Starting phenix.real_space_refine
on Tue Mar 11 23:05:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qhp_18415/03_2025/8qhp_18415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qhp_18415/03_2025/8qhp_18415.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qhp_18415/03_2025/8qhp_18415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qhp_18415/03_2025/8qhp_18415.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qhp_18415/03_2025/8qhp_18415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qhp_18415/03_2025/8qhp_18415.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      22      5.16       5
     C    4392      2.51       5
     N    1128      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6788
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3393
          Classifications: {'peptide': 410}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3393
          Classifications: {'peptide': 410}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    236  SG  CYS A  28      36.433  38.017  33.062  1.00137.77           S
  ATOM   1644  SG  CYS A 208      33.883  39.740  30.430  1.00155.64           S
  ATOM   3629  SG  CYS B  28      36.336  40.874  90.477  1.00138.97           S
  ATOM   5037  SG  CYS B 208      37.721  38.524  92.922  1.00158.95           S

  Time building chain proxies: 4.73, per 1000 atoms: 0.70
  Number of scatterers: 6788
  At special positions: 0
  Unit cell: (67.518, 71.148, 124.872, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      22     16.00
     O    1244      8.00
     N    1128      7.00
     C    4392      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: 1.71
  Conformation dependent library (CDL) restraints added in 932.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 208 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 233 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A  28 "
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B  28 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 208 "
        pdb="ZN    ZN B 501 " - pdb=" ND1 HIS B 233 "


  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1520

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      55.7% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 57
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 86 through 103
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 148
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 3.540A  pdb=" N   LEU A 162 " --> pdb=" O   LYS A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.974A  pdb=" N   SER A 209 " --> pdb=" O   HIS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.679A  pdb=" N   PHE A 231 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 232 through 246
    Processing helix  chain 'A' and resid 275 through 281
    Processing helix  chain 'A' and resid 284 through 294
    Processing helix  chain 'A' and resid 304 through 329
    Processing helix  chain 'A' and resid 339 through 362
    Processing helix  chain 'A' and resid 365 through 387
    Processing helix  chain 'A' and resid 391 through 410
      removed outlier: 3.502A  pdb=" N   LEU A 395 " --> pdb=" O   LYS A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 418
      removed outlier: 3.715A  pdb=" N   GLU A 418 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 57
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 84 through 103
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 158 through 163
      removed outlier: 3.572A  pdb=" N   LEU B 162 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 216
      removed outlier: 3.927A  pdb=" N   SER B 209 " --> pdb=" O   HIS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 232 through 246
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'B' and resid 284 through 294
    Processing helix  chain 'B' and resid 304 through 332
      removed outlier: 3.710A  pdb=" N   ARG B 330 " --> pdb=" O   ARG B 326 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASN B 331 " --> pdb=" O   VAL B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 362
    Processing helix  chain 'B' and resid 365 through 387
    Processing helix  chain 'B' and resid 391 through 410
    Processing helix  chain 'B' and resid 412 through 418
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65
      removed outlier: 9.433A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LYS A  24 " --> pdb=" O   PHE A 220 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ASP A 221 " --> pdb=" O   TYR A 252 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   LEU A 254 " --> pdb=" O   ASP A 221 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   HIS A 223 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   THR A 256 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   GLY A 225 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136
      removed outlier: 6.453A  pdb=" N   ILE A 141 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 180 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65
      removed outlier: 11.532A  pdb=" N   GLU B  22 " --> pdb=" O   PHE B 220 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   ILE B 222 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   GLY B 224 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TYR B  26 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
      removed outlier: 8.652A  pdb=" N   GLY B 226 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASP B 221 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU B 254 " --> pdb=" O   ASP B 221 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   HIS B 223 " --> pdb=" O   LEU B 254 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   THR B 256 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   GLY B 225 " --> pdb=" O   THR B 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 136
      removed outlier: 6.385A  pdb=" N   ILE B 141 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE B 180 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265

