Starting phenix.real_space_refine
on Sun Apr 27 18:46:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dax_46701/04_2025/9dax_46701.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dax_46701/04_2025/9dax_46701.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dax_46701/04_2025/9dax_46701.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dax_46701/04_2025/9dax_46701.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dax_46701/04_2025/9dax_46701.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dax_46701/04_2025/9dax_46701.cif"
  }
  resolution = 3.3
  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=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Mg      1      5.21       5
     S      26      5.16       5
     C    4037      2.51       5
     N    1091      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6401
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3468
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 451, 3460
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 26, 'TRANS': 424}
      Conformer: "B"
        Number of residues, atoms: 451, 3460
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 26, 'TRANS': 424}
          bond proxies already assigned to first conformer: 3546
    Chain: "B"
      Number of atoms: 2920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2920
          Classifications: {'peptide': 374}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 355}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3, 'water': 6}
          Link IDs: {None: 8}
  Time building chain proxies: 6.30, per 1000 atoms: 0.98
  Number of scatterers: 6401
  At special positions: 0
  Unit cell: (65.36, 104.06, 84.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      26     16.00
     Mg      1     11.99
     O    1240      8.00
     N    1091      7.00
     C    4037      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " distance=2.03

  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: 1.40
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 14 sheets defined
      13.1% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 151 through 159
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 200 through 206
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 3.524A  pdb=" N   PHE A 231 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 80
    Processing helix  chain 'B' and resid 121 through 123
      No H-bonds generated for 'chain 'B' and resid 121 through 123'
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.855A  pdb=" N   LEU B 128 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TRP B 129 " --> pdb=" O   LYS B 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 124 through 129'
    Processing helix  chain 'B' and resid 133 through 144
      removed outlier: 4.032A  pdb=" N   LYS B 144 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 207
      removed outlier: 3.983A  pdb=" N   ASN B 204 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 232
      removed outlier: 3.811A  pdb=" N   ALA B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   CYS B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 291 through 296
      removed outlier: 3.590A  pdb=" N   THR B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
      removed outlier: 3.638A  pdb=" N   TYR B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 353
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63
      removed outlier: 3.653A  pdb=" N   ILE A 436 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 420 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79
      removed outlier: 3.537A  pdb=" N   GLU A  75 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100
    Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133
    Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 242
    Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA9, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 364
      removed outlier: 3.618A  pdb=" N   ALA A 361 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ASP A 373 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLN A 405 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 65
      removed outlier: 6.368A  pdb=" N   ARG B  87 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE B  88 " --> pdb=" O   ILE B 426 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 102
    Processing sheet with id=AB5, first strand: chain 'B' and resid 194 through 197
      removed outlier: 4.164A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   ILE B 151 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASP B 113 " --> pdb=" O   SER B 243 " (cutoff:3.500A)

    188 hydrogen bonds defined for protein.
