Starting phenix.real_space_refine
on Thu Jun  5 11:41:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i4g_35172/06_2025/8i4g_35172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i4g_35172/06_2025/8i4g_35172.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i4g_35172/06_2025/8i4g_35172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i4g_35172/06_2025/8i4g_35172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i4g_35172/06_2025/8i4g_35172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i4g_35172/06_2025/8i4g_35172.cif"
  }
  resolution = 3.68
  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=   0.001 sd=   0.029
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: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3878      2.51       5
     N    1005      2.21       5
     O    1149      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6057
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 922
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 5135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 5135
          Classifications: {'peptide': 649}
          Link IDs: {'PTRANS': 34, 'TRANS': 614}
  Time building chain proxies: 4.22, per 1000 atoms: 0.70
  Number of scatterers: 6057
  At special positions: 0
  Unit cell: (69.9, 94.132, 133.276, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1149      8.00
     N    1005      7.00
     C    3878      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 137 " - pdb=" SG  CYS A 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 297 " - pdb=" SG  CYS A 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 385 " - pdb=" SG  CYS A 438 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 486 " - pdb=" SG  CYS A 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 544 " - pdb=" SG  CYS A 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 623 " - pdb=" SG  CYS A 655 " 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: 1.27
  Conformation dependent library (CDL) restraints added in 969.2 milliseconds
  

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 13 sheets defined
      4.8% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 300 through 310
      removed outlier: 3.965A  pdb=" N   GLU A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 348
    Processing helix  chain 'A' and resid 370 through 375
      removed outlier: 3.994A  pdb=" N   VAL A 373 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A 375 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 413
      No H-bonds generated for 'chain 'A' and resid 411 through 413'
    Processing helix  chain 'A' and resid 625 through 630
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.619A  pdb=" N   VAL C   5 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASP C  73 " --> pdb=" O   THR C  78 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER C  71 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.773A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   THR C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   MET C  34 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 39
      removed outlier: 3.640A  pdb=" N   VAL A  70 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER A  68 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 273 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   PHE A  73 " --> pdb=" O   TYR A 271 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 63
      removed outlier: 3.741A  pdb=" N   HIS A  57 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP A  61 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A  63 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LEU A 282 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   ALA A 294 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LYS A 284 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 91
      removed outlier: 3.782A  pdb=" N   GLY A 109 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   CYS A 137 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133
      removed outlier: 3.782A  pdb=" N   GLY A 109 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   LEU A 147 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 100
      removed outlier: 3.641A  pdb=" N   VAL A  96 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER A 100 " --> pdb=" O   ARG A 196 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 214 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLU A 197 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS A 212 " --> pdb=" O   GLU A 197 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A 199 " --> pdb=" O   TYR A 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320
      removed outlier: 3.555A  pdb=" N   TYR A 618 " --> pdb=" O   CYS A 655 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 364
      removed outlier: 3.567A  pdb=" N   ALA A 403 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 364
      removed outlier: 3.567A  pdb=" N   ALA A 403 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 368
      removed outlier: 6.868A  pdb=" N   CYS A 367 " --> pdb=" O   CYS A 531 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 458 through 460
      removed outlier: 3.662A  pdb=" N   TYR A 459 " --> pdb=" O   GLN A 499 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 544 through 547
      removed outlier: 4.008A  pdb=" N   VAL A 545 " --> pdb=" O   GLY A 556 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY A 556 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)

    117 hydrogen bonds defined for protein.
    270 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1937
        1.34 -     1.46: 1565
        1.46 -     1.58: 2688
        1.58 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 6219
  Sorted by residual:
  bond pdb=" C   GLN A 179 "
       pdb=" N   PRO A 180 "
    ideal  model  delta    sigma   weight residual
    1.332  1.361 -0.030 1.30e-02 5.92e+03 5.18e+00
  bond pdb=" C   PHE A 335 "
       pdb=" N   PRO A 336 "
    ideal  model  delta    sigma   weight residual
    1.328  1.351 -0.023 1.25e-02 6.40e+03 3.26e+00
  bond pdb=" CA  ILE A 203 "
       pdb=" CB  ILE A 203 "
    ideal  model  delta    sigma   weight residual
    1.528  1.541 -0.013 1.34e-02 5.57e+03 9.54e-01
  bond pdb=" CA  ILE A 125 "
       pdb=" CB  ILE A 125 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.31e-02 5.83e+03 9.05e-01
  bond pdb=" CA  HIS A 631 "
       pdb=" C   HIS A 631 "
    ideal  model  delta    sigma   weight residual
    1.532  1.524  0.009 9.60e-03 1.09e+04 8.52e-01
  ... (remaining 6214 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 7860
        1.13 -     2.27: 480
        2.27 -     3.40: 111
        3.40 -     4.53: 13
        4.53 -     5.66: 4
  Bond angle restraints: 8468
  Sorted by residual:
  angle pdb=" N   VAL A 326 "
