Starting phenix.real_space_refine
on Thu Jun  5 03:53:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wop_32654/06_2025/7wop_32654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wop_32654/06_2025/7wop_32654.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wop_32654/06_2025/7wop_32654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wop_32654/06_2025/7wop_32654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wop_32654/06_2025/7wop_32654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wop_32654/06_2025/7wop_32654.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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      23      5.16       5
     C    3212      2.51       5
     N     863      2.21       5
     O    1009      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5107
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1588
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1754
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 225}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1765
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 223}
          Chain breaks: 1
  Time building chain proxies: 5.66, per 1000 atoms: 1.11
  Number of scatterers: 5107
  At special positions: 0
  Unit cell: (86.184, 78.736, 102.144, 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      23     16.00
     O    1009      8.00
     N     863      7.00
     C    3212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 148 " - pdb=" SG  CYS B 221 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 220 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 710.6 milliseconds
  

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1190

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 10 sheets defined
      5.5% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.655A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.830A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.546A  pdb=" N   GLU A 406 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 84
      removed outlier: 3.500A  pdb=" N   GLU C  84 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 156
      removed outlier: 3.500A  pdb=" N   HIS C 156 " --> pdb=" O   PHE C 153 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50
      removed outlier: 6.502A  pdb=" N   TRP B  37 " --> pdb=" O   MET B  49 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR B 106 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 69
      removed outlier: 5.110A  pdb=" N   SER B  65 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER B  67 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 177
      removed outlier: 5.785A  pdb=" N   TRP B 173 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ARG B 164 " --> pdb=" O   TRP B 173 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET B 160 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 23
    Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 49
      removed outlier: 6.716A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASN C  97 " --> pdb=" O   ASP C  93 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 49
      removed outlier: 6.716A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR C  87 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 143 through 144
    Processing sheet with id=AB1, first strand: chain 'C' and resid 182 through 184
      removed outlier: 3.696A  pdb=" N   TYR C 183 " --> pdb=" O   VAL C 174 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   TRP C 160 " --> pdb=" O   VAL C 172 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   VAL C 174 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   MET C 158 " --> pdb=" O   VAL C 174 " (cutoff:3.500A)

    87 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1663
        1.35 -     1.46: 1355
        1.46 -     1.58: 2187
        1.58 -     1.70: 0
        1.70 -     1.81: 30
  Bond restraints: 5235
  Sorted by residual:
  bond pdb=" N   GLY C 237 "
       pdb=" CA  GLY C 237 "
    ideal  model  delta    sigma   weight residual
    1.458  1.447  0.011 9.20e-03 1.18e+04 1.34e+00
  bond pdb=" CA  PRO B 228 "
       pdb=" C   PRO B 228 "
    ideal  model  delta    sigma   weight residual
    1.526  1.518  0.008 8.50e-03 1.38e+04 8.29e-01
  bond pdb=" C   ILE B 226 "
       pdb=" O   ILE B 226 "
    ideal  model  delta    sigma   weight residual
    1.232  1.242 -0.010 1.15e-02 7.56e+03 7.95e-01
  bond pdb=" CA  GLY A 476 "
       pdb=" C   GLY A 476 "
    ideal  model  delta    sigma   weight residual
    1.514  1.527 -0.012 1.41e-02 5.03e+03 7.51e-01
  bond pdb=" N   THR B  19 "
       pdb=" CA  THR B  19 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.011 1.42e-02 4.96e+03 5.62e-01
  ... (remaining 5230 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 6811
        1.15 -     2.30: 229
        2.30 -     3.44: 61
        3.44 -     4.59: 12
        4.59 -     5.74: 3
  Bond angle restraints: 7116
  Sorted by residual:
  angle pdb=" C   SER C  51 "
        pdb=" N   ASN C  52 "
        pdb=" CA  ASN C  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.03   -5.49 1.91e+00 2.74e-01 8.25e+00