    476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        0.90 -     1.09: 2
        1.09 -     1.28: 1084
        1.28 -     1.46: 2576
        1.46 -     1.65: 2835
        1.65 -     1.84: 39
  Bond restraints: 6536
  Sorted by residual:
  bond pdb=" CB  PRO A 410 "
       pdb=" CG  PRO A 410 "
    ideal  model  delta    sigma   weight residual
    1.492  0.899  0.593 5.00e-02 4.00e+02 1.41e+02
  bond pdb=" C   LYS B 298 "
       pdb=" O   LYS B 298 "
    ideal  model  delta    sigma   weight residual
    1.235  1.086  0.149 1.26e-02 6.30e+03 1.40e+02
  bond pdb=" N   LYS B 298 "
       pdb=" CA  LYS B 298 "
    ideal  model  delta    sigma   weight residual
    1.457  1.325  0.132 1.29e-02 6.01e+03 1.05e+02
  bond pdb=" CG  PRO A 410 "
       pdb=" CD  PRO A 410 "
    ideal  model  delta    sigma   weight residual
    1.503  1.234  0.269 3.40e-02 8.65e+02 6.26e+01
  bond pdb=" N   LEU B 299 "
       pdb=" CA  LEU B 299 "
    ideal  model  delta    sigma   weight residual
    1.456  1.544 -0.088 1.32e-02 5.74e+03 4.43e+01
  ... (remaining 6531 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.62: 8872
       11.62 -    23.23: 6
       23.23 -    34.85: 3
       34.85 -    46.46: 0
       46.46 -    58.08: 1
  Bond angle restraints: 8882
  Sorted by residual:
  angle pdb=" N   PRO A 410 "
        pdb=" CD  PRO A 410 "
        pdb=" CG  PRO A 410 "
      ideal   model   delta    sigma   weight residual
     103.20   75.64   27.56 1.50e+00 4.44e-01 3.38e+02
  angle pdb=" CB  PRO A 410 "
        pdb=" CG  PRO A 410 "
        pdb=" CD  PRO A 410 "
      ideal   model   delta    sigma   weight residual
     106.10  164.18  -58.08 3.20e+00 9.77e-02 3.29e+02
  angle pdb=" CA  PRO A 410 "
        pdb=" CB  PRO A 410 "
        pdb=" CG  PRO A 410 "
      ideal   model   delta    sigma   weight residual
     104.50   70.31   34.19 1.90e+00 2.77e-01 3.24e+02
  angle pdb=" N   GLU B 297 "
        pdb=" CA  GLU B 297 "
        pdb=" C   GLU B 297 "
      ideal   model   delta    sigma   weight residual
     110.80   86.71   24.09 2.13e+00 2.20e-01 1.28e+02
  angle pdb=" N   LEU B 299 "
        pdb=" CA  LEU B 299 "
        pdb=" CB  LEU B 299 "
      ideal   model   delta    sigma   weight residual
     110.53  123.48  -12.95 1.47e+00 4.63e-01 7.76e+01
  ... (remaining 8877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.35: 3382
       19.35 -    38.69: 398
       38.69 -    58.04: 93
       58.04 -    77.38: 17
       77.38 -    96.73: 9
  Dihedral angle restraints: 3899
    sinusoidal: 1539
      harmonic: 2360
  Sorted by residual:
  dihedral pdb=" N   LEU B 299 "
           pdb=" C   LEU B 299 "
           pdb=" CA  LEU B 299 "
           pdb=" CB  LEU B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  155.80  -33.00     0      2.50e+00 1.60e-01 1.74e+02
  dihedral pdb=" C   LEU B 299 "
           pdb=" N   LEU B 299 "
           pdb=" CA  LEU B 299 "
           pdb=" CB  LEU B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -152.97   30.37     0      2.50e+00 1.60e-01 1.48e+02
  dihedral pdb=" CB  CYS A 107 "
           pdb=" SG  CYS A 107 "
           pdb=" SG  CYS A 130 "
           pdb=" CB  CYS A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.66   81.34     1      1.00e+01 1.00e-02 8.15e+01
  ... (remaining 3896 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.283: 968
       0.283 -    0.565: 2
       0.565 -    0.848: 0
       0.848 -    1.131: 0
       1.131 -    1.414: 1
  Chirality restraints: 971
  Sorted by residual:
  chirality pdb=" CA  LEU B 299 "
            pdb=" N   LEU B 299 "
            pdb=" C   LEU B 299 "
            pdb=" CB  LEU B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 5.00e+01
  chirality pdb=" CA  MET B 295 "
            pdb=" N   MET B 295 "
            pdb=" C   MET B 295 "
            pdb=" CB  MET B 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.96e+00
  chirality pdb=" CA  GLU B 297 "
            pdb=" N   GLU B 297 "
            pdb=" C   GLU B 297 "
            pdb=" CB  GLU B 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.97   -0.46 2.00e-01 2.50e+01 5.35e+00
  ... (remaining 968 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 110 "    0.071 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO B 111 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO B 111 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B 111 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  56 "   -0.054 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO A  57 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A  57 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A  57 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 294 "    0.017 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   LEU B 294 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   LEU B 294 "    0.020 2.00e-02 2.50e+03
