Starting phenix.real_space_refine
on Thu Jun  5 22:44:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qhp_18415/06_2025/8qhp_18415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qhp_18415/06_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_18415/06_2025/8qhp_18415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qhp_18415/06_2025/8qhp_18415.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qhp_18415/06_2025/8qhp_18415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qhp_18415/06_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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.76, per 1000 atoms: 0.85
  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 1.1 seconds
  
  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: 0.73
  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: 2.26

  Time building geometry restraints manager: 2.07 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: 0.04
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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.460
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.220
-------------------------------------------------------------------------------
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   6968  Z= 0.105
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12780 (  363)
  hydrogen bonds       : angle       5.33363 ( 1071)
  metal coordination   : bond        0.00185 (    6)
  covalent geometry    : bond        0.00221 ( 6962)
  covalent geometry    : angle       0.38369 ( 9370)

*********************** 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  : 0.737 
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: 1.4181
  time to fit residues: 161.5902
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  : 0.800 
-------------------------------------------------------------------------------
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      :  0.024   1.921   6968  Z= 0.804
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  363)
  hydrogen bonds       : angle       4.46849 ( 1071)
  metal coordination   : bond        0.78419 (    6)
  covalent geometry    : bond        0.00564 ( 6962)
  covalent geometry    : angle       0.51329 ( 9370)

*********************** 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  : 0.742 
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: 1.5181
  time to fit residues: 144.4005
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  : 0.837 
-------------------------------------------------------------------------------
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   0.070   6968  Z= 0.164
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 (  363)
  hydrogen bonds       : angle       4.16557 ( 1071)
  metal coordination   : bond        0.03554 (    6)
  covalent geometry    : bond        0.00376 ( 6962)
  covalent geometry    : angle       0.46492 ( 9370)

*********************** 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  : 0.756 
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: 1.4658
  time to fit residues: 135.3411
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  : 0.807 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0060
   chunk 59 optimal weight:    0.5980
   chunk 16 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8798

-------------------------------------------------------------------------------
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 = 0.113352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.075658 restraints weight = 9323.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.95
r_work: 0.2701 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6968  Z= 0.134
  Angle     :  0.443  11.898   9370  Z= 0.231
  Chirality :  0.039   0.139    956
  Planarity :  0.003   0.033   1202
  Dihedral  :  3.761  14.887    902
  Min Nonbonded Distance : 1.648

Molprobity Statistics.
  All-atom Clashscore : 4.83
  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:  2.24 (0.25), residues: 442
  sheet: -0.08 (0.50), residues: 92
  loop :  1.10 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.011   0.001   HIS B 233 
 PHE   0.010   0.001   PHE A  92 
 TYR   0.012   0.001   TYR B 111 
 ARG   0.005   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  363)
  hydrogen bonds       : angle       4.00321 ( 1071)
  metal coordination   : bond        0.02322 (    6)
  covalent geometry    : bond        0.00308 ( 6962)
  covalent geometry    : angle       0.44320 ( 9370)

*********************** 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  : 0.811 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8245 (mt-10)
REVERT: A   63 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8488 (tmm)
REVERT: A   86 LYS cc_start: 0.8425 (tttt) cc_final: 0.8140 (tppt)
REVERT: A  123 GLU cc_start: 0.9054 (tt0) cc_final: 0.8336 (tp30)
REVERT: A  185 LYS cc_start: 0.9024 (mttt) cc_final: 0.8687 (mtmm)
REVERT: A  199 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7916 (mt-10)
REVERT: A  260 MET cc_start: 0.7888 (mmt) cc_final: 0.7191 (mmm)
REVERT: A  266 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7776 (tpp)
REVERT: B   63 MET cc_start: 0.9218 (ttm) cc_final: 0.8730 (ttp)
REVERT: B   71 ASP cc_start: 0.8579 (t0) cc_final: 0.8267 (t0)
REVERT: B   90 GLU cc_start: 0.8450 (tt0) cc_final: 0.7895 (tm-30)
REVERT: B  144 GLU cc_start: 0.7943 (tt0) cc_final: 0.7583 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 82
  average time/residue: 1.3277
  time to fit residues: 114.4936
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  : 0.814 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0000
   chunk 51 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.0988

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.112330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.074796 restraints weight = 9263.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.81
r_work: 0.2687 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6968  Z= 0.152
  Angle     :  0.442  11.911   9370  Z= 0.231
  Chirality :  0.039   0.147    956
  Planarity :  0.003   0.032   1202
  Dihedral  :  3.734  15.161    902
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.43 %
    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:  2.41 (0.30), residues: 812
  helix:  2.35 (0.25), residues: 438
  sheet: -0.09 (0.51), residues: 92
  loop :  1.16 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 197 
 HIS   0.002   0.000   HIS A  37 
 PHE   0.032   0.002   PHE A 273 
 TYR   0.011   0.001   TYR B  44 
 ARG   0.009   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03873 (  363)
  hydrogen bonds       : angle       4.00326 ( 1071)
  metal coordination   : bond        0.00312 (    6)
  covalent geometry    : bond        0.00356 ( 6962)
  covalent geometry    : angle       0.44227 ( 9370)