    363 hydrogen bonds defined for protein.
    1071 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: 2.39

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2164
        1.34 -     1.46: 1623
        1.46 -     1.58: 3137
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 6962
  Sorted by residual:
  bond pdb=" N   VAL B  32 "
       pdb=" CA  VAL B  32 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.017 1.57e-02 4.06e+03 1.15e+00
  bond pdb=" CA  VAL A  32 "
       pdb=" C   VAL A  32 "
    ideal  model  delta    sigma   weight residual
    1.526  1.535 -0.008 9.00e-03 1.23e+04 8.57e-01
  bond pdb=" CG  ARG A  51 "
       pdb=" CD  ARG A  51 "
    ideal  model  delta    sigma   weight residual
    1.520  1.498  0.022 3.00e-02 1.11e+03 5.18e-01
  bond pdb=" CG1 ILE B  93 "
       pdb=" CD1 ILE B  93 "
    ideal  model  delta    sigma   weight residual
    1.513  1.487  0.026 3.90e-02 6.57e+02 4.51e-01
  bond pdb=" C   ASP A  84 "
       pdb=" N   PRO A  85 "
    ideal  model  delta    sigma   weight residual
    1.336  1.342 -0.007 1.08e-02 8.57e+03 3.82e-01
  ... (remaining 6957 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.85: 9020
        0.85 -     1.70: 300
        1.70 -     2.56: 23
        2.56 -     3.41: 26
        3.41 -     4.26: 1
  Bond angle restraints: 9370
  Sorted by residual:
  angle pdb=" N   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     106.21  110.47   -4.26 1.07e+00 8.73e-01 1.58e+01
  angle pdb=" C   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" CB  VAL B  32 "
      ideal   model   delta    sigma   weight residual
     113.22  110.73    2.49 1.12e+00 7.97e-01 4.93e+00
  angle pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
        pdb=" O   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     122.63  120.99    1.64 8.70e-01 1.32e+00 3.56e+00
  angle pdb=" CA  TYR A  44 "
        pdb=" CB  TYR A  44 "
        pdb=" CG  TYR A  44 "
      ideal   model   delta    sigma   weight residual
     113.90  111.19    2.71 1.80e+00 3.09e-01 2.27e+00
  angle pdb=" CA  TYR B  44 "
        pdb=" CB  TYR B  44 "
        pdb=" CG  TYR B  44 "
      ideal   model   delta    sigma   weight residual
     113.90  111.31    2.59 1.80e+00 3.09e-01 2.07e+00
  ... (remaining 9365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.35: 3658
       12.35 -    24.70: 347
       24.70 -    37.05: 86
       37.05 -    49.40: 34
       49.40 -    61.75: 19
  Dihedral angle restraints: 4144
    sinusoidal: 1762
      harmonic: 2382
  Sorted by residual:
  dihedral pdb=" CA  LYS B  57 "
           pdb=" CB  LYS B  57 "
           pdb=" CG  LYS B  57 "
           pdb=" CD  LYS B  57 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.56   59.56     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LYS A 295 "
           pdb=" CB  LYS A 295 "
           pdb=" CG  LYS A 295 "
           pdb=" CD  LYS A 295 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.96   58.96     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  ARG A  51 "
           pdb=" CB  ARG A  51 "
           pdb=" CG  ARG A  51 "
           pdb=" CD  ARG A  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.05  -56.95     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 4141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 570
       0.027 -    0.054: 237
       0.054 -    0.082: 109
       0.082 -    0.109: 33
       0.109 -    0.136: 7
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CA  ILE B 141 "
            pdb=" N   ILE B 141 "
            pdb=" C   ILE B 141 "
            pdb=" CB  ILE B 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE A 141 "
            pdb=" N   ILE A 141 "
            pdb=" C   ILE A 141 "
            pdb=" CB  ILE A 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  PHE A  92 "
            pdb=" N   PHE A  92 "
            pdb=" C   PHE A  92 "
            pdb=" CB  PHE A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 953 not shown)