  angle pdb=" N   ASN A 481 "
        pdb=" CA  ASN A 481 "
        pdb=" C   ASN A 481 "
      ideal   model   delta    sigma   weight residual
     113.15  109.85    3.30 1.19e+00 7.06e-01 7.69e+00
  angle pdb=" N   GLY A 504 "
        pdb=" CA  GLY A 504 "
        pdb=" C   GLY A 504 "
      ideal   model   delta    sigma   weight residual
     113.79  110.74    3.05 1.17e+00 7.31e-01 6.81e+00
  angle pdb=" N   GLY B  95 "
        pdb=" CA  GLY B  95 "
        pdb=" C   GLY B  95 "
      ideal   model   delta    sigma   weight residual
     111.36  114.27   -2.91 1.17e+00 7.31e-01 6.17e+00
  angle pdb=" N   THR B  25 "
        pdb=" CA  THR B  25 "
        pdb=" C   THR B  25 "
      ideal   model   delta    sigma   weight residual
     114.09  110.45    3.64 1.55e+00 4.16e-01 5.51e+00
  ... (remaining 7111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 2847
       16.21 -    32.42: 166
       32.42 -    48.63: 36
       48.63 -    64.84: 8
       64.84 -    81.05: 4
  Dihedral angle restraints: 3061
    sinusoidal: 1163
      harmonic: 1898
  Sorted by residual:
  dihedral pdb=" CA  CYS A 336 "
           pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   20.34   58.66     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  PRO B 228 "
           pdb=" C   PRO B 228 "
           pdb=" N   TYR B 229 "
           pdb=" CA  TYR B 229 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.60  -16.40     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" N   PHE B 193 "
           pdb=" CA  PHE B 193 "
           pdb=" CB  PHE B 193 "
           pdb=" CG  PHE B 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -120.02  -59.98     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3058 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 425
       0.029 -    0.057: 221
       0.057 -    0.086: 65
       0.086 -    0.115: 36
       0.115 -    0.143: 6
  Chirality restraints: 753
  Sorted by residual:
  chirality pdb=" CA  VAL A 483 "
            pdb=" N   VAL A 483 "
            pdb=" C   VAL A 483 "
            pdb=" CB  VAL A 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CB  VAL A 433 "
            pdb=" CA  VAL A 433 "
            pdb=" CG1 VAL A 433 "
            pdb=" CG2 VAL A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.04e-01
  chirality pdb=" CA  ILE B  50 "
            pdb=" N   ILE B  50 "
            pdb=" C   ILE B  50 "
            pdb=" CB  ILE B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.89e-01
  ... (remaining 750 not shown)

  Planarity restraints: 932
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B   7 "   -0.032 5.00e-02 4.00e+02   4.94e-02 3.91e+00
        pdb=" N   PRO B   8 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B   8 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B   8 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 166 "    0.032 5.00e-02 4.00e+02   4.84e-02 3.75e+00
        pdb=" N   PRO B 167 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 167 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 167 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C   6 "   -0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO C   7 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C   7 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C   7 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 929 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 413
        2.74 -     3.28: 5253
        3.28 -     3.82: 8454
        3.82 -     4.36: 9662
        4.36 -     4.90: 16798
  Nonbonded interactions: 40580
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  36 "
            pdb=" OG  SER B  91 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   THR C  33 "
            pdb=" OH  TYR C 236 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER C  27 "
            pdb=" OD1 ASP C  94 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   LEU A 455 "
            pdb=" OH  TYR B 159 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" OG1 THR B 203 "
     model   vdw
     2.328 3.040
  ... (remaining 40575 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:             50.900
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.380
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   74.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6451
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   0.037   5243  Z= 0.101
  Angle     :  0.536   5.738   7132  Z= 0.311
  Chirality :  0.040   0.143    753
  Planarity :  0.004   0.049    932
  Dihedral  : 10.828  81.052   1847
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.38 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  9.21 %
    Allowed  :  8.48 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.81 (0.27), residues: 659
  helix: -4.90 (0.33), residues: 26
  sheet: -2.57 (0.38), residues: 157
  loop : -3.60 (0.23), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  98 
 HIS   0.001   0.000   HIS C 159 
 PHE   0.005   0.001   PHE C 153 
 TYR   0.006   0.001   TYR B  51 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19869 (   78)
