Starting phenix.real_space_refine
on Fri Aug 22 16:47:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i4g_35172/08_2025/8i4g_35172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i4g_35172/08_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_35172/08_2025/8i4g_35172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i4g_35172/08_2025/8i4g_35172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i4g_35172/08_2025/8i4g_35172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i4g_35172/08_2025/8i4g_35172.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.37, per 1000 atoms: 0.23
  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: 0.38
  Conformation dependent library (CDL) restraints added in 340.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.23
  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: 0.68

  Time building geometry restraints manager: 0.57 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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.680
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.900
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 325 
 TYR   0.006   0.001   TYR A 271 
 PHE   0.007   0.001   PHE A 406 
 TRP   0.004   0.001   TRP A 359 
 HIS   0.001   0.000   HIS A 525 

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

*********************** 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  : 0.179 
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: 0.7149 (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: 0.8046 (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: 0.4545 (tp)
REVERT: A  299 LEU cc_start: 0.7945 (tp) cc_final: 0.7719 (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: 0.7838 (mmmt)
REVERT: A  473 ASP cc_start: 0.8178 (t0) cc_final: 0.6692 (m-30)
REVERT: A  495 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6590 (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: 0.7023 (t)
REVERT: A  523 LEU cc_start: 0.7889 (tp) cc_final: 0.7405 (tp)
REVERT: A  525 HIS cc_start: 0.6133 (p-80) cc_final: 0.5860 (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: 0.8379 (m)
REVERT: A  638 THR cc_start: 0.7661 (p) cc_final: 0.7428 (p)
REVERT: A  670 ILE cc_start: 0.8518 (mt) cc_final: 0.8315 (tt)
  outliers start: 38
  outliers final: 22
  residues processed: 259
  average time/residue: 0.0747
  time to fit residues: 25.0437
Evaluate side-chains
  231 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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
A 415 GLN
A 420 GLN
A 445 ASN
A 548 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.158923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.137793 restraints weight = 10664.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.142929 restraints weight = 5562.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.146346 restraints weight = 3423.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.148648 restraints weight = 2338.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.150345 restraints weight = 1734.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6228  Z= 0.136
  Angle     :  0.622  11.946   8486  Z= 0.313
  Chirality :  0.044   0.172    921
  Planarity :  0.005   0.049   1100
  Dihedral  :  9.022  88.302    899
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 15.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.17 (0.26), residues: 764
  helix: -3.09 (0.85), residues: 28
  sheet: -2.28 (0.33), residues: 195
  loop : -3.17 (0.23), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  42 
 TYR   0.022   0.001   TYR C  94 
 PHE   0.031   0.002   PHE A 568 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.002   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6219)
  covalent geometry    : angle       0.61335 ( 8468)
  SS BOND              : bond        0.00382 (    9)
  SS BOND              : angle       2.32299 (   18)
  hydrogen bonds       : bond        0.03438 (  103)
  hydrogen bonds       : angle       6.80336 (  270)

*********************** 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
  243 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 199
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 TYR cc_start: 0.7579 (p90) cc_final: 0.6998 (p90)
REVERT: C   77 ASN cc_start: 0.8316 (t0) cc_final: 0.7736 (t0)
REVERT: C   99 ARG cc_start: 0.7536 (ptt90) cc_final: 0.7270 (ppt170)
REVERT: A   40 PHE cc_start: 0.8357 (m-80) cc_final: 0.8038 (m-10)
REVERT: A   42 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7783 (ttm110)
REVERT: A   52 ARG cc_start: 0.7415 (mtt180) cc_final: 0.7213 (mtt180)
REVERT: A   60 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6559 (tm-30)
REVERT: A  119 LYS cc_start: 0.7695 (tppt) cc_final: 0.6961 (tppt)
REVERT: A  134 ILE cc_start: 0.7679 (mt) cc_final: 0.7298 (tt)
REVERT: A  250 LEU cc_start: 0.7994 (tp) cc_final: 0.7549 (tp)
REVERT: A  255 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4604 (tp)
REVERT: A  299 LEU cc_start: 0.8137 (tp) cc_final: 0.7862 (tp)
REVERT: A  302 LEU cc_start: 0.7730 (tp) cc_final: 0.7403 (tt)
REVERT: A  320 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7333 (mm-40)
REVERT: A  346 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7947 (mm-30)
REVERT: A  362 LYS cc_start: 0.7494 (tmtt) cc_final: 0.6848 (tmtt)
REVERT: A  398 PHE cc_start: 0.8206 (m-10) cc_final: 0.7949 (m-10)
REVERT: A  430 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7408 (mmmt)
REVERT: A  434 ASP cc_start: 0.6951 (t0) cc_final: 0.6475 (t0)
REVERT: A  466 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7701 (mmmm)
REVERT: A  472 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7413 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8457 (t0) cc_final: 0.7070 (m-30)
REVERT: A  495 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6660 (p90)
REVERT: A  518 VAL cc_start: 0.8519 (t) cc_final: 0.8244 (p)
REVERT: A  520 SER cc_start: 0.7636 (m) cc_final: 0.6911 (p)
REVERT: A  523 LEU cc_start: 0.7833 (tp) cc_final: 0.7621 (tp)
REVERT: A  534 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8297 (mmtp)
REVERT: A  542 ASN cc_start: 0.8257 (m-40) cc_final: 0.8019 (m110)
REVERT: A  543 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7216 (ttmm)
REVERT: A  580 ASP cc_start: 0.6879 (t70) cc_final: 0.6372 (t0)
REVERT: A  593 ILE cc_start: 0.8549 (mt) cc_final: 0.8329 (mt)
REVERT: A  598 PHE cc_start: 0.7300 (t80) cc_final: 0.7045 (t80)
  outliers start: 44
  outliers final: 27
  residues processed: 225
  average time/residue: 0.0792
  time to fit residues: 23.0609
Evaluate side-chains
  212 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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  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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0050
   chunk 33 optimal weight:    0.2980
   chunk 42 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.5394