  Planarity restraints: 1202
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 195 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.46e+00
        pdb=" N   PRO A 196 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 196 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 196 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 201 "    0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO A 202 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 202 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 202 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 148 "    0.018 5.00e-02 4.00e+02   2.70e-02 1.16e+00
        pdb=" N   PRO B 149 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B 149 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 149 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1199 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 235
        2.72 -     3.27: 6703
        3.27 -     3.81: 11579
        3.81 -     4.36: 14304
        4.36 -     4.90: 24475
  Nonbonded interactions: 57296
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 237 "
            pdb="ZN    ZN B 501 "
     model   vdw
     2.176 2.230
  nonbonded pdb=" OG  SER B 195 "
            pdb=" O   GLY B 198 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OE1 GLU B 286 "
            pdb=" OH  TYR B 319 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OG  SER A 335 "
            pdb=" O   ASP B 109 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD1 ASP A 139 "
            pdb=" OH  TYR A 142 "
     model   vdw
     2.219 3.040
  ... (remaining 57291 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.280
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
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      :  0.002   0.026   6962  Z= 0.141
  Angle     :  0.384   4.260   9370  Z= 0.218
  Chirality :  0.038   0.136    956
  Planarity :  0.003   0.030   1202
  Dihedral  : 11.643  61.754   2624
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.77 (0.29), residues: 812
  helix:  1.87 (0.25), residues: 424
  sheet:  0.25 (0.53), residues: 84
  loop :  0.61 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 249 
 HIS   0.001   0.000   HIS A  40 
 PHE   0.007   0.001   PHE B 356 
 TYR   0.010   0.001   TYR A  44 
 ARG   0.002   0.000   ARG A  51 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.792 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8638 (tttt) cc_final: 0.8371 (tppt)
REVERT: A  185 LYS cc_start: 0.9067 (mttt) cc_final: 0.8815 (mtmm)
REVERT: A  199 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8222 (mt-10)
REVERT: B   76 LYS cc_start: 0.8952 (tppp) cc_final: 0.8701 (ttmm)
REVERT: B   90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7956 (tm-30)
REVERT: B  207 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7598 (pt0)
REVERT: B  382 LYS cc_start: 0.8817 (tttt) cc_final: 0.8560 (tppp)
REVERT: B  386 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8662 (mt-10)
REVERT: B  414 ASP cc_start: 0.8827 (m-30) cc_final: 0.8347 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 1.4791
  time to fit residues: 168.4673
Evaluate side-chains
  78 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  11 GLN
B  66 ASN
B 233 HIS
B 309 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.110309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.073374 restraints weight = 9835.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.86
r_work: 0.2640 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   6962  Z= 0.362
  Angle     :  0.513  11.467   9370  Z= 0.268
  Chirality :  0.042   0.159    956
  Planarity :  0.004   0.035   1202
  Dihedral  :  3.974  16.051    902
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.80 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.89 (0.29), residues: 812
  helix:  1.84 (0.24), residues: 442
  sheet:  0.08 (0.50), residues: 92
  loop :  0.92 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 249 
 HIS   0.003   0.001   HIS B 255 
 PHE   0.013   0.002   PHE A  92 
 TYR   0.018   0.001   TYR B  44 
 ARG   0.004   0.001   ARG A  77 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8494 (tmm)
REVERT: A   86 LYS cc_start: 0.8486 (tttt) cc_final: 0.8162 (tppt)
REVERT: A  123 GLU cc_start: 0.9056 (tt0) cc_final: 0.8367 (tp30)
REVERT: A  185 LYS cc_start: 0.9008 (mttt) cc_final: 0.8678 (mtmm)
REVERT: A  199 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: B   90 GLU cc_start: 0.8470 (tt0) cc_final: 0.7955 (tm-30)
  outliers start: 14
  outliers final: 3
  residues processed: 91
  average time/residue: 1.4847
  time to fit residues: 141.2818
Evaluate side-chains
  75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  11 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.074537 restraints weight = 9427.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.96
r_work: 0.2678 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6962  Z= 0.242
  Angle     :  0.465  12.179   9370  Z= 0.242
  Chirality :  0.040   0.144    956
  Planarity :  0.003   0.037   1202
  Dihedral  :  3.847  15.136    902
  Min Nonbonded Distance : 1.580