  hydrogen bonds       : angle      10.35855 (  195)
  SS BOND              : bond        0.00149 (    8)
  SS BOND              : angle       0.61254 (   16)
  covalent geometry    : bond        0.00192 ( 5235)
  covalent geometry    : angle       0.53586 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 158
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 ASN cc_start: 0.8461 (m110) cc_final: 0.8186 (m-40)
REVERT: A  365 TYR cc_start: 0.8197 (m-80) cc_final: 0.7844 (m-80)
REVERT: A  395 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7770 (m)
REVERT: A  399 SER cc_start: 0.8050 (m) cc_final: 0.7262 (t)
REVERT: A  453 TYR cc_start: 0.7655 (p90) cc_final: 0.7269 (p90)
REVERT: A  454 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7978 (tpp-160)
REVERT: A  493 ARG cc_start: 0.6932 (ttt180) cc_final: 0.6692 (ttt180)
REVERT: B   60 VAL cc_start: 0.6133 (OUTLIER) cc_final: 0.5759 (m)
REVERT: B  108 VAL cc_start: 0.6482 (OUTLIER) cc_final: 0.5849 (t)
REVERT: B  193 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6774 (m-80)
REVERT: C   36 TRP cc_start: 0.7702 (m100) cc_final: 0.7418 (m100)
REVERT: C  195 SER cc_start: 0.7910 (p) cc_final: 0.7658 (m)
  outliers start: 51
  outliers final: 19
  residues processed: 197
  average time/residue: 0.2087
  time to fit residues: 52.1683
Evaluate side-chains
  162 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0040
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 30 optimal weight:    0.0570
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.2908

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 409 GLN
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  39 GLN
B  40 GLN
B 165 GLN
B 199 ASN
B 202 ASN
** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
C  80 GLN
C  97 ASN
C 137 GLN
** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 206 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.170110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.154576 restraints weight = 8349.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.158940 restraints weight = 4138.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.161747 restraints weight = 2403.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6513
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5243  Z= 0.125
  Angle     :  0.622   7.161   7132  Z= 0.319
  Chirality :  0.044   0.213    753
  Planarity :  0.005   0.049    932
  Dihedral  :  7.333  56.794    782
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.96 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 16.79 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.31 (0.28), residues: 659
  helix: -4.04 (0.53), residues: 34
  sheet: -1.97 (0.40), residues: 157
  loop : -3.35 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  98 
 HIS   0.004   0.001   HIS B  41 
 PHE   0.020   0.002   PHE C 153 
 TYR   0.020   0.001   TYR B 220 
 ARG   0.004   0.001   ARG B 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02905 (   78)
  hydrogen bonds       : angle       7.01565 (  195)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       0.64798 (   16)
  covalent geometry    : bond        0.00282 ( 5235)
  covalent geometry    : angle       0.62217 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.8484 (m-80) cc_final: 0.7965 (m-80)
REVERT: A  378 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8182 (ttmt)
REVERT: A  423 TYR cc_start: 0.7820 (t80) cc_final: 0.7405 (t80)
REVERT: A  453 TYR cc_start: 0.7809 (p90) cc_final: 0.7103 (p90)
REVERT: A  474 GLN cc_start: 0.7735 (tt0) cc_final: 0.7522 (tt0)
REVERT: A  493 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6833 (ttt180)
REVERT: B   60 VAL cc_start: 0.6144 (OUTLIER) cc_final: 0.5876 (m)
REVERT: B   91 SER cc_start: 0.7550 (p) cc_final: 0.6782 (t)
REVERT: B  163 VAL cc_start: 0.8371 (m) cc_final: 0.8041 (p)
REVERT: B  185 TYR cc_start: 0.6690 (m-80) cc_final: 0.6360 (m-80)
REVERT: B  195 ILE cc_start: 0.7031 (mt) cc_final: 0.6560 (tt)
REVERT: B  229 TYR cc_start: 0.7644 (t80) cc_final: 0.7365 (t80)
REVERT: C  192 PHE cc_start: 0.6743 (m-80) cc_final: 0.6261 (m-10)
  outliers start: 37
  outliers final: 23
  residues processed: 169
  average time/residue: 0.1969
  time to fit residues: 42.1788
Evaluate side-chains
  162 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 ASN
A 360 ASN
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 ASN
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 GLN
B 207 GLN
B 209 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.158909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.143047 restraints weight = 8355.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.147503 restraints weight = 4166.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.150166 restraints weight = 2425.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   5243  Z= 0.279
  Angle     :  0.732   7.183   7132  Z= 0.386
  Chirality :  0.050   0.236    753
  Planarity :  0.005   0.048    932
  Dihedral  :  7.299  46.017    775
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.08 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  7.22 %