        pdb=" CA  VAL A 326 "
        pdb=" C   VAL A 326 "
      ideal   model   delta    sigma   weight residual
     112.96  108.47    4.49 1.00e+00 1.00e+00 2.01e+01
  angle pdb=" N   THR A 308 "
        pdb=" CA  THR A 308 "
        pdb=" C   THR A 308 "
      ideal   model   delta    sigma   weight residual
     114.39  110.19    4.20 1.45e+00 4.76e-01 8.40e+00
  angle pdb=" C   SER A 178 "
        pdb=" N   GLN A 179 "
        pdb=" CA  GLN A 179 "
      ideal   model   delta    sigma   weight residual
     119.78  123.34   -3.56 1.24e+00 6.50e-01 8.26e+00
  angle pdb=" N   ARG C  67 "
        pdb=" CA  ARG C  67 "
        pdb=" C   ARG C  67 "
      ideal   model   delta    sigma   weight residual
     114.56  111.01    3.55 1.27e+00 6.20e-01 7.80e+00
  angle pdb=" N   SER A 643 "
        pdb=" CA  SER A 643 "
        pdb=" C   SER A 643 "
      ideal   model   delta    sigma   weight residual
     107.32  111.90   -4.58 1.65e+00 3.67e-01 7.72e+00
  ... (remaining 8463 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 3422
       16.72 -    33.44: 171
       33.44 -    50.15: 38
       50.15 -    66.87: 10
       66.87 -    83.59: 1
  Dihedral angle restraints: 3642
    sinusoidal: 1412
      harmonic: 2230
  Sorted by residual:
  dihedral pdb=" SG  CYS A 137 "
           pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" CA  CYS A 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   23.14   55.86     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CB  GLU A 102 "
           pdb=" CG  GLU A 102 "
           pdb=" CD  GLU A 102 "
           pdb=" OE1 GLU A 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.59   83.59     1      3.00e+01 1.11e-03 9.48e+00
  dihedral pdb=" N   TYR A 495 "
           pdb=" CA  TYR A 495 "
           pdb=" CB  TYR A 495 "
           pdb=" CG  TYR A 495 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    3.61   56.39     3      1.50e+01 4.44e-03 9.40e+00
  ... (remaining 3639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 538
       0.025 -    0.050: 207
       0.050 -    0.075: 91
       0.075 -    0.100: 57
       0.100 -    0.124: 28
  Chirality restraints: 921
  Sorted by residual:
  chirality pdb=" CB  ILE A 416 "
            pdb=" CA  ILE A 416 "
            pdb=" CG1 ILE A 416 "
            pdb=" CG2 ILE A 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE A 209 "
            pdb=" N   ILE A 209 "
            pdb=" C   ILE A 209 "
            pdb=" CB  ILE A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  ILE A 216 "
            pdb=" N   ILE A 216 "
            pdb=" C   ILE A 216 "
            pdb=" CB  ILE A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.54e-01
  ... (remaining 918 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 605 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 606 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 606 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 606 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 342 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO A 343 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 343 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 343 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 532 "   -0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO A 533 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 533 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 533 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1144
        2.78 -     3.31: 5520
        3.31 -     3.84: 10051
        3.84 -     4.37: 11282
        4.37 -     4.90: 19539
  Nonbonded interactions: 47536
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 286 "
            pdb=" OG1 THR A 292 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NH1 ARG A  42 "
            pdb=" OG  SER A 227 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   VAL A 136 "
            pdb=" OG1 THR A 173 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG1 THR A 256 "
            pdb=" OD1 ASP A 259 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER A 118 "
            pdb=" OE1 GLN A 140 "
     model   vdw
     2.285 3.040
  ... (remaining 47531 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             25.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6423
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6228  Z= 0.147
  Angle     :  0.631   5.665   8486  Z= 0.405
  Chirality :  0.040   0.124    921
  Planarity :  0.003   0.030   1100
  Dihedral  : 10.191  83.589   2197
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  :  9.62 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.78 (0.24), residues: 764
  helix: -4.28 (0.42), residues: 40
  sheet: -2.50 (0.33), residues: 174
  loop : -3.60 (0.22), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 359 
 HIS   0.001   0.000   HIS A 525 
 PHE   0.007   0.001   PHE A 406 
 TYR   0.006   0.001   TYR A 271 
 ARG   0.002   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30077 (  103)
  hydrogen bonds       : angle      11.61967 (  270)
  SS BOND              : bond        0.00146 (    9)
  SS BOND              : angle       0.64596 (   18)
  covalent geometry    : bond        0.00232 ( 6219)
  covalent geometry    : angle       0.63067 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 237
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.7431 (tp) cc_final: 0.7113 (tp)
REVERT: C   31 TYR cc_start: 0.7516 (p90) cc_final: 0.7150 (p90)
REVERT: C   77 ASN cc_start: 0.7701 (t0) cc_final: 0.7033 (t0)
REVERT: C   83 MET cc_start: 0.6665 (mtt) cc_final: 0.6329 (mtt)
REVERT: C  100 SER cc_start: 0.8672 (t) cc_final: 0.8044 (t)
REVERT: A   40 PHE cc_start: 0.8285 (m-80) cc_final: 0.7997 (m-10)
REVERT: A   60 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6593 (tm-30)
REVERT: A   72 TRP cc_start: 0.7879 (t60) cc_final: 0.7594 (t60)
REVERT: A   89 VAL cc_start: 0.8032 (t) cc_final: 0.7814 (p)
REVERT: A  105 ASN cc_start: 0.7580 (m-40) cc_final: 0.7091 (p0)
REVERT: A  119 LYS cc_start: 0.7801 (tppt) cc_final: 0.7004 (tppt)
REVERT: A  195 LEU cc_start: 0.8091 (tp) cc_final: 0.7838 (mp)
REVERT: A  250 LEU cc_start: 0.7825 (tp) cc_final: 0.7346 (tp)
REVERT: A  255 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4544 (tp)
REVERT: A  299 LEU cc_start: 0.7945 (tp) cc_final: 0.7721 (tp)
REVERT: A  302 LEU cc_start: 0.7791 (tp) cc_final: 0.7425 (tt)
REVERT: A  362 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7149 (tmtt)
REVERT: A  420 GLN cc_start: 0.7527 (mm110) cc_final: 0.7313 (mm110)
REVERT: A  430 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7837 (mmmt)
REVERT: A  473 ASP cc_start: 0.8178 (t0) cc_final: 0.6691 (m-30)
REVERT: A  495 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6591 (p90)
REVERT: A  516 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7129 (p)