-------------------------------------------------------------------------------
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 213 HIS
A 548 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.157751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.137181 restraints weight = 10620.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.142015 restraints weight = 5720.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.145290 restraints weight = 3572.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.147479 restraints weight = 2467.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.148994 restraints weight = 1843.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6228  Z= 0.128
  Angle     :  0.621  11.785   8486  Z= 0.308
  Chirality :  0.044   0.180    921
  Planarity :  0.004   0.042   1100
  Dihedral  :  8.726  87.026    890
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 17.14 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.74 (0.27), residues: 764
  helix: -2.00 (1.23), residues: 22
  sheet: -1.72 (0.34), residues: 192
  loop : -3.03 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.014   0.001   TYR A  97 
 PHE   0.025   0.002   PHE A 649 
 TRP   0.009   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6219)
  covalent geometry    : angle       0.61324 ( 8468)
  SS BOND              : bond        0.00414 (    9)
  SS BOND              : angle       2.18994 (   18)
  hydrogen bonds       : bond        0.03026 (  103)
  hydrogen bonds       : angle       6.07897 (  270)

*********************** 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
  243 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 196
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   31 TYR cc_start: 0.7571 (p90) cc_final: 0.7033 (p90)
REVERT: C   77 ASN cc_start: 0.8301 (t0) cc_final: 0.7639 (t0)
REVERT: C   83 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6137 (mpp)
REVERT: A   40 PHE cc_start: 0.8338 (m-80) cc_final: 0.8057 (m-10)
REVERT: A   60 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6548 (tm-30)
REVERT: A   72 TRP cc_start: 0.8000 (t60) cc_final: 0.7679 (t60)
REVERT: A  119 LYS cc_start: 0.7754 (tppt) cc_final: 0.7051 (tppt)
REVERT: A  250 LEU cc_start: 0.8055 (tp) cc_final: 0.7575 (tp)
REVERT: A  255 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4349 (tp)
REVERT: A  302 LEU cc_start: 0.7780 (tp) cc_final: 0.7467 (tt)
REVERT: A  319 TYR cc_start: 0.7266 (m-10) cc_final: 0.6953 (m-10)
REVERT: A  320 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7200 (mm-40)
REVERT: A  346 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7810 (mm-30)
REVERT: A  362 LYS cc_start: 0.7639 (tmtt) cc_final: 0.7029 (tmtt)
REVERT: A  430 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7460 (mmmt)
REVERT: A  466 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7707 (mmmm)
REVERT: A  472 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7566 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8417 (t0) cc_final: 0.7058 (m-30)
REVERT: A  495 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.6626 (p90)
REVERT: A  520 SER cc_start: 0.7803 (m) cc_final: 0.7080 (p)
REVERT: A  523 LEU cc_start: 0.8056 (tp) cc_final: 0.7849 (tp)
REVERT: A  534 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8329 (mmtp)
REVERT: A  542 ASN cc_start: 0.8271 (m-40) cc_final: 0.8046 (m110)
REVERT: A  568 PHE cc_start: 0.7308 (t80) cc_final: 0.6920 (t80)
REVERT: A  580 ASP cc_start: 0.7047 (t70) cc_final: 0.6262 (t0)
REVERT: A  592 ASP cc_start: 0.7564 (t70) cc_final: 0.7228 (t0)
REVERT: A  598 PHE cc_start: 0.7560 (t80) cc_final: 0.7334 (t80)
REVERT: A  649 PHE cc_start: 0.5337 (t80) cc_final: 0.4729 (t80)
REVERT: A  661 TYR cc_start: 0.6868 (t80) cc_final: 0.6403 (t80)
REVERT: A  670 ILE cc_start: 0.8474 (mt) cc_final: 0.8231 (tt)
  outliers start: 47
  outliers final: 32
  residues processed: 219
  average time/residue: 0.0800
  time to fit residues: 22.3207
Evaluate side-chains
  222 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 187
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  114 THR
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  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  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  333 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  565 PHE
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0170
   chunk 41 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8024

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.153090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.133086 restraints weight = 10703.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.137863 restraints weight = 5704.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.141026 restraints weight = 3550.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.143073 restraints weight = 2444.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.144610 restraints weight = 1840.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6643
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6228  Z= 0.158
  Angle     :  0.667  11.934   8486  Z= 0.332
  Chirality :  0.045   0.174    921
  Planarity :  0.005   0.046   1100
  Dihedral  :  8.399  87.373    884
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.13 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  7.52 %
    Allowed  : 17.14 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.73 (0.28), residues: 764
  helix: -1.70 (1.29), residues: 22
  sheet: -1.76 (0.34), residues: 197
  loop : -3.02 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  42 
 TYR   0.014   0.001   TYR A 642 
 PHE   0.016   0.002   PHE A 112 
 TRP   0.013   0.001   TRP A 359 
 HIS   0.002   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6219)
  covalent geometry    : angle       0.66137 ( 8468)
  SS BOND              : bond        0.00240 (    9)
  SS BOND              : angle       1.95216 (   18)
  hydrogen bonds       : bond        0.02992 (  103)
  hydrogen bonds       : angle       5.76502 (  270)