        pdb=" N   MET B 295 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        0.91 -     1.71: 3
        1.71 -     2.51: 105
        2.51 -     3.30: 7238
        3.30 -     4.10: 15863
        4.10 -     4.90: 29247
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 52456
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU B 299 "
            pdb=" CG2 ILE B 304 "
     model   vdw
     0.912 3.880
  nonbonded pdb=" CD1 LEU B 299 "
            pdb=" CB  ILE B 304 "
     model   vdw
     1.453 3.890
  nonbonded pdb=" CG  LEU B 299 "
            pdb=" CG2 ILE B 304 "
     model   vdw
     1.571 3.890
  nonbonded pdb=" CB  ILE B 226 "
            pdb=" CE  MET B 295 "
     model   vdw
     1.840 3.890
  nonbonded pdb=" CG2 ILE B 226 "
            pdb=" CE  MET B 295 "
     model   vdw
     1.863 3.880
  ... (remaining 52451 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.40 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:             4.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.840
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
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      :  0.010   0.593   6542  Z= 0.373
  Angle     :  1.227  58.077   8894  Z= 0.622
  Chirality :  0.069   1.414    971
  Planarity :  0.007   0.103   1170
  Dihedral  : 17.643  96.728   2381
  Min Nonbonded Distance : 0.912

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  4.51 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 24.89 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.40 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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 (0.28), residues: 822
  helix: -1.81 (0.49), residues: 88
  sheet: -1.23 (0.31), residues: 252
  loop : -1.45 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 260 
 HIS   0.006   0.001   HIS B 192 
 PHE   0.019   0.002   PHE B 414 
 TYR   0.017   0.001   TYR A 288 
 ARG   0.006   0.001   ARG B 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26885 (  188)
  hydrogen bonds       : angle      10.66624 (  476)
  SS BOND              : bond        0.00502 (    6)
  SS BOND              : angle       1.24819 (   12)
  covalent geometry    : bond        0.00965 ( 6536)
  covalent geometry    : angle       1.22694 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.2055
  time to fit residues: 16.7584
Evaluate side-chains
  55 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  298 LYS
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  304 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 62 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
A 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.238343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.204244 restraints weight = 15837.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.4532 rms_B_bonded: 5.26
r_work (final): 0.4532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4532 r_free = 0.4532    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4532 r_free = 0.4532    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   6542  Z= 0.176
  Angle     :  0.769  16.642   8894  Z= 0.395
  Chirality :  0.048   0.200    971
  Planarity :  0.006   0.070   1170
  Dihedral  :  5.413  36.796    915
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  6.21 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.01 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -1.85 (0.28), residues: 822
  helix: -1.25 (0.50), residues: 80
  sheet: -1.21 (0.31), residues: 258
  loop : -1.19 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 260 
 HIS   0.007   0.001   HIS A 291 
 PHE   0.018   0.002   PHE A  19 
 TYR   0.022   0.002   TYR A 288 
 ARG   0.003   0.001   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  188)
  hydrogen bonds       : angle       7.57230 (  476)
  SS BOND              : bond        0.00407 (    6)
  SS BOND              : angle       1.44933 (   12)
  covalent geometry    : bond        0.00420 ( 6536)
  covalent geometry    : angle       0.76773 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5587 (m)
REVERT: A  410 PRO cc_start: 0.7542 (OUTLIER) cc_final: 0.7174 (Cg_exo)
REVERT: B  181 LYS cc_start: 0.7346 (mtpp) cc_final: 0.6902 (tppt)
REVERT: B  321 TYR cc_start: 0.3201 (OUTLIER) cc_final: 0.2147 (t80)
  outliers start: 19
  outliers final: 6
  residues processed: 77
  average time/residue: 0.1767
  time to fit residues: 18.8240
Evaluate side-chains
  63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 333 GLN
A 443 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.234863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.200128 restraints weight = 15850.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.4482 rms_B_bonded: 5.71