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.45 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.15 (0.30), residues: 812
  helix:  2.09 (0.25), residues: 442
  sheet: -0.02 (0.50), residues: 92
  loop :  1.05 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.019   0.001   HIS B 233 
 PHE   0.028   0.001   PHE A 273 
 TYR   0.013   0.001   TYR A  44 
 ARG   0.007   0.000   ARG A  77 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8517 (tmm)
REVERT: A   86 LYS cc_start: 0.8457 (tttt) cc_final: 0.8162 (tppt)
REVERT: A  123 GLU cc_start: 0.9046 (tt0) cc_final: 0.8356 (tp30)
REVERT: A  185 LYS cc_start: 0.9033 (mttt) cc_final: 0.8721 (mtmm)
REVERT: A  199 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: A  260 MET cc_start: 0.7919 (mmt) cc_final: 0.7206 (mmm)
REVERT: A  266 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7824 (tpp)
REVERT: B   71 ASP cc_start: 0.8528 (t0) cc_final: 0.8178 (t0)
REVERT: B   90 GLU cc_start: 0.8479 (tt0) cc_final: 0.7916 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 88
  average time/residue: 1.3894
  time to fit residues: 128.2712
Evaluate side-chains
  73 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0060
   chunk 59 optimal weight:    0.0050
   chunk 16 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9012

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
B  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.113296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.075603 restraints weight = 9318.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.95
r_work: 0.2699 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6962  Z= 0.202
  Angle     :  0.444  12.006   9370  Z= 0.231
  Chirality :  0.039   0.139    956
  Planarity :  0.003   0.034   1202
  Dihedral  :  3.763  14.917    902
  Min Nonbonded Distance : 1.647

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.57 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.29 (0.30), residues: 812
  helix:  2.23 (0.25), residues: 442
  sheet: -0.08 (0.50), residues: 92
  loop :  1.11 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.012   0.001   HIS B 233 
 PHE   0.010   0.001   PHE A  92 
 TYR   0.012   0.001   TYR B 111 
 ARG   0.004   0.000   ARG A  19 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8277 (mt-10)
REVERT: A   63 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8487 (tmm)
REVERT: A   86 LYS cc_start: 0.8425 (tttt) cc_final: 0.8137 (tppt)
REVERT: A  123 GLU cc_start: 0.9055 (tt0) cc_final: 0.8338 (tp30)
REVERT: A  185 LYS cc_start: 0.9027 (mttt) cc_final: 0.8690 (mtmm)
REVERT: A  199 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7917 (mt-10)
REVERT: A  260 MET cc_start: 0.7878 (mmt) cc_final: 0.7178 (mmm)
REVERT: A  266 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7775 (tpp)
REVERT: B   63 MET cc_start: 0.9219 (ttm) cc_final: 0.8732 (ttp)
REVERT: B   71 ASP cc_start: 0.8580 (t0) cc_final: 0.8269 (t0)
REVERT: B   90 GLU cc_start: 0.8451 (tt0) cc_final: 0.7896 (tm-30)
REVERT: B  144 GLU cc_start: 0.7945 (tt0) cc_final: 0.7584 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 82
  average time/residue: 1.3139
  time to fit residues: 113.4134
Evaluate side-chains
  76 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 77 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0370
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.5464