*********************** 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
  256 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 206
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.7865 (t80) cc_final: 0.7404 (t80)
REVERT: C   31 TYR cc_start: 0.7552 (p90) cc_final: 0.7132 (p90)
REVERT: C   52 SER cc_start: 0.8366 (t) cc_final: 0.7695 (p)
REVERT: C   77 ASN cc_start: 0.8300 (t0) cc_final: 0.7742 (t0)
REVERT: C   93 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6976 (tt)
REVERT: A   41 THR cc_start: 0.7561 (p) cc_final: 0.7287 (t)
REVERT: A   44 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8292 (t)
REVERT: A   60 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6509 (tm-30)
REVERT: A   72 TRP cc_start: 0.8014 (t60) cc_final: 0.7678 (t60)
REVERT: A  119 LYS cc_start: 0.7684 (tppt) cc_final: 0.6954 (tppt)
REVERT: A  212 LYS cc_start: 0.8071 (tppt) cc_final: 0.7711 (tptp)
REVERT: A  250 LEU cc_start: 0.8128 (tp) cc_final: 0.7645 (tp)
REVERT: A  255 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4579 (tp)
REVERT: A  316 LYS cc_start: 0.6554 (mtmt) cc_final: 0.5863 (mtmt)
REVERT: A  319 TYR cc_start: 0.7294 (m-10) cc_final: 0.6968 (m-10)
REVERT: A  320 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7277 (mm-40)
REVERT: A  346 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7815 (mm-30)
REVERT: A  356 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8248 (p)
REVERT: A  362 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7397 (tptp)
REVERT: A  430 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7445 (mmmt)
REVERT: A  472 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7560 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8404 (t0) cc_final: 0.7098 (m-30)
REVERT: A  495 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.6748 (p90)
REVERT: A  520 SER cc_start: 0.8055 (m) cc_final: 0.7490 (p)
REVERT: A  534 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8377 (mmtp)
REVERT: A  538 ASN cc_start: 0.7182 (t0) cc_final: 0.6945 (t0)
REVERT: A  543 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7543 (ttmm)
REVERT: A  568 PHE cc_start: 0.7380 (t80) cc_final: 0.7095 (t80)
REVERT: A  580 ASP cc_start: 0.7206 (t70) cc_final: 0.6352 (t0)
REVERT: A  592 ASP cc_start: 0.7557 (t70) cc_final: 0.7303 (t0)
REVERT: A  593 ILE cc_start: 0.8630 (mt) cc_final: 0.8385 (mt)
REVERT: A  639 TRP cc_start: 0.6331 (OUTLIER) cc_final: 0.5971 (t60)
REVERT: A  649 PHE cc_start: 0.6032 (t80) cc_final: 0.5262 (t80)
REVERT: A  661 TYR cc_start: 0.6862 (t80) cc_final: 0.6416 (t80)
  outliers start: 50
  outliers final: 33
  residues processed: 229
  average time/residue: 0.0706
  time to fit residues: 20.9659
Evaluate side-chains
  237 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 198
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
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   89 VAL
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  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  393 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  465 SER
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  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  651 THR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 105 ASN
A 349 ASN
A 411 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.152757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.130780 restraints weight = 10724.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.135903 restraints weight = 5715.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.139265 restraints weight = 3560.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.141647 restraints weight = 2478.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143227 restraints weight = 1856.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.4136

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= 0.156
  Angle     :  0.670  11.205   8486  Z= 0.337
  Chirality :  0.045   0.161    921
  Planarity :  0.004   0.041   1100
  Dihedral  :  8.425  87.035    884
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 20.45 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.68 (0.28), residues: 764
  helix: -1.31 (1.42), residues: 22
  sheet: -1.70 (0.34), residues: 205
  loop : -3.03 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  42 
 TYR   0.015   0.001   TYR A 642 
 PHE   0.015   0.001   PHE A 353 
 TRP   0.013   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6219)
  covalent geometry    : angle       0.66329 ( 8468)
  SS BOND              : bond        0.00233 (    9)
  SS BOND              : angle       2.15761 (   18)
  hydrogen bonds       : bond        0.02971 (  103)
  hydrogen bonds       : angle       5.74330 (  270)