*********************** 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
  89 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8476 (ttm)
REVERT: A   86 LYS cc_start: 0.8415 (tttt) cc_final: 0.8075 (tppt)
REVERT: A  113 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6697 (mtp85)
REVERT: A  123 GLU cc_start: 0.9055 (tt0) cc_final: 0.8334 (tp30)
REVERT: A  185 LYS cc_start: 0.9015 (mttt) cc_final: 0.8657 (mtmm)
REVERT: A  199 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: A  260 MET cc_start: 0.7843 (mmt) cc_final: 0.7164 (mmm)
REVERT: A  266 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7774 (tpp)
REVERT: B   90 GLU cc_start: 0.8463 (tt0) cc_final: 0.7887 (tm-30)
REVERT: B  144 GLU cc_start: 0.7971 (tt0) cc_final: 0.7586 (tp30)
  outliers start: 12
  outliers final: 4
  residues processed: 83
  average time/residue: 1.4396
  time to fit residues: 125.3729
Evaluate side-chains
  77 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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  113 ARG
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=3.00
-------------------------------------------------------------------------------
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:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.112843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.075327 restraints weight = 9279.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.81
r_work: 0.2690 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6968  Z= 0.142
  Angle     :  0.446  11.417   9370  Z= 0.232
  Chirality :  0.039   0.167    956
  Planarity :  0.003   0.031   1202
  Dihedral  :  3.705  14.741    902
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.27 %
    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:  2.45 (0.30), residues: 812
  helix:  2.40 (0.25), residues: 438
  sheet: -0.09 (0.52), residues: 92
  loop :  1.14 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.001   0.000   HIS B 255 
 PHE   0.010   0.001   PHE B  67 
 TYR   0.011   0.001   TYR A  44 
 ARG   0.008   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  363)
  hydrogen bonds       : angle       3.96586 ( 1071)
  metal coordination   : bond        0.00308 (    6)
  covalent geometry    : bond        0.00333 ( 6962)
  covalent geometry    : angle       0.44627 ( 9370)

*********************** 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
  85 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8321 (ttm)
REVERT: A   86 LYS cc_start: 0.8386 (tttt) cc_final: 0.8046 (tppt)
REVERT: A  123 GLU cc_start: 0.9047 (tt0) cc_final: 0.8333 (tp30)
REVERT: A  185 LYS cc_start: 0.8997 (mttt) cc_final: 0.8701 (mttp)
REVERT: A  199 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: A  266 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7810 (tpp)
REVERT: B   71 ASP cc_start: 0.8588 (t0) cc_final: 0.8214 (t0)
REVERT: B   90 GLU cc_start: 0.8460 (tt0) cc_final: 0.7875 (tm-30)
REVERT: B  218 GLU cc_start: 0.8929 (tp30) cc_final: 0.8367 (tp30)
REVERT: B  382 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8411 (tttp)
REVERT: B  386 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8748 (mt-10)
  outliers start: 12
  outliers final: 5
  residues processed: 79
  average time/residue: 1.4032
  time to fit residues: 116.6101
Evaluate side-chains
  80 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3445 r_free = 0.3445 target = 0.113241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.075874 restraints weight = 9059.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.77
r_work: 0.2701 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6968  Z= 0.130
  Angle     :  0.441  11.202   9370  Z= 0.229
  Chirality :  0.039   0.161    956
  Planarity :  0.003   0.027   1202
  Dihedral  :  3.653  14.791    902
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.41 %
    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: -0.15 (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   0.031   0.001   PHE A 273 
 TYR   0.011   0.001   TYR A  44 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  363)
  hydrogen bonds       : angle       3.92677 ( 1071)
  metal coordination   : bond        0.00316 (    6)
  covalent geometry    : bond        0.00304 ( 6962)
  covalent geometry    : angle       0.44085 ( 9370)