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 294 GLN
B  11 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.110697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.073233 restraints weight = 9321.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.79
r_work: 0.2659 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6962  Z= 0.301
  Angle     :  0.469  12.061   9370  Z= 0.244
  Chirality :  0.040   0.148    956
  Planarity :  0.003   0.029   1202
  Dihedral  :  3.822  15.891    902
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.01 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.39 (0.30), residues: 812
  helix:  2.28 (0.25), residues: 438
  sheet:  0.49 (0.59), residues: 72
  loop :  0.97 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.002   0.001   HIS B 233 
 PHE   0.030   0.002   PHE A 273 
 TYR   0.014   0.001   TYR B  44 
 ARG   0.008   0.000   ARG A 417 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8468 (ttm)
REVERT: A   86 LYS cc_start: 0.8422 (tttt) cc_final: 0.8062 (tppt)
REVERT: A  123 GLU cc_start: 0.9053 (tt0) cc_final: 0.8333 (tp30)
REVERT: A  185 LYS cc_start: 0.9024 (mttt) cc_final: 0.8677 (mtmm)
REVERT: A  199 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7954 (mt-10)
REVERT: A  266 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7833 (tpp)
REVERT: B   63 MET cc_start: 0.9184 (ttm) cc_final: 0.8704 (ttp)
REVERT: B   90 GLU cc_start: 0.8489 (tt0) cc_final: 0.7902 (tm-30)
REVERT: B  382 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8568 (tppp)
  outliers start: 15
  outliers final: 5
  residues processed: 80
  average time/residue: 1.5394
  time to fit residues: 129.0729
Evaluate side-chains
  73 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 58 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 294 GLN
B  11 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.112966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.075507 restraints weight = 9252.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 2.81
r_work: 0.2678 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6962  Z= 0.182
  Angle     :  0.443  11.458   9370  Z= 0.231
  Chirality :  0.039   0.164    956
  Planarity :  0.003   0.031   1202
  Dihedral  :  3.715  14.712    902
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 13.55 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.43 (0.30), residues: 812
  helix:  2.39 (0.25), residues: 438
  sheet: -0.14 (0.52), residues: 92
  loop :  1.15 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.002   0.000   HIS A 255 
 PHE   0.021   0.001   PHE B 273 
 TYR   0.011   0.001   TYR B 111 
 ARG   0.006   0.000   ARG A 417 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8399 (tmm)
REVERT: A   66 ASN cc_start: 0.8328 (p0) cc_final: 0.7749 (p0)
REVERT: A   86 LYS cc_start: 0.8367 (tttt) cc_final: 0.8053 (tppt)
REVERT: A  123 GLU cc_start: 0.9056 (tt0) cc_final: 0.8319 (tp30)
REVERT: A  185 LYS cc_start: 0.9006 (mttt) cc_final: 0.8653 (mtmm)
REVERT: A  199 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7933 (mt-10)
REVERT: A  260 MET cc_start: 0.8124 (mmm) cc_final: 0.7361 (mmm)
REVERT: A  266 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7769 (tpp)
REVERT: B   71 ASP cc_start: 0.8568 (t0) cc_final: 0.8194 (t0)
REVERT: B   90 GLU cc_start: 0.8467 (tt0) cc_final: 0.7867 (tm-30)
REVERT: B  218 GLU cc_start: 0.8934 (tp30) cc_final: 0.8369 (tp30)
REVERT: B  382 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8537 (tppp)
  outliers start: 10
  outliers final: 5
  residues processed: 84
  average time/residue: 1.4557
  time to fit residues: 128.0822
Evaluate side-chains
  81 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  11 GLN
B 233 HIS
B 309 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.113101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.075781 restraints weight = 9053.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 2.78
r_work: 0.2704 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6962  Z= 0.191
  Angle     :  0.444  11.253   9370  Z= 0.231
  Chirality :  0.039   0.163    956
  Planarity :  0.003   0.027   1202
  Dihedral  :  3.659  14.841    902
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.25 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.45 (0.30), residues: 812
  helix:  2.41 (0.25), residues: 438
  sheet: -0.16 (0.52), residues: 92
  loop :  1.16 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.001   0.000   HIS B 255 
 PHE   0.032   0.001   PHE A 273 
 TYR   0.011   0.001   TYR B 111 
 ARG   0.005   0.000   ARG A 417 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.8385 (tttt) cc_final: 0.8058 (tppt)
REVERT: A  123 GLU cc_start: 0.9059 (tt0) cc_final: 0.8346 (tp30)
REVERT: A  185 LYS cc_start: 0.9018 (mttt) cc_final: 0.8732 (mttp)
REVERT: A  199 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7945 (mt-10)
REVERT: A  211 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5936 (mtt)
REVERT: A  218 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8118 (mm-30)
REVERT: B   63 MET cc_start: 0.9338 (ttp) cc_final: 0.8707 (ttm)
REVERT: B   71 ASP cc_start: 0.8606 (t0) cc_final: 0.8258 (t0)
REVERT: B   90 GLU cc_start: 0.8485 (tt0) cc_final: 0.7889 (tm-30)
REVERT: B  218 GLU cc_start: 0.8952 (tp30) cc_final: 0.8425 (tp30)
REVERT: B  382 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8332 (tttp)
REVERT: B  386 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8750 (pt0)
  outliers start: 11
  outliers final: 4
  residues processed: 86
  average time/residue: 1.4214
  time to fit residues: 128.0625
Evaluate side-chains
  82 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
B  11 GLN
B 309 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.113775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.076229 restraints weight = 9133.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 3.05
r_work: 0.2708 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6962  Z= 0.199
  Angle     :  0.463  11.104   9370  Z= 0.239
  Chirality :  0.039   0.128    956
  Planarity :  0.003   0.034   1202
  Dihedral  :  3.641  15.355    902
  Min Nonbonded Distance : 1.498

