
  residues processed: 122
  average time/residue: 0.2488
  time to fit residues: 37.4895
Evaluate side-chains
  127 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  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  238 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  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  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:    0.0870
   chunk 2 optimal weight:    0.6980
   chunk 22 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.168289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.144043 restraints weight = 10356.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.71
r_work: 0.3823 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.3483

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= 0.191
  Angle     :  0.682  12.713   8455  Z= 0.320
  Chirality :  0.043   0.398    945
  Planarity :  0.003   0.027   1064
  Dihedral  :  9.373  87.247    973
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 24.79 %
    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:  1.54 (0.32), residues: 753
  helix:  2.00 (0.23), residues: 516
  sheet:  1.29 (0.65), residues: 59
  loop : -2.15 (0.46), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  61 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.016   0.001   PHE A  81 
 TYR   0.009   0.001   TYR A 244 
 ARG   0.009   0.000   ARG A 391 

*********************** 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
  137 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8251 (p) cc_final: 0.7844 (p)
REVERT: A   85 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6115 (tp)
REVERT: A  185 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6354 (tm-30)
REVERT: A  288 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7849 (mm)
REVERT: A  377 ARG cc_start: 0.8048 (tpm-80) cc_final: 0.7718 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6665 (mp)
REVERT: B   41 PHE cc_start: 0.7606 (t80) cc_final: 0.7319 (t80)
REVERT: B   63 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6885 (tp)
REVERT: B   85 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6132 (tt)
REVERT: B  209 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7172 (tp)
REVERT: B  278 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6847 (m-70)
REVERT: B  290 GLN cc_start: 0.7329 (mp10) cc_final: 0.6985 (mp10)
REVERT: B  308 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6768 (ptm160)
REVERT: B  332 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7299 (ptt-90)
  outliers start: 32
  outliers final: 21
  residues processed: 127
  average time/residue: 0.2392
  time to fit residues: 37.7333
Evaluate side-chains
  136 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
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   85 LEU
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  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  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:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.4254 r_free = 0.4254 target = 0.167275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.142414 restraints weight = 10372.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 2.73
r_work: 0.3801 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6212  Z= 0.231
  Angle     :  0.702  11.919   8455  Z= 0.329
  Chirality :  0.044   0.399    945
  Planarity :  0.004   0.093   1064
  Dihedral  :  9.424  86.148    973
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 24.79 %
    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:  1.43 (0.31), residues: 753
  helix:  1.93 (0.23), residues: 516
  sheet:  1.21 (0.64), residues: 59
  loop : -2.22 (0.45), residues: 178

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   0.015   0.002   PHE A  81 
 TYR   0.008   0.001   TYR A 244 
 ARG   0.006   0.000   ARG B 391 

*********************** 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
  134 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 SER cc_start: 0.8263 (p) cc_final: 0.7848 (p)
REVERT: A   85 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6130 (tp)
REVERT: A   91 MET cc_start: 0.5467 (mmp) cc_final: 0.5267 (mmp)
REVERT: A  185 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6531 (tm-30)
REVERT: A  288 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7845 (mm)
REVERT: A  377 ARG cc_start: 0.8063 (tpm-80) cc_final: 0.7735 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (mp)
REVERT: B   63 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6882 (tp)
REVERT: B   85 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6169 (tp)
REVERT: B  209 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7140 (tp)
REVERT: B  223 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7106 (ptp-170)
REVERT: B  278 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6902 (m-70)
REVERT: B  290 GLN cc_start: 0.7413 (mp10) cc_final: 0.7062 (mp10)
REVERT: B  308 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6772 (ptm160)
REVERT: B  332 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7320 (ptt-90)
  outliers start: 32
  outliers final: 21
  residues processed: 124
  average time/residue: 0.2523
  time to fit residues: 38.4823
Evaluate side-chains
  132 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
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   85 LEU
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  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  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:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    0.3980
   chunk 47 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.167965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.143246 restraints weight = 10268.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 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: 0.7203
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6212  Z= 0.223
  Angle     :  0.710  11.465   8455  Z= 0.335
  Chirality :  0.044   0.395    945
  Planarity :  0.005   0.127   1064
  Dihedral  :  9.370  85.465    973
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 25.12 %
    Favored  : 69.55 %
  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:  1.37 (0.31), residues: 753
  helix:  1.92 (0.23), residues: 516
  sheet:  0.73 (0.63), residues: 63
  loop : -2.26 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.015   0.002   PHE A  81 
 TYR   0.009   0.001   TYR A 244 
 ARG   0.012   0.001   ARG A 334 

********************** 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
  138 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7101 (pm20) cc_final: 0.6831 (pm20)
REVERT: A   46 SER cc_start: 0.8242 (p) cc_final: 0.7846 (p)
REVERT: A   85 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.5945 (tp)
REVERT: A  185 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6424 (tm-30)
REVERT: A  228 MET cc_start: 0.7990 (ttm) cc_final: 0.7646 (ttm)
REVERT: A  288 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7831 (mm)
REVERT: A  377 ARG cc_start: 0.8099 (tpm-80) cc_final: 0.7757 (tpm-80)
REVERT: B   28 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6700 (mp)
REVERT: B   85 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6149 (tp)
REVERT: B  209 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7135 (tp)
REVERT: B  223 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7072 (ptp-170)
REVERT: B  278 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6915 (m-70)
REVERT: B  290 GLN cc_start: 0.7423 (mp10) cc_final: 0.7068 (mp10)
REVERT: B  308 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6874 (ptm160)
REVERT: B  332 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7344 (ptt-90)
REVERT: B  366 MET cc_start: 0.7660 (tmm) cc_final: 0.7379 (tmm)
  outliers start: 32
  outliers final: 21
  residues processed: 127
  average time/residue: 0.2510
  time to fit residues: 39.1226
Evaluate side-chains
  131 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
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   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  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  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:    0.6980
   chunk 41 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.168504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.144454 restraints weight = 10453.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.73
r_work: 0.3811 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6212  Z= 0.230
  Angle     :  0.732  11.319   8455  Z= 0.340
  Chirality :  0.044   0.397    945
  Planarity :  0.004   0.083   1064
  Dihedral  :  9.390  86.696    973
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 25.46 %
    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:  1.30 (0.31), residues: 753
  helix:  1.89 (0.23), residues: 516
  sheet:  0.69 (0.64), residues: 63
  loop : -2.36 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  61 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.015   0.002   PHE A  81 
 TYR   0.010   0.001   TYR A 244 
 ARG   0.007   0.001   ARG B 334 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2830.73 seconds
wall clock time: 51 minutes 12.57 seconds (3072.57 seconds total)