*********************** 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
  97 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8320 (ttm)
REVERT: A   66 ASN cc_start: 0.8368 (p0) cc_final: 0.8083 (p0)
REVERT: A   79 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8593 (mtp180)
REVERT: A   86 LYS cc_start: 0.8369 (tttt) cc_final: 0.8027 (tppt)
REVERT: A  113 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6678 (mtp85)
REVERT: A  123 GLU cc_start: 0.9047 (tt0) cc_final: 0.8330 (tp30)
REVERT: A  185 LYS cc_start: 0.8999 (mttt) cc_final: 0.8708 (mttp)
REVERT: A  199 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7890 (mt-10)
REVERT: A  207 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6556 (pp20)
REVERT: A  218 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8092 (mm-30)
REVERT: A  260 MET cc_start: 0.8128 (mmm) cc_final: 0.7382 (mmm)
REVERT: B   71 ASP cc_start: 0.8585 (t0) cc_final: 0.8223 (t0)
REVERT: B   90 GLU cc_start: 0.8470 (tt0) cc_final: 0.7875 (tm-30)
REVERT: B  144 GLU cc_start: 0.7964 (tt0) cc_final: 0.7635 (tp30)
REVERT: B  218 GLU cc_start: 0.8938 (tp30) cc_final: 0.8397 (tp30)
REVERT: B  382 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8371 (tttp)
REVERT: B  386 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8609 (mt-10)
  outliers start: 17
  outliers final: 6
  residues processed: 90
  average time/residue: 1.4015
  time to fit residues: 132.1819
Evaluate side-chains
  84 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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   79 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  207 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.112806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.075245 restraints weight = 9221.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.80
r_work: 0.2674 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6968  Z= 0.145
  Angle     :  0.457  11.054   9370  Z= 0.236
  Chirality :  0.039   0.134    956
  Planarity :  0.003   0.027   1202
  Dihedral  :  3.656  15.417    902
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.83 %
    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:  2.44 (0.25), residues: 438
  sheet: -0.16 (0.52), residues: 92
  loop :  1.11 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.002   0.000   HIS A 296 
 PHE   0.010   0.001   PHE B  67 
 TYR   0.011   0.001   TYR A  44 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03714 (  363)
  hydrogen bonds       : angle       3.93436 ( 1071)
  metal coordination   : bond        0.00362 (    6)
  covalent geometry    : bond        0.00340 ( 6962)
  covalent geometry    : angle       0.45655 ( 9370)

*********************** 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
  91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A   63 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8323 (ttm)
REVERT: A   66 ASN cc_start: 0.8390 (p0) cc_final: 0.8087 (p0)
REVERT: A   79 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8595 (mtp180)
REVERT: A   86 LYS cc_start: 0.8343 (tttt) cc_final: 0.8005 (tppt)
REVERT: A  113 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6685 (mtp85)
REVERT: A  123 GLU cc_start: 0.9045 (tt0) cc_final: 0.8321 (tp30)
REVERT: A  185 LYS cc_start: 0.9002 (mttt) cc_final: 0.8716 (mttp)
REVERT: A  199 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7911 (mt-10)
REVERT: A  207 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6656 (pp20)
REVERT: A  218 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8105 (mm-30)
REVERT: B   63 MET cc_start: 0.9380 (ttp) cc_final: 0.8851 (ttm)
REVERT: B   71 ASP cc_start: 0.8576 (t0) cc_final: 0.8228 (t0)
REVERT: B   90 GLU cc_start: 0.8472 (tt0) cc_final: 0.7872 (tm-30)
REVERT: B  144 GLU cc_start: 0.7958 (tt0) cc_final: 0.7628 (tp30)
REVERT: B  218 GLU cc_start: 0.8936 (tp30) cc_final: 0.8522 (tp30)
REVERT: B  260 MET cc_start: 0.8085 (mmt) cc_final: 0.7727 (mmt)
REVERT: B  266 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7165 (tpp)
REVERT: B  382 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8363 (tttp)
REVERT: B  386 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8630 (mt-10)
  outliers start: 14
  outliers final: 6
  residues processed: 84
  average time/residue: 1.4027
  time to fit residues: 123.4778
Evaluate side-chains
  88 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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   79 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  207 GLU
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  266 MET
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:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 69 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 233 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.113555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.076055 restraints weight = 9210.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 2.80
r_work: 0.2708 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.022   1.814   6968  Z= 0.735
  Angle     :  0.445  10.951   9370  Z= 0.231
  Chirality :  0.039   0.129    956
  Planarity :  0.003   0.027   1202
  Dihedral  :  3.604  14.753    902
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.66 %
    Favored  : 83.94 %
  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:  2.47 (0.30), residues: 812
  helix:  2.48 (0.24), residues: 438
  sheet: -0.22 (0.52), residues: 92
  loop :  1.11 (0.39), 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   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03565 (  363)
  hydrogen bonds       : angle       3.88119 ( 1071)
  metal coordination   : bond        0.74038 (    6)
  covalent geometry    : bond        0.00290 ( 6962)
  covalent geometry    : angle       0.44507 ( 9370)