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.53 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.44 (0.30), residues: 812
  helix:  2.43 (0.25), residues: 438
  sheet: -0.16 (0.52), residues: 92
  loop :  1.10 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.024   0.001   HIS B 233 
 PHE   0.009   0.001   PHE B  67 
 TYR   0.010   0.001   TYR B 111 
 ARG   0.006   0.000   ARG A 417 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8596 (mtp180)
REVERT: A   86 LYS cc_start: 0.8358 (tttt) cc_final: 0.8032 (tppt)
REVERT: A  123 GLU cc_start: 0.9051 (tt0) cc_final: 0.8352 (tp30)
REVERT: A  185 LYS cc_start: 0.8994 (mttt) cc_final: 0.8716 (mttp)
REVERT: A  199 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7886 (mt-10)
REVERT: A  211 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5104 (mmt)
REVERT: A  218 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8089 (mm-30)
REVERT: B   71 ASP cc_start: 0.8572 (t0) cc_final: 0.8221 (t0)
REVERT: B   90 GLU cc_start: 0.8466 (tt0) cc_final: 0.7866 (tm-30)
REVERT: B  144 GLU cc_start: 0.7961 (tt0) cc_final: 0.7630 (tp30)
REVERT: B  218 GLU cc_start: 0.8938 (tp30) cc_final: 0.8518 (tp30)
REVERT: B  382 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8533 (tppp)
  outliers start: 13
  outliers final: 6
  residues processed: 88
  average time/residue: 1.3613
  time to fit residues: 125.6566
Evaluate side-chains
  81 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  131 LYS
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  11 GLN
B 236 ASN
B 309 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.075124 restraints weight = 9237.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.93
r_work: 0.2685 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6962  Z= 0.233
  Angle     :  0.478  10.876   9370  Z= 0.248
  Chirality :  0.039   0.127    956
  Planarity :  0.003   0.036   1202
  Dihedral  :  3.692  15.309    902
  Min Nonbonded Distance : 1.491