*********************** 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
  249 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 200
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8183 (tp) cc_final: 0.7307 (tp)
REVERT: C   27 PHE cc_start: 0.8141 (t80) cc_final: 0.7793 (t80)
REVERT: C   31 TYR cc_start: 0.7670 (p90) cc_final: 0.7181 (p90)
REVERT: C   52 SER cc_start: 0.8320 (t) cc_final: 0.7508 (p)
REVERT: C   77 ASN cc_start: 0.8457 (t0) cc_final: 0.7798 (t0)
REVERT: C   93 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6712 (tt)
REVERT: C   99 ARG cc_start: 0.7909 (ptt90) cc_final: 0.7385 (ppt170)
REVERT: A   41 THR cc_start: 0.7632 (p) cc_final: 0.7321 (t)
REVERT: A   44 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (t)
REVERT: A   60 GLN cc_start: 0.7468 (tm-30) cc_final: 0.6592 (tm-30)
REVERT: A   72 TRP cc_start: 0.8066 (t60) cc_final: 0.7676 (t60)
REVERT: A  119 LYS cc_start: 0.7792 (tppt) cc_final: 0.7038 (tppt)
REVERT: A  173 THR cc_start: 0.7809 (p) cc_final: 0.7541 (p)
REVERT: A  182 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6962 (mt)
REVERT: A  201 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.5037 (ptpt)
REVERT: A  212 LYS cc_start: 0.7995 (tppt) cc_final: 0.7617 (tptp)
REVERT: A  250 LEU cc_start: 0.8114 (tp) cc_final: 0.7595 (tp)
REVERT: A  255 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4573 (tp)
REVERT: A  302 LEU cc_start: 0.7518 (tp) cc_final: 0.7138 (tt)
REVERT: A  316 LYS cc_start: 0.6412 (mtmt) cc_final: 0.5769 (mtpt)
REVERT: A  319 TYR cc_start: 0.7318 (m-10) cc_final: 0.6990 (m-10)
REVERT: A  320 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7246 (mm-40)
REVERT: A  325 ARG cc_start: 0.7480 (ptp-170) cc_final: 0.7136 (ptt180)
REVERT: A  346 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7914 (mm-30)
REVERT: A  356 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8188 (p)
REVERT: A  362 LYS cc_start: 0.7608 (tmtt) cc_final: 0.7238 (tptp)
REVERT: A  429 TYR cc_start: 0.7574 (t80) cc_final: 0.7313 (t80)
REVERT: A  430 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7751 (mmmt)
REVERT: A  459 TYR cc_start: 0.7448 (p90) cc_final: 0.6492 (p90)
REVERT: A  472 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7576 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8403 (t0) cc_final: 0.7180 (m-30)
REVERT: A  495 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.6752 (p90)
REVERT: A  496 PHE cc_start: 0.8374 (t80) cc_final: 0.8172 (t80)
REVERT: A  518 VAL cc_start: 0.8503 (t) cc_final: 0.8044 (p)
REVERT: A  520 SER cc_start: 0.8013 (m) cc_final: 0.7521 (p)
REVERT: A  534 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8340 (mmtp)
REVERT: A  538 ASN cc_start: 0.7242 (t0) cc_final: 0.6950 (t0)
REVERT: A  543 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7428 (ttmm)
REVERT: A  568 PHE cc_start: 0.7515 (t80) cc_final: 0.7078 (t80)
REVERT: A  580 ASP cc_start: 0.7136 (t70) cc_final: 0.6271 (t0)
REVERT: A  592 ASP cc_start: 0.7518 (t70) cc_final: 0.7276 (t0)
REVERT: A  649 PHE cc_start: 0.6108 (t80) cc_final: 0.5381 (t80)
REVERT: A  661 TYR cc_start: 0.7000 (t80) cc_final: 0.6448 (t80)
REVERT: A  670 ILE cc_start: 0.8349 (mm) cc_final: 0.8045 (tt)
  outliers start: 49
  outliers final: 32
  residues processed: 223
  average time/residue: 0.0762
  time to fit residues: 21.7626
Evaluate side-chains
  236 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 197
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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  138 GLU
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  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  349 ASN
Chi-restraints excluded: chain A residue  352 THR
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  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  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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0370
   chunk 44 optimal weight:    0.0000
   chunk 5 optimal weight:    2.9990
   chunk 71 optimal weight:    0.1980
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4064

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** 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 = 0.4030 r_free = 0.4030 target = 0.154509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.132431 restraints weight = 10624.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.137430 restraints weight = 5734.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.140864 restraints weight = 3612.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.143257 restraints weight = 2523.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.144845 restraints weight = 1892.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6228  Z= 0.124
  Angle     :  0.665  11.687   8486  Z= 0.331
  Chirality :  0.045   0.182    921
  Planarity :  0.004   0.038   1100
  Dihedral  :  8.190  86.235    881
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 21.20 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.45 (0.28), residues: 764
  helix: -1.40 (1.32), residues: 22
  sheet: -1.44 (0.36), residues: 196
  loop : -2.88 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  42 
 TYR   0.014   0.001   TYR A 618 
 PHE   0.012   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 359 
 HIS   0.011   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6219)
  covalent geometry    : angle       0.65819 ( 8468)
  SS BOND              : bond        0.00323 (    9)
  SS BOND              : angle       2.11261 (   18)
  hydrogen bonds       : bond        0.02898 (  103)
  hydrogen bonds       : angle       5.51223 (  270)