REVERT: A  520 SER cc_start: 0.7335 (m) cc_final: 0.7022 (t)
REVERT: A  523 LEU cc_start: 0.7889 (tp) cc_final: 0.7404 (tp)
REVERT: A  525 HIS cc_start: 0.6133 (p-80) cc_final: 0.5862 (p-80)
REVERT: A  534 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8262 (mmtp)
REVERT: A  535 LYS cc_start: 0.8136 (pptt) cc_final: 0.7639 (pptt)
REVERT: A  580 ASP cc_start: 0.6577 (t70) cc_final: 0.5915 (t0)
REVERT: A  592 ASP cc_start: 0.7649 (t70) cc_final: 0.7267 (t0)
REVERT: A  593 ILE cc_start: 0.8225 (mt) cc_final: 0.7959 (mt)
REVERT: A  594 THR cc_start: 0.8769 (p) cc_final: 0.8380 (m)
REVERT: A  638 THR cc_start: 0.7661 (p) cc_final: 0.7429 (p)
REVERT: A  670 ILE cc_start: 0.8518 (mt) cc_final: 0.8312 (tt)
  outliers start: 38
  outliers final: 22
  residues processed: 259
  average time/residue: 0.2261
  time to fit residues: 77.0386
Evaluate side-chains
  232 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain A residue  484 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.2980
   chunk 56 optimal weight:    0.0060
   chunk 31 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 415 GLN
A 420 GLN
A 445 ASN
A 548 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.162387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.141208 restraints weight = 10563.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.146196 restraints weight = 5643.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.149578 restraints weight = 3530.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6228  Z= 0.122
  Angle     :  0.608  11.888   8486  Z= 0.305
  Chirality :  0.044   0.169    921
  Planarity :  0.004   0.044   1100
  Dihedral  :  8.945  88.562    899
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 15.79 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.14 (0.26), residues: 764
  helix: -3.16 (0.83), residues: 28
  sheet: -2.25 (0.33), residues: 195
  loop : -3.15 (0.23), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 110 
 HIS   0.002   0.001   HIS A 213 
 PHE   0.029   0.002   PHE A 568 
 TYR   0.020   0.001   TYR C  94 
 ARG   0.005   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03199 (  103)
  hydrogen bonds       : angle       6.71738 (  270)
  SS BOND              : bond        0.00386 (    9)
  SS BOND              : angle       2.09184 (   18)
  covalent geometry    : bond        0.00271 ( 6219)
  covalent geometry    : angle       0.60131 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 202
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 TYR cc_start: 0.7537 (p90) cc_final: 0.6979 (p90)
REVERT: C   77 ASN cc_start: 0.8217 (t0) cc_final: 0.7647 (t0)
REVERT: A   40 PHE cc_start: 0.8299 (m-80) cc_final: 0.8053 (m-10)
REVERT: A   42 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7553 (ttm110)
REVERT: A   60 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6532 (tm-30)
REVERT: A  119 LYS cc_start: 0.7688 (tppt) cc_final: 0.6884 (tppt)
REVERT: A  134 ILE cc_start: 0.7685 (mt) cc_final: 0.7323 (tt)
REVERT: A  250 LEU cc_start: 0.8002 (tp) cc_final: 0.7541 (tp)
REVERT: A  255 LEU cc_start: 0.4948 (OUTLIER) cc_final: 0.4624 (tp)
REVERT: A  299 LEU cc_start: 0.8161 (tp) cc_final: 0.7871 (tp)
REVERT: A  302 LEU cc_start: 0.7760 (tp) cc_final: 0.7429 (tt)
REVERT: A  320 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7250 (mm-40)
REVERT: A  346 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7896 (mm-30)
REVERT: A  362 LYS cc_start: 0.7586 (tmtt) cc_final: 0.6980 (tmtt)
REVERT: A  398 PHE cc_start: 0.8213 (m-10) cc_final: 0.7995 (m-10)
REVERT: A  430 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7308 (mmmt)
REVERT: A  434 ASP cc_start: 0.6917 (t0) cc_final: 0.6441 (t0)
REVERT: A  472 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7559 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8421 (t0) cc_final: 0.6645 (m-30)
REVERT: A  495 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6568 (p90)
REVERT: A  518 VAL cc_start: 0.8556 (t) cc_final: 0.8286 (p)
REVERT: A  520 SER cc_start: 0.7563 (m) cc_final: 0.7269 (t)
REVERT: A  534 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8320 (mmtp)
REVERT: A  535 LYS cc_start: 0.8148 (pptt) cc_final: 0.7715 (pptt)
REVERT: A  542 ASN cc_start: 0.8190 (m-40) cc_final: 0.7967 (m110)
REVERT: A  543 LYS cc_start: 0.7610 (ttmt) cc_final: 0.7149 (ttmm)
REVERT: A  580 ASP cc_start: 0.6958 (t70) cc_final: 0.6444 (t0)
REVERT: A  593 ILE cc_start: 0.8616 (mt) cc_final: 0.8390 (mt)
REVERT: A  598 PHE cc_start: 0.7092 (t80) cc_final: 0.6796 (t80)
  outliers start: 45
  outliers final: 30
  residues processed: 227
  average time/residue: 0.2754
  time to fit residues: 81.6171
Evaluate side-chains
  220 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 188
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain A residue  484 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  672 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C  84 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.151166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130247 restraints weight = 10695.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.135056 restraints weight = 5756.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.138303 restraints weight = 3621.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6228  Z= 0.202
  Angle     :  0.681  11.528   8486  Z= 0.347
  Chirality :  0.045   0.196    921
  Planarity :  0.005   0.043   1100
  Dihedral  :  9.119  87.977    894
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  7.82 %
    Allowed  : 17.59 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.27), residues: 764
  helix: -1.94 (1.24), residues: 22
  sheet: -2.02 (0.33), residues: 198
  loop : -3.08 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 359 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.025   0.002   PHE A 496 
 TYR   0.019   0.002   TYR A 642 
 ARG   0.004   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  103)
  hydrogen bonds       : angle       6.19206 (  270)
  SS BOND              : bond        0.00483 (    9)
  SS BOND              : angle       2.56780 (   18)
  covalent geometry    : bond        0.00435 ( 6219)
  covalent geometry    : angle       0.67123 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 210
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8073 (tp) cc_final: 0.7501 (tp)
REVERT: C   27 PHE cc_start: 0.7929 (t80) cc_final: 0.7332 (t80)
REVERT: C   29 PHE cc_start: 0.7444 (m-10) cc_final: 0.6921 (m-10)
REVERT: C   31 TYR cc_start: 0.7586 (p90) cc_final: 0.7149 (p90)
REVERT: C   52 SER cc_start: 0.8383 (t) cc_final: 0.7700 (p)
REVERT: C   77 ASN cc_start: 0.8472 (t0) cc_final: 0.7793 (t0)
REVERT: C   83 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.6078 (mpp)
REVERT: A   40 PHE cc_start: 0.8402 (m-80) cc_final: 0.8069 (m-10)