*********************** 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: 10
    poor density    : 77
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8323 (p0) cc_final: 0.8008 (p0)
REVERT: A   86 LYS cc_start: 0.8360 (tttt) cc_final: 0.8008 (tppt)
REVERT: A   90 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: A  113 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.6727 (mtp85)
REVERT: A  123 GLU cc_start: 0.9058 (tt0) cc_final: 0.8324 (tp30)
REVERT: A  185 LYS cc_start: 0.9009 (mttt) cc_final: 0.8740 (mttp)
REVERT: A  199 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: A  218 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8146 (mm-30)
REVERT: B   63 MET cc_start: 0.9346 (ttp) cc_final: 0.8680 (ttm)
REVERT: B   71 ASP cc_start: 0.8582 (t0) cc_final: 0.8284 (t0)
REVERT: B   90 GLU cc_start: 0.8476 (tt0) cc_final: 0.7879 (tm-30)
REVERT: B  144 GLU cc_start: 0.7978 (tt0) cc_final: 0.7653 (tp30)
REVERT: B  218 GLU cc_start: 0.8951 (tp30) cc_final: 0.8488 (mm-30)
REVERT: B  260 MET cc_start: 0.8042 (mmt) cc_final: 0.7673 (mmt)
REVERT: B  382 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8363 (tttp)
REVERT: B  386 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8580 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 84
  average time/residue: 1.5156
  time to fit residues: 133.2374
Evaluate side-chains
  85 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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  113 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.0160

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.113197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.075649 restraints weight = 9170.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.92
r_work: 0.2676 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   6968  Z= 0.154
  Angle     :  0.478  10.898   9370  Z= 0.248
  Chirality :  0.039   0.132    956
  Planarity :  0.003   0.038   1202
  Dihedral  :  3.659  15.403    902
  Min Nonbonded Distance : 1.433

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.66 %
    Favored  : 83.80 %
  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:  2.46 (0.25), residues: 438
  sheet: -0.20 (0.52), residues: 92
  loop :  1.04 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 197 
 HIS   0.026   0.001   HIS B 233 
 PHE   0.010   0.001   PHE B  67 
 TYR   0.011   0.001   TYR B  44 
 ARG   0.006   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03719 (  363)
  hydrogen bonds       : angle       3.92029 ( 1071)
  metal coordination   : bond        0.04549 (    6)
  covalent geometry    : bond        0.00347 ( 6962)
  covalent geometry    : angle       0.47773 ( 9370)

********************** 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
  89 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A   66 ASN cc_start: 0.8422 (p0) cc_final: 0.8089 (p0)
REVERT: A   86 LYS cc_start: 0.8334 (tttt) cc_final: 0.7988 (tppt)
REVERT: A   90 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: A  113 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6681 (mtp85)
REVERT: A  123 GLU cc_start: 0.9049 (tt0) cc_final: 0.8310 (tp30)
REVERT: A  185 LYS cc_start: 0.8994 (mttt) cc_final: 0.8721 (mttp)
REVERT: A  199 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7906 (mt-10)
REVERT: A  218 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8129 (mm-30)
REVERT: A  266 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7734 (tpp)
REVERT: B   71 ASP cc_start: 0.8565 (t0) cc_final: 0.8270 (t0)
REVERT: B   90 GLU cc_start: 0.8465 (tt0) cc_final: 0.7863 (tm-30)
REVERT: B  144 GLU cc_start: 0.7979 (tt0) cc_final: 0.7651 (tp30)
REVERT: B  218 GLU cc_start: 0.8926 (tp30) cc_final: 0.8449 (mm-30)
REVERT: B  382 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8328 (tttp)
REVERT: B  386 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8540 (mt-10)
  outliers start: 11
  outliers final: 6
  residues processed: 85
  average time/residue: 1.7598
  time to fit residues: 156.1546
Evaluate side-chains
  86 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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  113 ARG
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  131 LYS
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:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0000
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.6584

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.114819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.077325 restraints weight = 9132.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 2.93
r_work: 0.2722 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.099   6968  Z= 0.127
  Angle     :  0.459  10.662   9370  Z= 0.239
  Chirality :  0.039   0.134    956
  Planarity :  0.003   0.042   1202
  Dihedral  :  3.618  14.825    902
  Min Nonbonded Distance : 1.444

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.94 %
    Favored  : 83.80 %
  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:  2.49 (0.30), residues: 812
  helix:  2.53 (0.25), residues: 438
  sheet: -0.24 (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   0.027   0.001   HIS B 233 
 PHE   0.031   0.001   PHE A 273 
 TYR   0.010   0.001   TYR B 111 
 ARG   0.007   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  363)
  hydrogen bonds       : angle       3.86639 ( 1071)
  metal coordination   : bond        0.05175 (    6)
  covalent geometry    : bond        0.00269 ( 6962)
  covalent geometry    : angle       0.45920 ( 9370)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4691.45 seconds
wall clock time: 81 minutes 58.14 seconds (4918.14 seconds total)