*********************** 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
  248 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 203
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8057 (tp) cc_final: 0.7660 (tp)
REVERT: C   27 PHE cc_start: 0.8171 (t80) cc_final: 0.7785 (t80)
REVERT: C   31 TYR cc_start: 0.7656 (p90) cc_final: 0.7159 (p90)
REVERT: C   52 SER cc_start: 0.8261 (t) cc_final: 0.7444 (p)
REVERT: C   77 ASN cc_start: 0.8421 (t0) cc_final: 0.7766 (t0)
REVERT: C   83 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6146 (mtm)
REVERT: C   93 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6667 (tt)
REVERT: C   99 ARG cc_start: 0.7875 (ptt90) cc_final: 0.7466 (ppt170)
REVERT: A   41 THR cc_start: 0.7536 (p) cc_final: 0.7213 (t)
REVERT: A   44 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8208 (t)
REVERT: A   60 GLN cc_start: 0.7431 (tm-30) cc_final: 0.6578 (tm-30)
REVERT: A   72 TRP cc_start: 0.8025 (t60) cc_final: 0.7629 (t60)
REVERT: A  119 LYS cc_start: 0.7781 (tppt) cc_final: 0.6985 (tppt)
REVERT: A  201 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4954 (ptpt)
REVERT: A  212 LYS cc_start: 0.7995 (tppt) cc_final: 0.7558 (tptm)
REVERT: A  248 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7342 (mm)
REVERT: A  250 LEU cc_start: 0.8099 (tp) cc_final: 0.7560 (tp)
REVERT: A  302 LEU cc_start: 0.7409 (tp) cc_final: 0.7052 (tt)
REVERT: A  316 LYS cc_start: 0.6359 (mtmt) cc_final: 0.5869 (mtmt)
REVERT: A  319 TYR cc_start: 0.7305 (m-10) cc_final: 0.6916 (m-10)
REVERT: A  320 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7206 (mm-40)
REVERT: A  325 ARG cc_start: 0.7382 (ptp-170) cc_final: 0.7087 (ptt180)
REVERT: A  346 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7928 (mm-30)
REVERT: A  356 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (p)
REVERT: A  362 LYS cc_start: 0.7602 (tmtt) cc_final: 0.7214 (tptp)
REVERT: A  430 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7529 (mmmt)
REVERT: A  459 TYR cc_start: 0.7237 (p90) cc_final: 0.6492 (p90)
REVERT: A  472 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7583 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8411 (t0) cc_final: 0.7170 (m-30)
REVERT: A  493 ASN cc_start: 0.7493 (m-40) cc_final: 0.7264 (m-40)
REVERT: A  495 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.6804 (p90)
REVERT: A  496 PHE cc_start: 0.8342 (t80) cc_final: 0.8124 (t80)
REVERT: A  499 GLN cc_start: 0.6915 (tm-30) cc_final: 0.6712 (tm-30)
REVERT: A  518 VAL cc_start: 0.8423 (t) cc_final: 0.7986 (p)
REVERT: A  520 SER cc_start: 0.8039 (m) cc_final: 0.7423 (p)
REVERT: A  534 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8310 (mmtp)
REVERT: A  538 ASN cc_start: 0.7219 (t0) cc_final: 0.6885 (t0)
REVERT: A  543 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7420 (ttmm)
REVERT: A  568 PHE cc_start: 0.7478 (t80) cc_final: 0.7064 (t80)
REVERT: A  580 ASP cc_start: 0.7115 (t70) cc_final: 0.6208 (t0)
REVERT: A  592 ASP cc_start: 0.7462 (t70) cc_final: 0.7194 (t0)
REVERT: A  649 PHE cc_start: 0.6064 (t80) cc_final: 0.5302 (t80)
REVERT: A  661 TYR cc_start: 0.6949 (t80) cc_final: 0.6338 (t80)
  outliers start: 45
  outliers final: 29
  residues processed: 224
  average time/residue: 0.0858
  time to fit residues: 24.4842
Evaluate side-chains
  237 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 201
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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   83 MET
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  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  248 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  393 LEU
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  590 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0980
   chunk 25 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 127 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 = 0.4018 r_free = 0.4018 target = 0.153282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.131373 restraints weight = 10611.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.136473 restraints weight = 5689.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.139879 restraints weight = 3554.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.142134 restraints weight = 2465.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.143876 restraints weight = 1860.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.4462

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= 0.138
  Angle     :  0.670  12.783   8486  Z= 0.335
  Chirality :  0.045   0.193    921
  Planarity :  0.004   0.037   1100
  Dihedral  :  8.072  86.723    879
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.13 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 23.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.29), residues: 764
  helix: -0.30 (1.71), residues: 16
  sheet: -1.48 (0.34), residues: 204
  loop : -2.74 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  42 
 TYR   0.012   0.001   TYR A 642 
 PHE   0.013   0.001   PHE A 353 
 TRP   0.011   0.001   TRP A 359 
 HIS   0.010   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6219)
  covalent geometry    : angle       0.66585 ( 8468)
  SS BOND              : bond        0.00229 (    9)
  SS BOND              : angle       1.75571 (   18)
  hydrogen bonds       : bond        0.02906 (  103)
  hydrogen bonds       : angle       5.47816 (  270)

*********************** 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
  241 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 198
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8184 (tp) cc_final: 0.7748 (tp)
REVERT: C   27 PHE cc_start: 0.8116 (t80) cc_final: 0.7710 (t80)
REVERT: C   31 TYR cc_start: 0.7650 (p90) cc_final: 0.7159 (p90)
REVERT: C   52 SER cc_start: 0.8210 (t) cc_final: 0.7417 (p)
REVERT: C   77 ASN cc_start: 0.8436 (t0) cc_final: 0.7772 (t0)
REVERT: C   83 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6036 (mtm)
REVERT: C   93 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6668 (tt)
REVERT: C   99 ARG cc_start: 0.7880 (ptt90) cc_final: 0.7459 (ppt170)
REVERT: A   41 THR cc_start: 0.7572 (p) cc_final: 0.7265 (t)
REVERT: A   44 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8202 (t)
REVERT: A   60 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6570 (tm-30)
REVERT: A   72 TRP cc_start: 0.8044 (t60) cc_final: 0.7627 (t60)
REVERT: A  119 LYS cc_start: 0.7773 (tppt) cc_final: 0.7005 (tppt)
REVERT: A  182 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7109 (mt)
REVERT: A  183 MET cc_start: 0.5790 (tmt) cc_final: 0.5450 (tmt)
REVERT: A  201 LYS cc_start: 0.5520 (OUTLIER) cc_final: 0.5073 (ptpt)
REVERT: A  212 LYS cc_start: 0.7998 (tppt) cc_final: 0.7431 (tptm)
REVERT: A  248 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7335 (mm)
REVERT: A  250 LEU cc_start: 0.8119 (tp) cc_final: 0.7577 (tp)
REVERT: A  302 LEU cc_start: 0.7428 (tp) cc_final: 0.7071 (tt)
REVERT: A  319 TYR cc_start: 0.7299 (m-10) cc_final: 0.6938 (m-10)
REVERT: A  320 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7287 (mm-40)
REVERT: A  346 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7921 (mm-30)
REVERT: A  356 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8258 (p)
REVERT: A  362 LYS cc_start: 0.7615 (tmtt) cc_final: 0.7250 (tptp)
REVERT: A  430 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7784 (mmmt)
REVERT: A  459 TYR cc_start: 0.7185 (p90) cc_final: 0.6417 (p90)
REVERT: A  472 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7589 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8424 (t0) cc_final: 0.7204 (m-30)
REVERT: A  493 ASN cc_start: 0.7442 (m-40) cc_final: 0.7220 (m-40)
REVERT: A  495 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.6868 (p90)
REVERT: A  496 PHE cc_start: 0.8307 (t80) cc_final: 0.8103 (t80)
REVERT: A  499 GLN cc_start: 0.6949 (tm-30) cc_final: 0.6677 (tm-30)
REVERT: A  518 VAL cc_start: 0.8422 (t) cc_final: 0.7966 (p)
REVERT: A  520 SER cc_start: 0.8062 (m) cc_final: 0.7538 (p)
REVERT: A  534 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8313 (mmtp)
REVERT: A  538 ASN cc_start: 0.7295 (t0) cc_final: 0.6873 (t0)
REVERT: A  568 PHE cc_start: 0.7495 (t80) cc_final: 0.7076 (t80)
REVERT: A  580 ASP cc_start: 0.7108 (t70) cc_final: 0.6209 (t0)
REVERT: A  592 ASP cc_start: 0.7444 (t70) cc_final: 0.7241 (t0)
  outliers start: 43
  outliers final: 32
  residues processed: 219
  average time/residue: 0.0814
  time to fit residues: 22.7808
Evaluate side-chains
  237 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 197
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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   83 MET
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  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  248 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  386 TYR
Chi-restraints excluded: chain A residue  439 VAL
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  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  633 ASP
Chi-restraints excluded: chain A residue  639 TRP
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0000
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** 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 = 0.4006 r_free = 0.4006 target = 0.152184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130067 restraints weight = 10707.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.135068 restraints weight = 5762.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.138490 restraints weight = 3623.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.140871 restraints weight = 2524.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.142419 restraints weight = 1895.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.4695