REVERT: A   41 THR cc_start: 0.7571 (p) cc_final: 0.7314 (t)
REVERT: A   44 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8327 (t)
REVERT: A   60 GLN cc_start: 0.7437 (tm-30) cc_final: 0.6561 (tm-30)
REVERT: A   72 TRP cc_start: 0.8085 (t60) cc_final: 0.7729 (t60)
REVERT: A  119 LYS cc_start: 0.7860 (tppt) cc_final: 0.7148 (tppt)
REVERT: A  183 MET cc_start: 0.5997 (tmt) cc_final: 0.5621 (tmt)
REVERT: A  195 LEU cc_start: 0.8677 (tt) cc_final: 0.8424 (tt)
REVERT: A  212 LYS cc_start: 0.8006 (tptm) cc_final: 0.7761 (tptm)
REVERT: A  250 LEU cc_start: 0.8028 (tp) cc_final: 0.7586 (tp)
REVERT: A  255 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4500 (tp)
REVERT: A  299 LEU cc_start: 0.8196 (tp) cc_final: 0.7985 (tp)
REVERT: A  302 LEU cc_start: 0.7995 (tp) cc_final: 0.7270 (tt)
REVERT: A  305 THR cc_start: 0.8361 (m) cc_final: 0.8125 (p)
REVERT: A  319 TYR cc_start: 0.7354 (m-10) cc_final: 0.7102 (m-10)
REVERT: A  320 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7319 (mm-40)
REVERT: A  346 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7806 (mm-30)
REVERT: A  356 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8304 (p)
REVERT: A  361 ARG cc_start: 0.7737 (ttm170) cc_final: 0.6897 (ttm170)
REVERT: A  429 TYR cc_start: 0.7814 (t80) cc_final: 0.7563 (t80)
REVERT: A  430 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7573 (mmmt)
REVERT: A  472 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7588 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8440 (t0) cc_final: 0.7160 (m-30)
REVERT: A  495 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6732 (p90)
REVERT: A  520 SER cc_start: 0.8013 (m) cc_final: 0.7548 (p)
REVERT: A  523 LEU cc_start: 0.8053 (tp) cc_final: 0.7816 (tp)
REVERT: A  534 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8377 (mmtp)
REVERT: A  538 ASN cc_start: 0.7258 (t0) cc_final: 0.7044 (t0)
REVERT: A  543 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7496 (ttmm)
REVERT: A  568 PHE cc_start: 0.7347 (t80) cc_final: 0.6885 (t80)
REVERT: A  580 ASP cc_start: 0.7231 (t70) cc_final: 0.6409 (t0)
REVERT: A  592 ASP cc_start: 0.7538 (t70) cc_final: 0.7159 (t0)
REVERT: A  639 TRP cc_start: 0.6432 (OUTLIER) cc_final: 0.6017 (t60)
REVERT: A  670 ILE cc_start: 0.8503 (mt) cc_final: 0.8237 (tt)
  outliers start: 52
  outliers final: 31
  residues processed: 235
  average time/residue: 0.1917
  time to fit residues: 57.8079
Evaluate side-chains
  236 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 199
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  639 TRP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  672 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0980
   chunk 61 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
A  69 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.152278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.131841 restraints weight = 10787.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.136621 restraints weight = 5745.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.139876 restraints weight = 3565.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6228  Z= 0.138
  Angle     :  0.647  11.103   8486  Z= 0.329
  Chirality :  0.045   0.176    921
  Planarity :  0.004   0.041   1100
  Dihedral  :  8.586  88.163    886
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  7.22 %
    Allowed  : 20.15 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.75 (0.28), residues: 764
  helix: -1.70 (1.28), residues: 22
  sheet: -1.81 (0.35), residues: 194
  loop : -3.01 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.027   0.002   PHE A 649 
 TYR   0.013   0.001   TYR A 642 
 ARG   0.006   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  103)
  hydrogen bonds       : angle       5.86997 (  270)
  SS BOND              : bond        0.00269 (    9)
  SS BOND              : angle       2.10131 (   18)
  covalent geometry    : bond        0.00306 ( 6219)
  covalent geometry    : angle       0.64089 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 205
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8048 (tp) cc_final: 0.7530 (tp)
REVERT: C   27 PHE cc_start: 0.8010 (t80) cc_final: 0.7611 (t80)
REVERT: C   31 TYR cc_start: 0.7633 (p90) cc_final: 0.7198 (p90)
REVERT: C   34 MET cc_start: 0.5982 (mtp) cc_final: 0.5638 (mtp)
REVERT: C   52 SER cc_start: 0.8343 (t) cc_final: 0.7662 (p)
REVERT: C   69 THR cc_start: 0.7575 (m) cc_final: 0.7315 (p)
REVERT: C   77 ASN cc_start: 0.8370 (t0) cc_final: 0.7675 (t0)
REVERT: A   41 THR cc_start: 0.7601 (p) cc_final: 0.7326 (t)
REVERT: A   44 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8273 (t)
REVERT: A   60 GLN cc_start: 0.7409 (tm-30) cc_final: 0.6526 (tm-30)
REVERT: A   72 TRP cc_start: 0.8031 (t60) cc_final: 0.7706 (t60)
REVERT: A  119 LYS cc_start: 0.7701 (tppt) cc_final: 0.6992 (tppt)
REVERT: A  181 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.6070 (p90)
REVERT: A  183 MET cc_start: 0.5783 (tmt) cc_final: 0.5484 (tmt)
REVERT: A  250 LEU cc_start: 0.8146 (tp) cc_final: 0.7646 (tp)
REVERT: A  255 LEU cc_start: 0.4908 (OUTLIER) cc_final: 0.4560 (tp)
REVERT: A  302 LEU cc_start: 0.7940 (tp) cc_final: 0.7179 (tt)
REVERT: A  319 TYR cc_start: 0.7261 (m-10) cc_final: 0.6921 (m-10)
REVERT: A  320 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7273 (mm-40)
REVERT: A  346 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7846 (mm-30)
REVERT: A  356 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8235 (p)
REVERT: A  361 ARG cc_start: 0.7779 (ttm170) cc_final: 0.6960 (ttm170)
REVERT: A  362 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7430 (tptp)
REVERT: A  430 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7669 (mmmt)
REVERT: A  445 ASN cc_start: 0.8485 (p0) cc_final: 0.8236 (p0)
REVERT: A  472 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7577 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8351 (t0) cc_final: 0.7114 (m-30)
REVERT: A  495 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6613 (p90)
REVERT: A  520 SER cc_start: 0.8056 (m) cc_final: 0.7476 (p)
REVERT: A  534 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8251 (mmmm)
REVERT: A  538 ASN cc_start: 0.7179 (t0) cc_final: 0.6900 (t0)
REVERT: A  543 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7507 (ttmm)
REVERT: A  568 PHE cc_start: 0.7343 (t80) cc_final: 0.7065 (t80)
REVERT: A  580 ASP cc_start: 0.7159 (t70) cc_final: 0.6357 (t0)
REVERT: A  592 ASP cc_start: 0.7471 (t70) cc_final: 0.7269 (t0)
REVERT: A  639 TRP cc_start: 0.6389 (OUTLIER) cc_final: 0.5937 (t60)
  outliers start: 48
  outliers final: 31
  residues processed: 229
  average time/residue: 0.1936
  time to fit residues: 56.5648
Evaluate side-chains
  232 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 195