r_work (final): 0.4482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4481 r_free = 0.4481    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4481 r_free = 0.4481    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   6542  Z= 0.167
  Angle     :  0.757  15.984   8894  Z= 0.388
  Chirality :  0.047   0.189    971
  Planarity :  0.006   0.070   1170
  Dihedral  :  4.975  27.384    904
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.72 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.44 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.01 (0.28), residues: 822
  helix: -1.45 (0.45), residues: 93
  sheet: -1.19 (0.31), residues: 264
  loop : -1.36 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 260 
 HIS   0.007   0.001   HIS A 291 
 PHE   0.019   0.002   PHE B 431 
 TYR   0.020   0.002   TYR A 380 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03854 (  188)
  hydrogen bonds       : angle       7.20698 (  476)
  SS BOND              : bond        0.00460 (    6)
  SS BOND              : angle       1.46848 (   12)
  covalent geometry    : bond        0.00398 ( 6536)
  covalent geometry    : angle       0.75560 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5757 (m)
REVERT: A  410 PRO cc_start: 0.7551 (OUTLIER) cc_final: 0.7183 (Cg_exo)
REVERT: B  181 LYS cc_start: 0.7516 (mtpp) cc_final: 0.6929 (tppt)
REVERT: B  209 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7141 (pttm)
REVERT: B  321 TYR cc_start: 0.3302 (OUTLIER) cc_final: 0.2214 (t80)
REVERT: B  413 SER cc_start: 0.7085 (OUTLIER) cc_final: 0.6841 (t)
  outliers start: 23
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1942
  time to fit residues: 20.1077
Evaluate side-chains
  63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  413 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.233439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.205404 restraints weight = 6647.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.4547 rms_B_bonded: 1.61
r_work: 0.4325 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4345 r_free = 0.4345    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4345 r_free = 0.4345    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   6542  Z= 0.177
  Angle     :  0.761  16.050   8894  Z= 0.388
  Chirality :  0.047   0.216    971
  Planarity :  0.006   0.070   1170
  Dihedral  :  5.046  27.147    904
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.21 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 20.72 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -1.98 (0.28), residues: 822
  helix: -1.14 (0.49), residues: 91
  sheet: -1.12 (0.32), residues: 245
  loop : -1.45 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 260 
 HIS   0.004   0.001   HIS A 291 
 PHE   0.017   0.002   PHE A  19 
 TYR   0.024   0.002   TYR A 288 
 ARG   0.004   0.000   ARG A 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03576 (  188)
  hydrogen bonds       : angle       7.10730 (  476)
  SS BOND              : bond        0.00472 (    6)
  SS BOND              : angle       1.42952 (   12)
  covalent geometry    : bond        0.00422 ( 6536)
  covalent geometry    : angle       0.75973 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.3807 (OUTLIER) cc_final: 0.3248 (m-10)
REVERT: A  288 TYR cc_start: 0.2819 (OUTLIER) cc_final: 0.2377 (t80)
REVERT: A  410 PRO cc_start: 0.7312 (OUTLIER) cc_final: 0.6903 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4411 (OUTLIER) cc_final: 0.3860 (tt)
REVERT: B  181 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7038 (tppt)
REVERT: B  209 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7128 (pttm)
REVERT: B  215 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7608 (p0)
REVERT: B  413 SER cc_start: 0.6856 (OUTLIER) cc_final: 0.6493 (t)
  outliers start: 30
  outliers final: 13
  residues processed: 88
  average time/residue: 0.1804
  time to fit residues: 21.6303
Evaluate side-chains
  73 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  413 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 106 GLN
B 269 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.234088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.205145 restraints weight = 6537.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4552 rms_B_bonded: 1.86
r_work: 0.4289 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4292 r_free = 0.4292    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4292 r_free = 0.4292    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   6542  Z= 0.153
  Angle     :  0.742  16.103   8894  Z= 0.377
  Chirality :  0.048   0.235    971
  Planarity :  0.005   0.069   1170