    Allowed  : 18.95 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.26 (0.29), residues: 659
  helix: -3.65 (0.62), residues: 34
  sheet: -1.94 (0.39), residues: 160
  loop : -3.35 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP C 171 
 HIS   0.007   0.001   HIS B  41 
 PHE   0.031   0.002   PHE C 153 
 TYR   0.021   0.003   TYR A 453 
 ARG   0.004   0.001   ARG C 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (   78)
  hydrogen bonds       : angle       7.24861 (  195)
  SS BOND              : bond        0.00412 (    8)
  SS BOND              : angle       0.97919 (   16)
  covalent geometry    : bond        0.00609 ( 5235)
  covalent geometry    : angle       0.73125 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6302 (t80)
REVERT: A  375 PHE cc_start: 0.7724 (m-10) cc_final: 0.7451 (m-10)
REVERT: A  399 SER cc_start: 0.8245 (m) cc_final: 0.7514 (t)
REVERT: A  453 TYR cc_start: 0.8061 (p90) cc_final: 0.7336 (p90)
REVERT: A  454 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8131 (ttm170)
REVERT: A  458 LYS cc_start: 0.8164 (tppt) cc_final: 0.7861 (tppt)
REVERT: A  474 GLN cc_start: 0.7850 (tt0) cc_final: 0.7638 (tt0)
REVERT: A  493 ARG cc_start: 0.7286 (ttt180) cc_final: 0.6957 (ttt180)
REVERT: A  506 GLN cc_start: 0.8508 (mt0) cc_final: 0.8167 (mt0)
REVERT: B   60 VAL cc_start: 0.6723 (OUTLIER) cc_final: 0.6513 (m)
REVERT: B  193 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7042 (m-80)
REVERT: B  195 ILE cc_start: 0.7272 (mt) cc_final: 0.6717 (tt)
REVERT: B  227 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7040 (tp-100)
REVERT: B  230 TYR cc_start: 0.7428 (t80) cc_final: 0.7192 (t80)
REVERT: B  231 TYR cc_start: 0.6732 (t80) cc_final: 0.6436 (t80)
REVERT: C   28 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7626 (p0)
REVERT: C   29 ILE cc_start: 0.8779 (mt) cc_final: 0.8464 (tt)
REVERT: C   33 THR cc_start: 0.7736 (p) cc_final: 0.7455 (m)
REVERT: C   68 SER cc_start: 0.8673 (t) cc_final: 0.8411 (p)
REVERT: C  158 MET cc_start: 0.8266 (mmm) cc_final: 0.7826 (mmt)
REVERT: C  170 GLU cc_start: 0.7461 (pp20) cc_final: 0.6612 (pp20)
REVERT: C  171 TRP cc_start: 0.7529 (t60) cc_final: 0.7109 (t60)
REVERT: C  173 SER cc_start: 0.7682 (t) cc_final: 0.7376 (p)
REVERT: C  236 TYR cc_start: 0.8059 (p90) cc_final: 0.7482 (p90)
  outliers start: 40
  outliers final: 25
  residues processed: 188
  average time/residue: 0.1908
  time to fit residues: 45.6143
Evaluate side-chains
  184 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   28 ASN
Chi-restraints excluded: chain C residue  100 PHE
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 ASN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.159829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143720 restraints weight = 8519.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.148235 restraints weight = 4210.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.151079 restraints weight = 2438.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   5243  Z= 0.218
  Angle     :  0.707   7.496   7132  Z= 0.370
  Chirality :  0.048   0.262    753
  Planarity :  0.005   0.047    932
  Dihedral  :  7.299  45.878    774
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.78 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 21.84 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.29), residues: 659
  helix: -3.38 (0.70), residues: 34
  sheet: -1.76 (0.41), residues: 154
  loop : -3.25 (0.25), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C  98 
 HIS   0.005   0.001   HIS B  41 
 PHE   0.031   0.002   PHE C 153 
 TYR   0.028   0.002   TYR B  88 
 ARG   0.006   0.001   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (   78)
  hydrogen bonds       : angle       7.07814 (  195)
  SS BOND              : bond        0.00685 (    8)
  SS BOND              : angle       2.28595 (   16)
  covalent geometry    : bond        0.00485 ( 5235)
  covalent geometry    : angle       0.69914 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 147
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6734 (tmt90)
REVERT: A  357 ARG cc_start: 0.7272 (ptp-110) cc_final: 0.7032 (ptp-110)
REVERT: A  365 TYR cc_start: 0.8458 (m-80) cc_final: 0.7869 (m-80)
REVERT: A  378 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7811 (ttmt)
REVERT: A  399 SER cc_start: 0.8221 (m) cc_final: 0.7597 (p)
REVERT: A  403 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7873 (mtp-110)
REVERT: A  423 TYR cc_start: 0.7858 (t80) cc_final: 0.7522 (t80)
REVERT: A  453 TYR cc_start: 0.8049 (p90) cc_final: 0.7328 (p90)
REVERT: A  458 LYS cc_start: 0.8081 (tppt) cc_final: 0.7677 (mmmt)
REVERT: A  493 ARG cc_start: 0.7273 (ttt180) cc_final: 0.7002 (ttt180)
REVERT: B   85 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5063 (pm20)
REVERT: B  185 TYR cc_start: 0.7150 (m-80) cc_final: 0.6683 (m-80)
REVERT: B  193 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7261 (m-80)
REVERT: B  195 ILE cc_start: 0.7288 (mt) cc_final: 0.6989 (tt)
REVERT: B  227 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6797 (tp-100)