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= 0.156
  Angle     :  0.697  13.971   8486  Z= 0.348
  Chirality :  0.046   0.207    921
  Planarity :  0.004   0.039   1100
  Dihedral  :  8.162  86.953    879
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 23.46 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.29), residues: 764
  helix: -0.17 (1.76), residues: 16
  sheet: -1.33 (0.34), residues: 212
  loop : -2.82 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  42 
 TYR   0.015   0.001   TYR A 429 
 PHE   0.017   0.001   PHE A 649 
 TRP   0.013   0.001   TRP A 359 
 HIS   0.009   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6219)
  covalent geometry    : angle       0.69235 ( 8468)
  SS BOND              : bond        0.00388 (    9)
  SS BOND              : angle       1.85584 (   18)
  hydrogen bonds       : bond        0.02941 (  103)
  hydrogen bonds       : angle       5.48326 (  270)

*********************** 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
  241 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 199
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 LEU cc_start: 0.8303 (tp) cc_final: 0.8062 (tp)
REVERT: C   27 PHE cc_start: 0.8126 (t80) cc_final: 0.7786 (t80)
REVERT: C   31 TYR cc_start: 0.7660 (p90) cc_final: 0.7136 (p90)
REVERT: C   52 SER cc_start: 0.8207 (t) cc_final: 0.7474 (p)
REVERT: C   72 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7405 (tpp80)
REVERT: C   77 ASN cc_start: 0.8513 (t0) cc_final: 0.7861 (t0)
REVERT: C   93 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6647 (tt)
REVERT: C   99 ARG cc_start: 0.7870 (ptt90) cc_final: 0.7373 (ppt170)
REVERT: A   41 THR cc_start: 0.7616 (p) cc_final: 0.7359 (t)
REVERT: A   60 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6577 (tm-30)
REVERT: A   72 TRP cc_start: 0.8028 (t60) cc_final: 0.7596 (t60)
REVERT: A  119 LYS cc_start: 0.7811 (tppt) cc_final: 0.7043 (tppt)
REVERT: A  182 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7131 (mt)
REVERT: A  183 MET cc_start: 0.5850 (tmt) cc_final: 0.5606 (tmt)
REVERT: A  201 LYS cc_start: 0.5537 (OUTLIER) cc_final: 0.5082 (ptpt)
REVERT: A  212 LYS cc_start: 0.7997 (tppt) cc_final: 0.7406 (tptm)
REVERT: A  250 LEU cc_start: 0.8074 (tp) cc_final: 0.7562 (tp)
REVERT: A  302 LEU cc_start: 0.7468 (tp) cc_final: 0.7100 (tt)
REVERT: A  319 TYR cc_start: 0.7297 (m-10) cc_final: 0.6937 (m-10)
REVERT: A  320 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7275 (mm-40)
REVERT: A  325 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.7178 (ptt180)
REVERT: A  346 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: A  356 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8283 (p)
REVERT: A  361 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7125 (ttm170)
REVERT: A  362 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7241 (tptp)
REVERT: A  430 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7642 (mmmt)
REVERT: A  434 ASP cc_start: 0.7069 (t0) cc_final: 0.6753 (t0)
REVERT: A  458 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6797 (mtp180)
REVERT: A  472 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7573 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8453 (t0) cc_final: 0.6939 (m-30)
REVERT: A  520 SER cc_start: 0.8047 (m) cc_final: 0.7517 (p)
REVERT: A  534 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8322 (mmtp)
REVERT: A  538 ASN cc_start: 0.7216 (t0) cc_final: 0.6801 (t0)
REVERT: A  568 PHE cc_start: 0.7501 (t80) cc_final: 0.7071 (t80)
REVERT: A  580 ASP cc_start: 0.7099 (t70) cc_final: 0.6196 (t0)
REVERT: A  649 PHE cc_start: 0.5910 (t80) cc_final: 0.5194 (t80)
REVERT: A  661 TYR cc_start: 0.7021 (t80) cc_final: 0.6487 (t80)
  outliers start: 42
  outliers final: 34
  residues processed: 220
  average time/residue: 0.0816
  time to fit residues: 22.9136
Evaluate side-chains
  234 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 196
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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   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  201 LYS
Chi-restraints excluded: chain A residue  248 LEU
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  386 TYR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  439 VAL
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  464 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  525 HIS
Chi-restraints excluded: chain A residue  535 LYS
Chi-restraints excluded: chain A residue  559 THR
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  651 THR
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  667 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0170
   chunk 59 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7818