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  535 LYS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  569 GLN
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  639 TRP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  672 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0030
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.153787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133062 restraints weight = 10521.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.137882 restraints weight = 5588.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.141137 restraints weight = 3471.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6228  Z= 0.132
  Angle     :  0.658  13.190   8486  Z= 0.331
  Chirality :  0.045   0.167    921
  Planarity :  0.004   0.044   1100
  Dihedral  :  8.402  88.328    882
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 21.65 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.28), residues: 764
  helix: -1.31 (1.40), residues: 22
  sheet: -1.52 (0.36), residues: 196
  loop : -2.98 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.026   0.002   PHE A 649 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.006   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02970 (  103)
  hydrogen bonds       : angle       5.69065 (  270)
  SS BOND              : bond        0.00183 (    9)
  SS BOND              : angle       2.16173 (   18)
  covalent geometry    : bond        0.00300 ( 6219)
  covalent geometry    : angle       0.65100 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 198
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8066 (tp) cc_final: 0.7312 (tp)
REVERT: C   27 PHE cc_start: 0.8068 (t80) cc_final: 0.7582 (t80)
REVERT: C   31 TYR cc_start: 0.7705 (p90) cc_final: 0.7230 (p90)
REVERT: C   52 SER cc_start: 0.8278 (t) cc_final: 0.7470 (p)
REVERT: C   77 ASN cc_start: 0.8466 (t0) cc_final: 0.7672 (t0)
REVERT: C   93 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6774 (tt)
REVERT: A   41 THR cc_start: 0.7545 (p) cc_final: 0.7258 (t)
REVERT: A   42 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7920 (ttm170)
REVERT: A   44 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8284 (t)
REVERT: A   60 GLN cc_start: 0.7454 (tm-30) cc_final: 0.6560 (tm-30)
REVERT: A   72 TRP cc_start: 0.8058 (t60) cc_final: 0.7680 (t60)
REVERT: A  119 LYS cc_start: 0.7765 (tppt) cc_final: 0.7008 (tppt)
REVERT: A  175 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: A  181 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.6055 (p90)
REVERT: A  183 MET cc_start: 0.5776 (tmt) cc_final: 0.5472 (tmt)
REVERT: A  201 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.5109 (ptpt)
REVERT: A  250 LEU cc_start: 0.8103 (tp) cc_final: 0.7593 (tp)
REVERT: A  302 LEU cc_start: 0.7513 (tp) cc_final: 0.7162 (tt)
REVERT: A  319 TYR cc_start: 0.7301 (m-10) cc_final: 0.6899 (m-10)
REVERT: A  320 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7205 (mm-40)
REVERT: A  325 ARG cc_start: 0.7480 (ptp-170) cc_final: 0.7192 (ptt180)
REVERT: A  346 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7950 (mm-30)
REVERT: A  356 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8208 (p)
REVERT: A  361 ARG cc_start: 0.7786 (ttm170) cc_final: 0.6975 (ttm170)
REVERT: A  362 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7320 (tptp)
REVERT: A  430 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7613 (mmmt)
REVERT: A  431 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8634 (mm)
REVERT: A  459 TYR cc_start: 0.7418 (p90) cc_final: 0.6590 (p90)
REVERT: A  472 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7566 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8398 (t0) cc_final: 0.7149 (m-30)
REVERT: A  495 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.6753 (p90)
REVERT: A  520 SER cc_start: 0.7997 (m) cc_final: 0.7493 (p)
REVERT: A  534 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8329 (mmtp)
REVERT: A  538 ASN cc_start: 0.7208 (t0) cc_final: 0.6887 (t0)
REVERT: A  543 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7490 (ttmm)
REVERT: A  568 PHE cc_start: 0.7442 (t80) cc_final: 0.7126 (t80)
REVERT: A  580 ASP cc_start: 0.7205 (t70) cc_final: 0.6324 (t0)
REVERT: A  592 ASP cc_start: 0.7533 (t70) cc_final: 0.7331 (t0)
REVERT: A  649 PHE cc_start: 0.5794 (t80) cc_final: 0.5185 (t80)
REVERT: A  661 TYR cc_start: 0.7015 (t80) cc_final: 0.6510 (t80)
REVERT: A  670 ILE cc_start: 0.8366 (mm) cc_final: 0.8043 (tp)
  outliers start: 46
  outliers final: 30
  residues processed: 220
  average time/residue: 0.1977
  time to fit residues: 55.3168
Evaluate side-chains
  230 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 TYR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  535 LYS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  672 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   overall best weight:    0.8420

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
A 609 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.151752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130798 restraints weight = 10466.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.135542 restraints weight = 5623.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.138716 restraints weight = 3524.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6228  Z= 0.167
  Angle     :  0.688  11.566   8486  Z= 0.350
  Chirality :  0.046   0.179    921
  Planarity :  0.004   0.040   1100
  Dihedral  :  8.198  88.866    878
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 22.56 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.28), residues: 764
  helix: -1.36 (1.32), residues: 22
  sheet: -1.50 (0.36), residues: 195
  loop : -2.94 (0.24), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.016   0.002   PHE A 353 
 TYR   0.017   0.001   TYR A 642 
 ARG   0.006   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03168 (  103)
  hydrogen bonds       : angle       5.68177 (  270)
  SS BOND              : bond        0.00427 (    9)
  SS BOND              : angle       2.38881 (   18)
  covalent geometry    : bond        0.00371 ( 6219)
  covalent geometry    : angle       0.68022 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 207
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8141 (t80) cc_final: 0.7723 (t80)
REVERT: C   31 TYR cc_start: 0.7699 (p90) cc_final: 0.7207 (p90)
REVERT: C   52 SER cc_start: 0.8237 (t) cc_final: 0.7517 (p)
REVERT: C   77 ASN cc_start: 0.8500 (t0) cc_final: 0.7780 (t0)
REVERT: C   93 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6804 (tt)
REVERT: A   41 THR cc_start: 0.7608 (p) cc_final: 0.7339 (t)
REVERT: A   42 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7951 (ttm170)
REVERT: A   44 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8228 (t)