REVERT: B  230 TYR cc_start: 0.7429 (t80) cc_final: 0.7162 (t80)
REVERT: B  231 TYR cc_start: 0.6952 (t80) cc_final: 0.6474 (t80)
REVERT: C   29 ILE cc_start: 0.8729 (mt) cc_final: 0.8470 (tt)
REVERT: C   33 THR cc_start: 0.7663 (p) cc_final: 0.7237 (m)
REVERT: C   68 SER cc_start: 0.8671 (t) cc_final: 0.8410 (p)
REVERT: C  158 MET cc_start: 0.8179 (mmm) cc_final: 0.7730 (mmt)
REVERT: C  170 GLU cc_start: 0.7635 (pp20) cc_final: 0.7101 (pp20)
REVERT: C  173 SER cc_start: 0.7721 (t) cc_final: 0.7373 (p)
REVERT: C  236 TYR cc_start: 0.8076 (p90) cc_final: 0.7309 (p90)
  outliers start: 35
  outliers final: 23
  residues processed: 175
  average time/residue: 0.1848
  time to fit residues: 40.7970
Evaluate side-chains
  175 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  188 SER
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 7 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.160825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.144830 restraints weight = 8402.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.149343 restraints weight = 4131.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.152152 restraints weight = 2397.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5243  Z= 0.184
  Angle     :  0.681   6.891   7132  Z= 0.357
  Chirality :  0.047   0.217    753
  Planarity :  0.005   0.046    932
  Dihedral  :  7.266  45.307    773
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.78 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  7.40 %
    Allowed  : 22.38 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.30), residues: 659
  helix: -3.05 (0.78), residues: 34
  sheet: -1.64 (0.41), residues: 153
  loop : -3.20 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C  98 
 HIS   0.004   0.001   HIS B  41 
 PHE   0.032   0.002   PHE C 153 
 TYR   0.033   0.002   TYR B  93 
 ARG   0.005   0.001   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03233 (   78)
  hydrogen bonds       : angle       6.95967 (  195)
  SS BOND              : bond        0.00598 (    8)
  SS BOND              : angle       1.84087 (   16)
  covalent geometry    : bond        0.00410 ( 5235)
  covalent geometry    : angle       0.67618 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 VAL cc_start: 0.7887 (m) cc_final: 0.7508 (p)
REVERT: A  355 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6828 (tmt90)
REVERT: A  357 ARG cc_start: 0.7267 (ptp-110) cc_final: 0.6960 (ptp-110)
REVERT: A  365 TYR cc_start: 0.8442 (m-80) cc_final: 0.7777 (m-80)
REVERT: A  378 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7811 (ttmt)
REVERT: A  403 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7765 (mtp-110)
REVERT: A  451 TYR cc_start: 0.7467 (m-80) cc_final: 0.7041 (m-80)
REVERT: A  453 TYR cc_start: 0.8014 (p90) cc_final: 0.7436 (p90)
REVERT: A  458 LYS cc_start: 0.7978 (tppt) cc_final: 0.7606 (tppt)
REVERT: A  493 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6933 (ttt180)
REVERT: B   25 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6870 (p)
REVERT: B   85 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.5001 (pm20)
REVERT: B  102 PHE cc_start: 0.8509 (m-80) cc_final: 0.8166 (m-10)
REVERT: B  185 TYR cc_start: 0.6954 (m-80) cc_final: 0.6528 (m-80)
REVERT: B  193 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7011 (m-80)
REVERT: B  195 ILE cc_start: 0.7228 (mt) cc_final: 0.6919 (tt)
REVERT: B  227 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6698 (tp-100)
REVERT: B  230 TYR cc_start: 0.7408 (t80) cc_final: 0.7068 (t80)
REVERT: C   17 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7707 (mtm110)
REVERT: C   33 THR cc_start: 0.7685 (p) cc_final: 0.7193 (m)
REVERT: C   68 SER cc_start: 0.8669 (t) cc_final: 0.8431 (p)
REVERT: C  171 TRP cc_start: 0.8051 (t60) cc_final: 0.7676 (t60)
REVERT: C  173 SER cc_start: 0.7718 (t) cc_final: 0.7376 (p)
REVERT: C  236 TYR cc_start: 0.7925 (p90) cc_final: 0.7243 (p90)
  outliers start: 41
  outliers final: 25
  residues processed: 178
  average time/residue: 0.2777
  time to fit residues: 63.0733
Evaluate side-chains
  177 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  188 SER
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0270
   chunk 49 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0980
   chunk 4 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.162191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.146091 restraints weight = 8410.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.150581 restraints weight = 4137.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.153472 restraints weight = 2397.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5243  Z= 0.144
  Angle     :  0.666   7.063   7132  Z= 0.350
  Chirality :  0.047   0.188    753
  Planarity :  0.005   0.047    932
  Dihedral  :  7.059  45.441    772
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.02 %
    Favored  : 84.98 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 24.19 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.86 (0.30), residues: 659
  helix: -2.83 (0.82), residues: 34
  sheet: -1.74 (0.41), residues: 162