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A  80 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.151920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.129763 restraints weight = 10759.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.134738 restraints weight = 5781.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.138205 restraints weight = 3630.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.140469 restraints weight = 2520.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.142213 restraints weight = 1906.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.4938

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= 0.161
  Angle     :  0.700  14.214   8486  Z= 0.350
  Chirality :  0.046   0.208    921
  Planarity :  0.004   0.039   1100
  Dihedral  :  8.280  87.332    879
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 23.91 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.32 (0.28), residues: 764
  helix: -1.44 (1.35), residues: 22
  sheet: -1.34 (0.34), residues: 217
  loop : -2.82 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  42 
 TYR   0.015   0.001   TYR A 642 
 PHE   0.015   0.001   PHE A 649 
 TRP   0.011   0.001   TRP A 359 
 HIS   0.008   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6219)
  covalent geometry    : angle       0.69619 ( 8468)
  SS BOND              : bond        0.00305 (    9)
  SS BOND              : angle       1.66255 (   18)
  hydrogen bonds       : bond        0.02926 (  103)
  hydrogen bonds       : angle       5.57694 (  270)

*********************** 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
  241 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8096 (t80) cc_final: 0.7799 (t80)
REVERT: C   31 TYR cc_start: 0.7664 (p90) cc_final: 0.7118 (p90)
REVERT: C   52 SER cc_start: 0.8168 (t) cc_final: 0.7443 (p)
REVERT: C   72 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7401 (tpp80)
REVERT: C   77 ASN cc_start: 0.8478 (t0) cc_final: 0.7901 (t0)
REVERT: C   93 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6740 (tt)
REVERT: C   99 ARG cc_start: 0.7854 (ptt90) cc_final: 0.7388 (ppt170)
REVERT: A   41 THR cc_start: 0.7663 (p) cc_final: 0.7440 (t)
REVERT: A   42 ARG cc_start: 0.8290 (ttm170) cc_final: 0.8021 (ttm170)
REVERT: A   60 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6554 (tm-30)
REVERT: A   72 TRP cc_start: 0.8037 (t60) cc_final: 0.7588 (t60)
REVERT: A  119 LYS cc_start: 0.7795 (tppt) cc_final: 0.7105 (tppt)
REVERT: A  182 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7128 (mt)
REVERT: A  201 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5102 (ptpt)
REVERT: A  212 LYS cc_start: 0.8085 (tppt) cc_final: 0.7643 (tppt)
REVERT: A  250 LEU cc_start: 0.8067 (tp) cc_final: 0.7507 (tp)
REVERT: A  302 LEU cc_start: 0.7485 (tp) cc_final: 0.7117 (tt)
REVERT: A  319 TYR cc_start: 0.7297 (m-10) cc_final: 0.6934 (m-10)
REVERT: A  320 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7238 (mm-40)
REVERT: A  325 ARG cc_start: 0.7527 (ptp-170) cc_final: 0.7303 (ptt180)
REVERT: A  346 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: A  360 ASN cc_start: 0.8501 (m-40) cc_final: 0.8032 (p0)
REVERT: A  361 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7132 (ttm170)
REVERT: A  362 LYS cc_start: 0.7626 (tmtt) cc_final: 0.7276 (tptp)
REVERT: A  434 ASP cc_start: 0.7078 (t0) cc_final: 0.6777 (t0)
REVERT: A  472 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7559 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8421 (t0) cc_final: 0.6949 (m-30)
REVERT: A  496 PHE cc_start: 0.8193 (t80) cc_final: 0.7866 (t80)
REVERT: A  520 SER cc_start: 0.8030 (m) cc_final: 0.7351 (p)
REVERT: A  534 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8318 (mmtp)
REVERT: A  538 ASN cc_start: 0.7281 (t0) cc_final: 0.7045 (t0)
REVERT: A  568 PHE cc_start: 0.7515 (t80) cc_final: 0.7086 (t80)
REVERT: A  580 ASP cc_start: 0.7000 (t70) cc_final: 0.6311 (t0)
REVERT: A  649 PHE cc_start: 0.6127 (t80) cc_final: 0.5289 (t80)
REVERT: A  661 TYR cc_start: 0.6991 (t80) cc_final: 0.6451 (t80)
  outliers start: 40
  outliers final: 29
  residues processed: 219
  average time/residue: 0.0836
  time to fit residues: 23.2881
Evaluate side-chains
  233 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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   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  201 LYS
Chi-restraints excluded: chain A residue  248 LEU
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  393 LEU
Chi-restraints excluded: chain A residue  439 VAL
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  464 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  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  651 THR
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 33 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0570
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6902

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** 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 = 0.4005 r_free = 0.4005 target = 0.152395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130169 restraints weight = 10740.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.135204 restraints weight = 5798.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.138684 restraints weight = 3650.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.140956 restraints weight = 2535.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.142205 restraints weight = 1917.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.5059