  Dihedral  :  4.920  29.359    904
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.63 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.44 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -1.93 (0.28), residues: 822
  helix: -1.15 (0.50), residues: 91
  sheet: -1.07 (0.33), residues: 245
  loop : -1.41 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 260 
 HIS   0.004   0.001   HIS A 291 
 PHE   0.016   0.002   PHE A 356 
 TYR   0.020   0.002   TYR A 380 
 ARG   0.003   0.000   ARG A 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03411 (  188)
  hydrogen bonds       : angle       6.90734 (  476)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       1.36303 (   12)
  covalent geometry    : bond        0.00369 ( 6536)
  covalent geometry    : angle       0.74082 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 54
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6439 (m)
REVERT: A  204 PHE cc_start: 0.3594 (OUTLIER) cc_final: 0.3086 (m-10)
REVERT: A  410 PRO cc_start: 0.7493 (OUTLIER) cc_final: 0.7077 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4329 (OUTLIER) cc_final: 0.3770 (tt)
REVERT: B  106 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8412 (mp10)
REVERT: B  181 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7062 (tppt)
REVERT: B  215 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7630 (p0)
REVERT: B  287 MET cc_start: 0.7209 (mmm) cc_final: 0.6997 (mmm)
REVERT: B  413 SER cc_start: 0.6863 (OUTLIER) cc_final: 0.6534 (t)
  outliers start: 29
  outliers final: 16
  residues processed: 81
  average time/residue: 0.1787
  time to fit residues: 19.5817
Evaluate side-chains
  77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.231592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.195728 restraints weight = 15841.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.4443 rms_B_bonded: 5.81
r_work: 0.4171 rms_B_bonded: 5.52 restraints_weight: 2.0000
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4170 r_free = 0.4170    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4170 r_free = 0.4170    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   6542  Z= 0.178
  Angle     :  0.768  16.080   8894  Z= 0.385
  Chirality :  0.048   0.206    971
  Planarity :  0.006   0.078   1170
  Dihedral  :  5.114  32.962    904
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.33 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 21.58 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.04 (0.28), residues: 822
  helix: -1.33 (0.49), residues: 91
  sheet: -1.13 (0.32), residues: 245
  loop : -1.47 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 260 
 HIS   0.007   0.001   HIS A 291 
 PHE   0.016   0.002   PHE A  19 
 TYR   0.020   0.002   TYR A 190 
 ARG   0.003   0.000   ARG A 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  188)
  hydrogen bonds       : angle       6.89314 (  476)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.45275 (   12)
  covalent geometry    : bond        0.00433 ( 6536)
  covalent geometry    : angle       0.76663 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.3582 (OUTLIER) cc_final: 0.3084 (m-10)
REVERT: A  410 PRO cc_start: 0.7390 (OUTLIER) cc_final: 0.6967 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4621 (OUTLIER) cc_final: 0.4051 (tt)
REVERT: B  181 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7051 (tppt)
REVERT: B  209 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6876 (pttm)
REVERT: B  390 LYS cc_start: 0.6479 (pptt) cc_final: 0.6255 (pptt)
REVERT: B  413 SER cc_start: 0.6685 (OUTLIER) cc_final: 0.6441 (t)
  outliers start: 32
  outliers final: 20
  residues processed: 90
  average time/residue: 0.2034
  time to fit residues: 24.2510
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 58
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  319 GLN
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    0.2980
   chunk 70 optimal weight:    0.0870
   chunk 77 optimal weight:    0.2980
   chunk 53 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.233138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.214632 restraints weight = 9462.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4655 rms_B_bonded: 0.98
r_work: 0.4377 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4413 r_free = 0.4413    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4413 r_free = 0.4413    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   6542  Z= 0.152
  Angle     :  0.744  16.127   8894  Z= 0.368
  Chirality :  0.046   0.175    971
  Planarity :  0.005   0.076   1170
  Dihedral  :  4.928  31.209    904
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.48 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.02 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.05 (0.28), residues: 822