  loop : -3.08 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.034   0.002   PHE C 153 
 TYR   0.044   0.002   TYR B  93 
 ARG   0.010   0.001   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03001 (   78)
  hydrogen bonds       : angle       6.51182 (  195)
  SS BOND              : bond        0.00767 (    8)
  SS BOND              : angle       1.59602 (   16)
  covalent geometry    : bond        0.00328 ( 5235)
  covalent geometry    : angle       0.66232 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 148
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 VAL cc_start: 0.7838 (m) cc_final: 0.7535 (p)
REVERT: A  357 ARG cc_start: 0.7239 (ptp-110) cc_final: 0.6857 (ptp-110)
REVERT: A  365 TYR cc_start: 0.8423 (m-80) cc_final: 0.7831 (m-80)
REVERT: A  378 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7847 (ttmt)
REVERT: A  451 TYR cc_start: 0.7343 (m-80) cc_final: 0.7004 (m-80)
REVERT: A  453 TYR cc_start: 0.7931 (p90) cc_final: 0.7504 (p90)
REVERT: A  454 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7645 (tpp80)
REVERT: A  474 GLN cc_start: 0.7619 (tt0) cc_final: 0.7350 (tt0)
REVERT: A  493 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6831 (ttt180)
REVERT: B   25 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6910 (p)
REVERT: B   85 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4971 (pm20)
REVERT: B  102 PHE cc_start: 0.8444 (m-80) cc_final: 0.8143 (m-10)
REVERT: B  185 TYR cc_start: 0.6751 (m-80) cc_final: 0.6351 (m-80)
REVERT: B  193 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7034 (m-80)
REVERT: B  195 ILE cc_start: 0.7278 (mt) cc_final: 0.7025 (tt)
REVERT: B  227 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6376 (tp-100)
REVERT: C   17 ARG cc_start: 0.7837 (mtp-110) cc_final: 0.7628 (mtm110)
REVERT: C   33 THR cc_start: 0.7653 (p) cc_final: 0.7144 (m)
REVERT: C   68 SER cc_start: 0.8621 (t) cc_final: 0.8360 (p)
REVERT: C  170 GLU cc_start: 0.7619 (pp20) cc_final: 0.7250 (pp20)
REVERT: C  171 TRP cc_start: 0.7984 (t60) cc_final: 0.7057 (t60)
REVERT: C  173 SER cc_start: 0.7664 (t) cc_final: 0.7262 (p)
REVERT: C  236 TYR cc_start: 0.7797 (p90) cc_final: 0.7261 (p90)
  outliers start: 37
  outliers final: 23
  residues processed: 174
  average time/residue: 0.2162
  time to fit residues: 48.5657
Evaluate side-chains
  175 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0870
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0270
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 45 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.2816

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.163908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.147798 restraints weight = 8231.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.152253 restraints weight = 4120.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.155088 restraints weight = 2414.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5243  Z= 0.125
  Angle     :  0.645   6.913   7132  Z= 0.334
  Chirality :  0.046   0.180    753
  Planarity :  0.005   0.046    932
  Dihedral  :  6.864  45.775    771
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.17 %
    Favored  : 84.83 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 23.83 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.68 (0.31), residues: 659
  helix: -3.42 (0.84), residues: 28
  sheet: -1.59 (0.42), residues: 162
  loop : -2.92 (0.26), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  98 
 HIS   0.002   0.001   HIS B  41 
 PHE   0.034   0.002   PHE C 153 
 TYR   0.039   0.002   TYR B  93 
 ARG   0.005   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02805 (   78)
  hydrogen bonds       : angle       6.39425 (  195)
  SS BOND              : bond        0.00585 (    8)
  SS BOND              : angle       1.39677 (   16)
  covalent geometry    : bond        0.00287 ( 5235)
  covalent geometry    : angle       0.64209 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 VAL cc_start: 0.7809 (m) cc_final: 0.7434 (p)
REVERT: A  357 ARG cc_start: 0.7140 (ptp-110) cc_final: 0.6742 (ptp-110)
REVERT: A  378 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7742 (ttmt)
REVERT: A  453 TYR cc_start: 0.7939 (p90) cc_final: 0.7663 (p90)
REVERT: A  454 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7934 (tpp-160)
REVERT: A  474 GLN cc_start: 0.7652 (tt0) cc_final: 0.7343 (tt0)
REVERT: B   25 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6843 (p)
REVERT: B   85 GLU cc_start: 0.5439 (OUTLIER) cc_final: 0.4982 (pm20)
REVERT: B  102 PHE cc_start: 0.8394 (m-80) cc_final: 0.8097 (m-10)
REVERT: B  111 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.4009 (tm)
REVERT: B  185 TYR cc_start: 0.6624 (m-80) cc_final: 0.6383 (m-80)
REVERT: B  193 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7011 (m-80)
REVERT: B  195 ILE cc_start: 0.7181 (mt) cc_final: 0.6686 (tt)
REVERT: B  227 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6263 (tp-100)
REVERT: C   33 THR cc_start: 0.7617 (p) cc_final: 0.7395 (m)
REVERT: C   68 SER cc_start: 0.8740 (t) cc_final: 0.8490 (p)
REVERT: C  158 MET cc_start: 0.8114 (mmm) cc_final: 0.7718 (mmt)