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= 0.152
  Angle     :  0.707  14.171   8486  Z= 0.352
  Chirality :  0.046   0.218    921
  Planarity :  0.004   0.039   1100
  Dihedral  :  8.059  86.663    877
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.04 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 24.81 %
    Favored  : 69.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.23 (0.28), residues: 764
  helix: -1.46 (1.35), residues: 22
  sheet: -1.21 (0.34), residues: 206
  loop : -2.77 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  42 
 TYR   0.014   0.001   TYR A 642 
 PHE   0.017   0.002   PHE A 226 
 TRP   0.010   0.001   TRP A 639 
 HIS   0.006   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6219)
  covalent geometry    : angle       0.70334 ( 8468)
  SS BOND              : bond        0.00367 (    9)
  SS BOND              : angle       1.68781 (   18)
  hydrogen bonds       : bond        0.02894 (  103)
  hydrogen bonds       : angle       5.59179 (  270)

********************** 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
  232 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 195
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   27 PHE cc_start: 0.8085 (t80) cc_final: 0.7832 (t80)
REVERT: C   52 SER cc_start: 0.8113 (t) cc_final: 0.7408 (p)
REVERT: C   72 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7374 (tpp80)
REVERT: C   77 ASN cc_start: 0.8516 (t0) cc_final: 0.7981 (t0)
REVERT: C   93 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6714 (tt)
REVERT: C   99 ARG cc_start: 0.7785 (ptt90) cc_final: 0.7343 (ppt170)
REVERT: A   41 THR cc_start: 0.7660 (p) cc_final: 0.7407 (t)
REVERT: A   60 GLN cc_start: 0.7311 (tm-30) cc_final: 0.6495 (tm-30)
REVERT: A   72 TRP cc_start: 0.8035 (t60) cc_final: 0.7590 (t60)
REVERT: A  119 LYS cc_start: 0.7824 (tppt) cc_final: 0.7126 (tppt)
REVERT: A  212 LYS cc_start: 0.8074 (tppt) cc_final: 0.7625 (tppt)
REVERT: A  250 LEU cc_start: 0.8028 (tp) cc_final: 0.7477 (tp)
REVERT: A  255 LEU cc_start: 0.5104 (tp) cc_final: 0.4688 (tt)
REVERT: A  302 LEU cc_start: 0.7468 (tp) cc_final: 0.7102 (tt)
REVERT: A  319 TYR cc_start: 0.7297 (m-10) cc_final: 0.6952 (m-10)
REVERT: A  320 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7212 (mm-40)
REVERT: A  325 ARG cc_start: 0.7505 (ptp-170) cc_final: 0.7298 (ptt180)
REVERT: A  346 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8001 (mm-30)
REVERT: A  356 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (p)
REVERT: A  360 ASN cc_start: 0.8504 (m-40) cc_final: 0.8043 (p0)
REVERT: A  361 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7159 (ttm170)
REVERT: A  362 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7289 (tptp)
REVERT: A  429 TYR cc_start: 0.7868 (t80) cc_final: 0.7512 (t80)
REVERT: A  434 ASP cc_start: 0.7059 (t0) cc_final: 0.6758 (t0)
REVERT: A  472 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7553 (ttm-80)
REVERT: A  473 ASP cc_start: 0.8430 (t0) cc_final: 0.6939 (m-30)
REVERT: A  496 PHE cc_start: 0.8288 (t80) cc_final: 0.7951 (t80)
REVERT: A  520 SER cc_start: 0.8060 (m) cc_final: 0.7311 (p)
REVERT: A  534 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8313 (mmtp)
REVERT: A  538 ASN cc_start: 0.7424 (t0) cc_final: 0.7081 (t0)
REVERT: A  568 PHE cc_start: 0.7477 (t80) cc_final: 0.7068 (t80)
REVERT: A  580 ASP cc_start: 0.6982 (t70) cc_final: 0.6315 (t0)
REVERT: A  649 PHE cc_start: 0.6354 (t80) cc_final: 0.5493 (t80)
REVERT: A  661 TYR cc_start: 0.7060 (t80) cc_final: 0.6446 (t80)
  outliers start: 37
  outliers final: 31
  residues processed: 214
  average time/residue: 0.0867
  time to fit residues: 23.5950
Evaluate side-chains
  226 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 193
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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   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  181 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  248 LEU
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  393 LEU
Chi-restraints excluded: chain A residue  439 VAL
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  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  525 HIS
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  651 THR
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 18 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 23 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 58 optimal weight:    0.1980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 681 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.150219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.128140 restraints weight = 10728.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.133096 restraints weight = 5786.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.136535 restraints weight = 3643.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.138782 restraints weight = 2535.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.140526 restraints weight = 1922.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.5308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6228  Z= 0.198
  Angle     :  0.748  14.147   8486  Z= 0.373
  Chirality :  0.047   0.215    921
  Planarity :  0.004   0.042   1100
  Dihedral  :  8.113  88.046    875
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.70 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 24.66 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.25 (0.28), residues: 764
  helix: -1.42 (1.39), residues: 22
  sheet: -1.22 (0.34), residues: 210
  loop : -2.79 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  42 
 TYR   0.018   0.002   TYR A 642 
 PHE   0.018   0.002   PHE A 226 
 TRP   0.014   0.002   TRP A 359 
 HIS   0.008   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 6219)
  covalent geometry    : angle       0.74291 ( 8468)
  SS BOND              : bond        0.00386 (    9)
  SS BOND              : angle       1.99556 (   18)
  hydrogen bonds       : bond        0.03106 (  103)
  hydrogen bonds       : angle       5.77306 (  270)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1166.73 seconds
wall clock time: 20 minutes 46.18 seconds (1246.18 seconds total)