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.80 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.40 (0.30), residues: 812
  helix:  2.43 (0.25), residues: 438
  sheet: -0.23 (0.52), residues: 92
  loop :  1.06 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.019   0.001   HIS B 233 
 PHE   0.032   0.001   PHE A 273 
 TYR   0.011   0.001   TYR B  44 
 ARG   0.006   0.000   ARG A 417 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (mtp180)
REVERT: A   86 LYS cc_start: 0.8386 (tttt) cc_final: 0.8061 (tppt)
REVERT: A  123 GLU cc_start: 0.9054 (tt0) cc_final: 0.8347 (tp30)
REVERT: A  185 LYS cc_start: 0.9008 (mttt) cc_final: 0.8728 (mttp)
REVERT: A  199 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7939 (mt-10)
REVERT: A  211 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5229 (mmt)
REVERT: A  218 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8119 (mm-30)
REVERT: B   71 ASP cc_start: 0.8593 (t0) cc_final: 0.8301 (t0)
REVERT: B   90 GLU cc_start: 0.8466 (tt0) cc_final: 0.7859 (tm-30)
REVERT: B  144 GLU cc_start: 0.8008 (tt0) cc_final: 0.7676 (tp30)
REVERT: B  218 GLU cc_start: 0.8927 (tp30) cc_final: 0.8453 (mm-30)
REVERT: B  266 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7493 (tpp)
REVERT: B  382 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (tppp)
  outliers start: 12
  outliers final: 6
  residues processed: 80
  average time/residue: 1.4770
  time to fit residues: 123.9216
Evaluate side-chains
  83 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  11 GLN
B 205 HIS
B 236 ASN
B 309 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.112691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.074854 restraints weight = 9261.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.97
r_work: 0.2700 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6962  Z= 0.240
  Angle     :  0.493  10.764   9370  Z= 0.255
  Chirality :  0.040   0.135    956
  Planarity :  0.003   0.042   1202
  Dihedral  :  3.711  16.050    902
  Min Nonbonded Distance : 1.406

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.94 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.37 (0.30), residues: 812
  helix:  2.41 (0.25), residues: 438
  sheet: -0.26 (0.52), residues: 92
  loop :  1.03 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.030   0.001   HIS B 233 
 PHE   0.010   0.001   PHE B  47 
 TYR   0.012   0.001   TYR B  44 
 ARG   0.006   0.000   ARG A 417 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 LYS cc_start: 0.8389 (tttt) cc_final: 0.8091 (tppt)
REVERT: A  113 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7531 (mtp85)
REVERT: A  123 GLU cc_start: 0.9050 (tt0) cc_final: 0.8343 (tp30)
REVERT: A  185 LYS cc_start: 0.9010 (mttt) cc_final: 0.8740 (mttp)
REVERT: A  199 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: A  211 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5258 (mmt)
REVERT: A  218 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8123 (mm-30)
REVERT: B   71 ASP cc_start: 0.8579 (t0) cc_final: 0.8291 (t0)
REVERT: B   90 GLU cc_start: 0.8469 (tt0) cc_final: 0.7869 (tm-30)
REVERT: B  218 GLU cc_start: 0.8928 (tp30) cc_final: 0.8449 (mm-30)
REVERT: B  266 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7516 (tpp)
REVERT: B  382 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8485 (tttp)
  outliers start: 10
  outliers final: 6
  residues processed: 80
  average time/residue: 1.4709
  time to fit residues: 123.4347
Evaluate side-chains
  80 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  382 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 240 GLN
A 294 GLN
B  11 GLN
B 309 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.113974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.076421 restraints weight = 9192.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 2.93
r_work: 0.2707 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6962  Z= 0.187
  Angle     :  0.472  10.415   9370  Z= 0.245
  Chirality :  0.039   0.129    956
  Planarity :  0.003   0.042   1202
  Dihedral  :  3.667  15.093    902
  Min Nonbonded Distance : 1.427

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.36 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.42 (0.30), residues: 812
  helix:  2.46 (0.25), residues: 438
  sheet: -0.26 (0.52), residues: 92
  loop :  1.04 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.029   0.001   HIS B 233 
 PHE   0.032   0.001   PHE A 273 
 TYR   0.011   0.001   TYR B 111 
 ARG   0.007   0.000   ARG A 417 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4314.27 seconds
wall clock time: 74 minutes 30.37 seconds (4470.37 seconds total)