REVERT: C  171 TRP cc_start: 0.7784 (t60) cc_final: 0.7440 (t60)
REVERT: C  173 SER cc_start: 0.7690 (t) cc_final: 0.7276 (p)
  outliers start: 39
  outliers final: 25
  residues processed: 172
  average time/residue: 0.1891
  time to fit residues: 42.4989
Evaluate side-chains
  169 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 28 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0770
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.164426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.148313 restraints weight = 8275.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.152763 restraints weight = 4095.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.155710 restraints weight = 2394.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5243  Z= 0.146
  Angle     :  0.677   7.080   7132  Z= 0.353
  Chirality :  0.047   0.167    753
  Planarity :  0.005   0.046    932
  Dihedral  :  6.942  45.329    771
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.17 %
    Favored  : 84.83 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 24.73 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.31), residues: 659
  helix: -3.29 (0.85), residues: 28
  sheet: -1.53 (0.42), residues: 164
  loop : -2.84 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.035   0.002   PHE C 153 
 TYR   0.045   0.002   TYR B  93 
 ARG   0.003   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02871 (   78)
  hydrogen bonds       : angle       6.44665 (  195)
  SS BOND              : bond        0.00753 (    8)
  SS BOND              : angle       1.49499 (   16)
  covalent geometry    : bond        0.00337 ( 5235)
  covalent geometry    : angle       0.67373 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 VAL cc_start: 0.7640 (m) cc_final: 0.7296 (p)
REVERT: A  357 ARG cc_start: 0.7154 (ptp-110) cc_final: 0.6726 (ptp-110)
REVERT: A  374 PHE cc_start: 0.7745 (m-10) cc_final: 0.7531 (m-10)
REVERT: A  378 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7862 (ttmt)
REVERT: B   25 THR cc_start: 0.7226 (OUTLIER) cc_final: 0.6913 (p)
REVERT: B   85 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.4967 (pm20)
REVERT: B  102 PHE cc_start: 0.8394 (m-80) cc_final: 0.8110 (m-10)
REVERT: B  111 LEU cc_start: 0.4458 (OUTLIER) cc_final: 0.4075 (tm)
REVERT: B  185 TYR cc_start: 0.6600 (m-80) cc_final: 0.6391 (m-80)
REVERT: B  193 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7213 (m-80)
REVERT: B  195 ILE cc_start: 0.7199 (mt) cc_final: 0.6710 (tt)
REVERT: B  227 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6307 (tp-100)
REVERT: C   33 THR cc_start: 0.7638 (p) cc_final: 0.7360 (m)
REVERT: C   68 SER cc_start: 0.8628 (t) cc_final: 0.8339 (p)
REVERT: C  158 MET cc_start: 0.8141 (mmm) cc_final: 0.7702 (mmt)
REVERT: C  171 TRP cc_start: 0.7753 (t60) cc_final: 0.7531 (t60)
REVERT: C  173 SER cc_start: 0.7695 (t) cc_final: 0.7290 (p)
  outliers start: 35
  outliers final: 24
  residues processed: 167
  average time/residue: 0.2091
  time to fit residues: 44.9421
Evaluate side-chains
  170 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 1.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 54 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0060
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.163802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.147750 restraints weight = 8206.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.152267 restraints weight = 4066.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.155130 restraints weight = 2361.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5243  Z= 0.150
  Angle     :  0.681   6.920   7132  Z= 0.356
  Chirality :  0.047   0.184    753
  Planarity :  0.005   0.046    932
  Dihedral  :  6.885  45.018    769
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.78 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 24.91 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.31), residues: 659
  helix: -3.28 (0.84), residues: 28
  sheet: -1.56 (0.42), residues: 164
  loop : -2.78 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.035   0.002   PHE C 153 
 TYR   0.044   0.002   TYR B  93 
 ARG   0.004   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02880 (   78)
  hydrogen bonds       : angle       6.39829 (  195)
  SS BOND              : bond        0.00630 (    8)
  SS BOND              : angle       1.35029 (   16)
  covalent geometry    : bond        0.00342 ( 5235)
  covalent geometry    : angle       0.67905 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7148 (ptp-110) cc_final: 0.6705 (ptp-110)
REVERT: A  378 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7828 (ttmt)
REVERT: A  438 SER cc_start: 0.8511 (p) cc_final: 0.8310 (t)
REVERT: A  452 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5932 (pp)
REVERT: A  493 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6962 (ttt180)
REVERT: B   25 THR cc_start: 0.7204 (OUTLIER) cc_final: 0.6895 (p)
REVERT: B   85 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.4969 (pm20)
REVERT: B  102 PHE cc_start: 0.8364 (m-80) cc_final: 0.8100 (m-10)