REVERT: A   60 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6563 (tm-30)
REVERT: A   72 TRP cc_start: 0.8083 (t60) cc_final: 0.7676 (t60)
REVERT: A  119 LYS cc_start: 0.7838 (tppt) cc_final: 0.7092 (tppt)
REVERT: A  181 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6232 (p90)
REVERT: A  201 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5143 (ptpt)
REVERT: A  212 LYS cc_start: 0.8173 (tppt) cc_final: 0.7575 (tptm)
REVERT: A  250 LEU cc_start: 0.8153 (tp) cc_final: 0.7627 (tp)
REVERT: A  291 ILE cc_start: 0.6526 (mm) cc_final: 0.6157 (mm)
REVERT: A  302 LEU cc_start: 0.7597 (tp) cc_final: 0.7240 (tt)
REVERT: A  316 LYS cc_start: 0.6435 (mtmt) cc_final: 0.5612 (mtpt)
REVERT: A  319 TYR cc_start: 0.7315 (m-10) cc_final: 0.6982 (m-10)
REVERT: A  320 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7299 (mm-40)
REVERT: A  325 ARG cc_start: 0.7563 (ptp-170) cc_final: 0.7318 (ptt180)
REVERT: A  346 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7932 (mm-30)
REVERT: A  356 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8238 (p)
REVERT: A  360 ASN cc_start: 0.8492 (m-40) cc_final: 0.7966 (p0)
REVERT: A  362 LYS cc_start: 0.7698 (tmtt) cc_final: 0.7324 (tptp)
REVERT: A  429 TYR cc_start: 0.7593 (t80) cc_final: 0.7325 (t80)
REVERT: A  430 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7775 (mmmt)
REVERT: A  472 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7608 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8424 (t0) cc_final: 0.7219 (m-30)
REVERT: A  495 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.6621 (p90)
REVERT: A  520 SER cc_start: 0.8091 (m) cc_final: 0.7628 (p)
REVERT: A  534 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8336 (mmtp)
REVERT: A  538 ASN cc_start: 0.7261 (t0) cc_final: 0.6881 (t0)
REVERT: A  543 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7559 (ttmm)
REVERT: A  568 PHE cc_start: 0.7478 (t80) cc_final: 0.7103 (t80)
REVERT: A  580 ASP cc_start: 0.7218 (t70) cc_final: 0.6295 (t0)
REVERT: A  639 TRP cc_start: 0.6474 (OUTLIER) cc_final: 0.6069 (t60)
REVERT: A  649 PHE cc_start: 0.6046 (t80) cc_final: 0.5394 (t80)
REVERT: A  661 TYR cc_start: 0.7043 (t80) cc_final: 0.6561 (t80)
  outliers start: 47
  outliers final: 33
  residues processed: 229
  average time/residue: 0.2093
  time to fit residues: 61.6292
Evaluate side-chains
  240 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 200
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   28 TYR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  639 TRP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  668 CYS
Chi-restraints excluded: chain A residue  672 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    0.2980
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN
A  69 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.152822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.130862 restraints weight = 10591.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.135897 restraints weight = 5768.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.139247 restraints weight = 3629.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.4658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6228  Z= 0.140
  Angle     :  0.680  11.221   8486  Z= 0.343
  Chirality :  0.045   0.185    921
  Planarity :  0.004   0.039   1100
  Dihedral  :  8.159  87.663    878
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.39 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 23.46 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.28), residues: 764
  helix: -1.32 (1.32), residues: 22
  sheet: -1.30 (0.35), residues: 198
  loop : -2.95 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.013   0.001   PHE A 649 
 TYR   0.016   0.001   TYR A 459 
 ARG   0.005   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02955 (  103)
  hydrogen bonds       : angle       5.63876 (  270)
  SS BOND              : bond        0.00461 (    9)
  SS BOND              : angle       2.02435 (   18)
  covalent geometry    : bond        0.00319 ( 6219)
  covalent geometry    : angle       0.67401 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8125 (t80) cc_final: 0.7646 (t80)
REVERT: C   31 TYR cc_start: 0.7697 (p90) cc_final: 0.7198 (p90)
REVERT: C   52 SER cc_start: 0.8169 (t) cc_final: 0.7458 (p)
REVERT: C   77 ASN cc_start: 0.8444 (t0) cc_final: 0.7650 (t0)
REVERT: C   93 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6746 (tt)
REVERT: A   41 THR cc_start: 0.7543 (p) cc_final: 0.7246 (t)
REVERT: A   42 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7927 (ttm170)
REVERT: A   44 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8209 (t)
REVERT: A   60 GLN cc_start: 0.7416 (tm-30) cc_final: 0.6559 (tm-30)
REVERT: A   72 TRP cc_start: 0.8059 (t60) cc_final: 0.7646 (t60)
REVERT: A  119 LYS cc_start: 0.7827 (tppt) cc_final: 0.7061 (tppt)
REVERT: A  181 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6125 (p90)
REVERT: A  201 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.5221 (ptpt)
REVERT: A  250 LEU cc_start: 0.8102 (tp) cc_final: 0.7598 (tp)
REVERT: A  302 LEU cc_start: 0.7496 (tp) cc_final: 0.7122 (tt)
REVERT: A  320 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7308 (mm-40)
REVERT: A  325 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7186 (ptt180)
REVERT: A  346 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7958 (mm-30)
REVERT: A  356 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (p)
REVERT: A  360 ASN cc_start: 0.8468 (m-40) cc_final: 0.8048 (p0)
REVERT: A  362 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7507 (tmtt)
REVERT: A  430 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7502 (mmmt)
REVERT: A  472 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7598 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8403 (t0) cc_final: 0.7201 (m-30)
REVERT: A  520 SER cc_start: 0.8100 (m) cc_final: 0.7632 (p)
REVERT: A  538 ASN cc_start: 0.7236 (t0) cc_final: 0.6826 (t0)
REVERT: A  568 PHE cc_start: 0.7454 (t80) cc_final: 0.7130 (t80)
REVERT: A  580 ASP cc_start: 0.7098 (t70) cc_final: 0.6428 (t0)
REVERT: A  639 TRP cc_start: 0.6464 (OUTLIER) cc_final: 0.6023 (t60)
REVERT: A  649 PHE cc_start: 0.5953 (t80) cc_final: 0.5374 (t80)
REVERT: A  661 TYR cc_start: 0.6985 (t80) cc_final: 0.6412 (t80)
  outliers start: 47
  outliers final: 33
  residues processed: 222
  average time/residue: 0.1934
  time to fit residues: 54.9771
Evaluate side-chains
  235 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 196
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 TYR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 ASN
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  639 TRP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0010