  helix: -1.34 (0.47), residues: 97
  sheet: -1.16 (0.32), residues: 246
  loop : -1.46 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 260 
 HIS   0.003   0.001   HIS B 274 
 PHE   0.016   0.002   PHE A 356 
 TYR   0.021   0.002   TYR A 380 
 ARG   0.005   0.000   ARG B  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  188)
  hydrogen bonds       : angle       6.75676 (  476)
  SS BOND              : bond        0.00434 (    6)
  SS BOND              : angle       1.32471 (   12)
  covalent geometry    : bond        0.00369 ( 6536)
  covalent geometry    : angle       0.74289 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.5358 (mp0) cc_final: 0.5060 (mp0)
REVERT: A  167 CYS cc_start: 0.6413 (OUTLIER) cc_final: 0.6203 (m)
REVERT: A  204 PHE cc_start: 0.4074 (OUTLIER) cc_final: 0.3577 (m-10)
REVERT: A  410 PRO cc_start: 0.7609 (OUTLIER) cc_final: 0.7203 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4654 (OUTLIER) cc_final: 0.4095 (tt)
REVERT: B  181 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7159 (tppt)
REVERT: B  209 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6352 (pttm)
REVERT: B  413 SER cc_start: 0.7068 (OUTLIER) cc_final: 0.6797 (t)
  outliers start: 23
  outliers final: 15
  residues processed: 79
  average time/residue: 0.2063
  time to fit residues: 21.6696
Evaluate side-chains
  77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    0.0070
   chunk 77 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 67 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 ASN
B 274 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.234446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.201014 restraints weight = 12064.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.4498 rms_B_bonded: 4.16
r_work: 0.4263 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4297 r_free = 0.4297    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4297 r_free = 0.4297    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4297
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   6542  Z= 0.136
  Angle     :  0.714  16.155   8894  Z= 0.355
  Chirality :  0.046   0.181    971
  Planarity :  0.005   0.068   1170
  Dihedral  :  4.772  29.310    904
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.36 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.74 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -1.99 (0.28), residues: 822
  helix: -1.28 (0.48), residues: 97
  sheet: -1.22 (0.32), residues: 259
  loop : -1.34 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 260 
 HIS   0.002   0.001   HIS A 291 
 PHE   0.017   0.002   PHE A 356 
 TYR   0.017   0.002   TYR A 380 
 ARG   0.004   0.000   ARG B  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03055 (  188)
  hydrogen bonds       : angle       6.55041 (  476)
  SS BOND              : bond        0.00413 (    6)
  SS BOND              : angle       1.23759 (   12)
  covalent geometry    : bond        0.00332 ( 6536)
  covalent geometry    : angle       0.71283 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 58
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6413 (m)
REVERT: A  204 PHE cc_start: 0.3712 (OUTLIER) cc_final: 0.3189 (m-10)
REVERT: A  333 GLN cc_start: 0.6856 (pt0) cc_final: 0.5990 (mm-40)
REVERT: A  410 PRO cc_start: 0.7359 (OUTLIER) cc_final: 0.6939 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4514 (OUTLIER) cc_final: 0.3956 (tt)
REVERT: B  181 LYS cc_start: 0.7723 (mtpp) cc_final: 0.7051 (tppt)
REVERT: B  209 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6615 (pttm)
REVERT: B  390 LYS cc_start: 0.6457 (pptt) cc_final: 0.6199 (pptt)
  outliers start: 25
  outliers final: 16
  residues processed: 81
  average time/residue: 0.2441
  time to fit residues: 28.4396
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.229521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.211324 restraints weight = 12101.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.4623 rms_B_bonded: 1.31
r_work: 0.4283 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4316 r_free = 0.4316    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4316 r_free = 0.4316    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   6542  Z= 0.181
  Angle     :  0.771  16.059   8894  Z= 0.385
  Chirality :  0.047   0.211    971
  Planarity :  0.006   0.061   1170
  Dihedral  :  5.084  27.794    904
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.82 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.46 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.11 (0.28), residues: 822
  helix: -1.48 (0.47), residues: 97
  sheet: -1.21 (0.32), residues: 250
  loop : -1.47 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 260 