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.152186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.130713 restraints weight = 10400.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135594 restraints weight = 5546.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.138932 restraints weight = 3453.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6713
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6228  Z= 0.155
  Angle     :  0.719  14.460   8486  Z= 0.356
  Chirality :  0.045   0.194    921
  Planarity :  0.004   0.039   1100
  Dihedral  :  8.026  88.441    874
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.13 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 24.21 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.28), residues: 764
  helix: -2.01 (1.09), residues: 28
  sheet: -1.17 (0.36), residues: 202
  loop : -2.92 (0.24), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C  36 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.013   0.001   PHE A 353 
 TYR   0.031   0.002   TYR A 459 
 ARG   0.004   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  103)
  hydrogen bonds       : angle       5.58730 (  270)
  SS BOND              : bond        0.00371 (    9)
  SS BOND              : angle       2.20042 (   18)
  covalent geometry    : bond        0.00348 ( 6219)
  covalent geometry    : angle       0.71276 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 198
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8146 (t80) cc_final: 0.7608 (t80)
REVERT: C   29 PHE cc_start: 0.7405 (m-10) cc_final: 0.6848 (m-10)
REVERT: C   31 TYR cc_start: 0.7693 (p90) cc_final: 0.7129 (p90)
REVERT: C   52 SER cc_start: 0.8162 (t) cc_final: 0.7420 (p)
REVERT: C   77 ASN cc_start: 0.8372 (t0) cc_final: 0.7712 (t0)
REVERT: C   93 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6655 (tt)
REVERT: A   41 THR cc_start: 0.7565 (p) cc_final: 0.7326 (t)
REVERT: A   42 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7767 (ttm110)
REVERT: A   44 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8224 (t)
REVERT: A   60 GLN cc_start: 0.7391 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: A   72 TRP cc_start: 0.8044 (t60) cc_final: 0.7589 (t60)
REVERT: A  119 LYS cc_start: 0.7849 (tppt) cc_final: 0.7146 (tppt)
REVERT: A  181 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6350 (p90)
REVERT: A  183 MET cc_start: 0.6038 (tmt) cc_final: 0.5698 (tmt)
REVERT: A  250 LEU cc_start: 0.8094 (tp) cc_final: 0.7585 (tp)
REVERT: A  302 LEU cc_start: 0.7504 (tp) cc_final: 0.7137 (tt)
REVERT: A  320 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7275 (mm-40)
REVERT: A  325 ARG cc_start: 0.7515 (ptp-170) cc_final: 0.7303 (ptt180)
REVERT: A  346 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7974 (mm-30)
REVERT: A  356 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8276 (p)
REVERT: A  360 ASN cc_start: 0.8478 (m-40) cc_final: 0.8069 (p0)
REVERT: A  430 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7709 (mmmt)
REVERT: A  472 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7583 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8425 (t0) cc_final: 0.6942 (m-30)
REVERT: A  496 PHE cc_start: 0.8341 (t80) cc_final: 0.8048 (t80)
REVERT: A  520 SER cc_start: 0.8188 (m) cc_final: 0.7636 (p)
REVERT: A  535 LYS cc_start: 0.8335 (mmmm) cc_final: 0.8032 (mmmm)
REVERT: A  538 ASN cc_start: 0.7277 (t0) cc_final: 0.6958 (t0)
REVERT: A  568 PHE cc_start: 0.7480 (t80) cc_final: 0.7109 (t80)
REVERT: A  580 ASP cc_start: 0.7052 (t70) cc_final: 0.6360 (t0)
REVERT: A  649 PHE cc_start: 0.6065 (t80) cc_final: 0.5455 (t80)
REVERT: A  661 TYR cc_start: 0.6954 (t80) cc_final: 0.6412 (t80)
  outliers start: 45
  outliers final: 32
  residues processed: 222
  average time/residue: 0.1978
  time to fit residues: 56.1286
Evaluate side-chains
  230 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 TYR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.148793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127238 restraints weight = 10633.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.132036 restraints weight = 5755.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.135320 restraints weight = 3638.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6228  Z= 0.224
  Angle     :  0.779  13.412   8486  Z= 0.392
  Chirality :  0.047   0.204    921
  Planarity :  0.005   0.050   1100
  Dihedral  :  8.394  90.294    874
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.61 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 26.17 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.28), residues: 764
  helix: -2.58 (0.96), residues: 34
  sheet: -1.09 (0.36), residues: 201
  loop : -2.98 (0.24), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP C  36 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.018   0.002   PHE A 112 
 TYR   0.029   0.002   TYR A 429 
 ARG   0.006   0.001   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  103)
  hydrogen bonds       : angle       5.85191 (  270)
  SS BOND              : bond        0.00392 (    9)
  SS BOND              : angle       2.18126 (   18)
  covalent geometry    : bond        0.00489 ( 6219)
  covalent geometry    : angle       0.77326 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8116 (t80) cc_final: 0.7834 (t80)
REVERT: C   31 TYR cc_start: 0.7721 (p90) cc_final: 0.7185 (p90)
REVERT: C   52 SER cc_start: 0.8095 (t) cc_final: 0.7400 (p)
REVERT: C   77 ASN cc_start: 0.8512 (t0) cc_final: 0.7840 (t0)
REVERT: C   93 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6623 (tt)
REVERT: C  107 PHE cc_start: 0.8536 (m-80) cc_final: 0.8125 (m-80)
REVERT: A   41 THR cc_start: 0.7720 (p) cc_final: 0.7445 (t)
REVERT: A   42 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7850 (ttm170)
REVERT: A   60 GLN cc_start: 0.7427 (tm-30) cc_final: 0.6570 (tm-30)
REVERT: A   72 TRP cc_start: 0.8121 (t60) cc_final: 0.7584 (t60)
REVERT: A  108 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7469 (mtm110)
REVERT: A  119 LYS cc_start: 0.7962 (tppt) cc_final: 0.7271 (tppt)
REVERT: A  181 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6463 (p90)
REVERT: A  250 LEU cc_start: 0.8132 (tp) cc_final: 0.7622 (tp)
REVERT: A  255 LEU cc_start: 0.5056 (tp) cc_final: 0.4536 (tt)
REVERT: A  302 LEU cc_start: 0.7613 (tp) cc_final: 0.7262 (tt)
REVERT: A  320 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7252 (mm-40)
REVERT: A  325 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7417 (ptt180)
REVERT: A  346 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: A  360 ASN cc_start: 0.8507 (m-40) cc_final: 0.8118 (p0)
REVERT: A  361 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7626 (ttm170)
REVERT: A  362 LYS cc_start: 0.7836 (tptm) cc_final: 0.7442 (tptp)
REVERT: A  427 TYR cc_start: 0.6560 (m-10) cc_final: 0.6307 (m-10)
REVERT: A  430 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7588 (mmmt)