 HIS   0.004   0.001   HIS A 291 
 PHE   0.021   0.002   PHE A 356 
 TYR   0.027   0.002   TYR A 288 
 ARG   0.004   0.000   ARG B  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  188)
  hydrogen bonds       : angle       6.79778 (  476)
  SS BOND              : bond        0.00537 (    6)
  SS BOND              : angle       1.48218 (   12)
  covalent geometry    : bond        0.00438 ( 6536)
  covalent geometry    : angle       0.76969 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.4108 (OUTLIER) cc_final: 0.3556 (m-10)
REVERT: A  333 GLN cc_start: 0.7280 (pt0) cc_final: 0.6542 (mm-40)
REVERT: A  410 PRO cc_start: 0.7570 (OUTLIER) cc_final: 0.7158 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4547 (tt)
REVERT: B  209 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6338 (pttm)
REVERT: B  215 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.8004 (p0)
  outliers start: 24
  outliers final: 16
  residues processed: 80
  average time/residue: 0.2161
  time to fit residues: 23.7562
Evaluate side-chains
  77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0670
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.229302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.194144 restraints weight = 15762.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 5.01
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4414 r_free = 0.4414    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4414 r_free = 0.4414    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.210   6542  Z= 0.247
  Angle     :  1.118  59.199   8894  Z= 0.619
  Chirality :  0.056   0.963    971
  Planarity :  0.006   0.060   1170
  Dihedral  :  5.154  27.604    904
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.58 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.03 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.16 (0.28), residues: 822
  helix: -1.48 (0.47), residues: 97
  sheet: -1.29 (0.32), residues: 250
  loop : -1.47 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 260 
 HIS   0.004   0.001   HIS A 291 
 PHE   0.020   0.002   PHE A 356 
 TYR   0.023   0.002   TYR A 288 
 ARG   0.014   0.001   ARG A 327 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  188)
  hydrogen bonds       : angle       6.80133 (  476)
  SS BOND              : bond        0.00553 (    6)
  SS BOND              : angle       1.48820 (   12)
  covalent geometry    : bond        0.00586 ( 6536)
  covalent geometry    : angle       1.11695 ( 8882)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.3709 (OUTLIER) cc_final: 0.3200 (m-10)
REVERT: A  333 GLN cc_start: 0.7121 (pt0) cc_final: 0.6305 (mm-40)
REVERT: A  410 PRO cc_start: 0.7467 (OUTLIER) cc_final: 0.7107 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4130 (OUTLIER) cc_final: 0.3651 (tt)
REVERT: B  209 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6707 (pttm)
REVERT: B  215 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7717 (p0)
  outliers start: 24
  outliers final: 15
  residues processed: 78
  average time/residue: 0.2893
  time to fit residues: 32.2418
Evaluate side-chains
  76 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0870
   chunk 80 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.229412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.196038 restraints weight = 9819.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4457 rms_B_bonded: 2.19
r_work: 0.4176 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4206 r_free = 0.4206    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4206 r_free = 0.4206    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.210   6542  Z= 0.247
  Angle     :  1.118  59.199   8894  Z= 0.619
  Chirality :  0.056   0.963    971
  Planarity :  0.006   0.060   1170
  Dihedral  :  5.154  27.604    904
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.58 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.60 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.16 (0.28), residues: 822
  helix: -1.48 (0.47), residues: 97
  sheet: -1.29 (0.32), residues: 250
  loop : -1.47 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 260 
 HIS   0.004   0.001   HIS A 291 
 PHE   0.020   0.002   PHE A 356 
 TYR   0.023   0.002   TYR A 288 
 ARG   0.014   0.001   ARG A 327 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  188)
  hydrogen bonds       : angle       6.80133 (  476)
  SS BOND              : bond        0.00553 (    6)
  SS BOND              : angle       1.48820 (   12)
  covalent geometry    : bond        0.00586 ( 6536)
  covalent geometry    : angle       1.11695 ( 8882)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3744.15 seconds
wall clock time: 67 minutes 16.01 seconds (4036.01 seconds total)