REVERT: A  434 ASP cc_start: 0.7172 (t0) cc_final: 0.6875 (t0)
REVERT: A  472 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7636 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8485 (t0) cc_final: 0.7378 (m-30)
REVERT: A  496 PHE cc_start: 0.8379 (t80) cc_final: 0.8097 (t80)
REVERT: A  520 SER cc_start: 0.8219 (m) cc_final: 0.7601 (p)
REVERT: A  538 ASN cc_start: 0.7415 (t0) cc_final: 0.7008 (t0)
REVERT: A  568 PHE cc_start: 0.7551 (t80) cc_final: 0.7179 (t80)
REVERT: A  580 ASP cc_start: 0.7045 (t70) cc_final: 0.6350 (t0)
REVERT: A  681 GLN cc_start: 0.7748 (mp10) cc_final: 0.7295 (mp10)
  outliers start: 38
  outliers final: 31
  residues processed: 219
  average time/residue: 0.2252
  time to fit residues: 63.3580
Evaluate side-chains
  231 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 198
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 TYR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  454 ASN
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    0.0570
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.150927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.129131 restraints weight = 10646.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.134081 restraints weight = 5750.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.137404 restraints weight = 3617.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.5412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6228  Z= 0.160
  Angle     :  0.763  15.447   8486  Z= 0.382
  Chirality :  0.047   0.208    921
  Planarity :  0.005   0.043   1100
  Dihedral  :  8.224  91.228    872
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 27.07 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.28), residues: 764
  helix: -2.03 (1.11), residues: 28
  sheet: -0.90 (0.37), residues: 194
  loop : -2.99 (0.24), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP C  36 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.022   0.002   PHE A 649 
 TYR   0.024   0.001   TYR A 459 
 ARG   0.005   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03199 (  103)
  hydrogen bonds       : angle       5.75412 (  270)
  SS BOND              : bond        0.00473 (    9)
  SS BOND              : angle       2.40853 (   18)
  covalent geometry    : bond        0.00363 ( 6219)
  covalent geometry    : angle       0.75599 ( 8468)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 189
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8138 (t80) cc_final: 0.7789 (t80)
REVERT: C   29 PHE cc_start: 0.7351 (m-10) cc_final: 0.6879 (m-10)
REVERT: C   31 TYR cc_start: 0.7711 (p90) cc_final: 0.7164 (p90)
REVERT: C   52 SER cc_start: 0.8066 (t) cc_final: 0.7356 (p)
REVERT: C   77 ASN cc_start: 0.8402 (t0) cc_final: 0.7745 (t0)
REVERT: C   93 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6612 (tt)
REVERT: A   41 THR cc_start: 0.7579 (p) cc_final: 0.7317 (t)
REVERT: A   60 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6534 (tm-30)
REVERT: A   72 TRP cc_start: 0.8058 (t60) cc_final: 0.7593 (t60)
REVERT: A  108 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7455 (mtm-85)
REVERT: A  119 LYS cc_start: 0.7908 (tppt) cc_final: 0.7200 (tppt)
REVERT: A  181 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6341 (p90)
REVERT: A  250 LEU cc_start: 0.8085 (tp) cc_final: 0.7599 (tp)
REVERT: A  255 LEU cc_start: 0.5147 (tp) cc_final: 0.4689 (tt)
REVERT: A  302 LEU cc_start: 0.7489 (tp) cc_final: 0.7128 (tt)
REVERT: A  320 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7178 (mm-40)
REVERT: A  346 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8116 (mm-30)
REVERT: A  360 ASN cc_start: 0.8513 (m-40) cc_final: 0.8043 (p0)
REVERT: A  362 LYS cc_start: 0.7758 (tptm) cc_final: 0.7408 (tttm)
REVERT: A  374 LEU cc_start: 0.7176 (mp) cc_final: 0.6973 (mt)
REVERT: A  427 TYR cc_start: 0.6562 (m-10) cc_final: 0.6331 (m-10)
REVERT: A  430 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7713 (mmmt)
REVERT: A  434 ASP cc_start: 0.7133 (t0) cc_final: 0.6827 (t0)
REVERT: A  472 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7611 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8437 (t0) cc_final: 0.7307 (m-30)
REVERT: A  496 PHE cc_start: 0.8426 (t80) cc_final: 0.8172 (t80)
REVERT: A  520 SER cc_start: 0.8192 (m) cc_final: 0.7473 (p)
REVERT: A  538 ASN cc_start: 0.7465 (t0) cc_final: 0.7084 (t0)
REVERT: A  543 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7566 (mtpp)
REVERT: A  568 PHE cc_start: 0.7489 (t80) cc_final: 0.7111 (t80)
REVERT: A  580 ASP cc_start: 0.7019 (t70) cc_final: 0.6335 (t0)
REVERT: A  649 PHE cc_start: 0.5784 (t80) cc_final: 0.5216 (t80)
REVERT: A  661 TYR cc_start: 0.6976 (t80) cc_final: 0.6496 (t80)
  outliers start: 35
  outliers final: 29
  residues processed: 205
  average time/residue: 0.2641
  time to fit residues: 70.3203
Evaluate side-chains
  221 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 190
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   28 TYR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain A residue   39 SER
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   84 ARG
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  306 LYS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  446 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  633 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  652 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.151502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.129367 restraints weight = 10768.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.134378 restraints weight = 5779.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.137741 restraints weight = 3630.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.5514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6228  Z= 0.154
  Angle     :  0.763  15.282   8486  Z= 0.378
  Chirality :  0.047   0.212    921
  Planarity :  0.005   0.046   1100
  Dihedral  :  8.040  94.704    870
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 28.12 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.28), residues: 764
  helix: -2.72 (0.92), residues: 34
  sheet: -0.79 (0.38), residues: 188
  loop : -2.90 (0.24), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C  36 
 HIS   0.003   0.001   HIS A 525 
 PHE   0.021   0.002   PHE A 649 
 TYR   0.015   0.001   TYR A 459 
 ARG   0.005   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03198 (  103)
  hydrogen bonds       : angle       5.68124 (  270)
  SS BOND              : bond        0.00362 (    9)
  SS BOND              : angle       2.31776 (   18)
  covalent geometry    : bond        0.00351 ( 6219)
  covalent geometry    : angle       0.75627 ( 8468)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2705.49 seconds
wall clock time: 48 minutes 24.34 seconds (2904.34 seconds total)