REVERT: B  111 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.4257 (tm)
REVERT: B  193 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7217 (m-80)
REVERT: B  195 ILE cc_start: 0.7203 (mt) cc_final: 0.6728 (tt)
REVERT: B  227 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6319 (tp-100)
REVERT: C   33 THR cc_start: 0.7633 (p) cc_final: 0.7110 (m)
REVERT: C   68 SER cc_start: 0.8630 (t) cc_final: 0.8350 (p)
REVERT: C  158 MET cc_start: 0.8123 (mmm) cc_final: 0.7712 (mmt)
REVERT: C  173 SER cc_start: 0.7718 (t) cc_final: 0.7308 (p)
REVERT: C  223 ASP cc_start: 0.7913 (t0) cc_final: 0.7662 (t0)
REVERT: C  236 TYR cc_start: 0.7786 (p90) cc_final: 0.7476 (p90)
  outliers start: 34
  outliers final: 27
  residues processed: 158
  average time/residue: 0.1875
  time to fit residues: 37.2652
Evaluate side-chains
  168 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  199 ASN
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0970
   chunk 51 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0970
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146607 restraints weight = 8286.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.151125 restraints weight = 4100.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.153996 restraints weight = 2384.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5243  Z= 0.155
  Angle     :  0.688   6.891   7132  Z= 0.359
  Chirality :  0.047   0.181    753
  Planarity :  0.005   0.046    932
  Dihedral  :  6.920  45.058    769
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.54 %
    Favored  : 83.46 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 24.55 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.31), residues: 659
  helix: -3.25 (0.84), residues: 28
  sheet: -1.44 (0.44), residues: 153
  loop : -2.83 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP C 171 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.036   0.002   PHE C 153 
 TYR   0.043   0.002   TYR B  93 
 ARG   0.004   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02906 (   78)
  hydrogen bonds       : angle       6.47687 (  195)
  SS BOND              : bond        0.00599 (    8)
  SS BOND              : angle       1.27857 (   16)
  covalent geometry    : bond        0.00353 ( 5235)
  covalent geometry    : angle       0.68613 ( 7116)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7217 (ptp-110) cc_final: 0.6836 (ptp-110)
REVERT: A  374 PHE cc_start: 0.7741 (m-10) cc_final: 0.7519 (m-10)
REVERT: A  378 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7918 (ttmt)
REVERT: A  452 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5916 (pp)
REVERT: B   25 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6855 (p)
REVERT: B   85 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.4951 (pm20)
REVERT: B  102 PHE cc_start: 0.8353 (m-80) cc_final: 0.8103 (m-10)
REVERT: B  111 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.4295 (tm)
REVERT: B  227 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6343 (tp-100)
REVERT: C   33 THR cc_start: 0.7669 (p) cc_final: 0.7126 (m)
REVERT: C   68 SER cc_start: 0.8581 (t) cc_final: 0.8293 (p)
REVERT: C  158 MET cc_start: 0.8148 (mmm) cc_final: 0.7702 (mmt)
REVERT: C  225 SER cc_start: 0.8559 (t) cc_final: 0.8343 (p)
REVERT: C  236 TYR cc_start: 0.7765 (p90) cc_final: 0.7380 (p90)
  outliers start: 36
  outliers final: 28
  residues processed: 164
  average time/residue: 0.1711
  time to fit residues: 35.8367
Evaluate side-chains
  170 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  175 SER
Chi-restraints excluded: chain B residue  199 ASN
Chi-restraints excluded: chain B residue  205 TYR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  227 GLN
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  247 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.160722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.144881 restraints weight = 8262.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.149314 restraints weight = 4104.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.152173 restraints weight = 2383.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5243  Z= 0.210
  Angle     :  0.745   7.664   7132  Z= 0.390
  Chirality :  0.049   0.206    753
  Planarity :  0.005   0.046    932
  Dihedral  :  7.179  46.320    769
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.21 %
    Favored  : 81.79 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 25.09 %
    Favored  : 68.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.31), residues: 659
  helix: -3.25 (0.82), residues: 28
  sheet: -1.46 (0.44), residues: 148
  loop : -2.87 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 171 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.037   0.002   PHE C 153 
 TYR   0.049   0.002   TYR B  93 
 ARG   0.005   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (   78)
  hydrogen bonds       : angle       6.64967 (  195)
  SS BOND              : bond        0.00599 (    8)
  SS BOND              : angle       1.37920 (   16)
  covalent geometry    : bond        0.00466 ( 5235)
  covalent geometry    : angle       0.74343 ( 7116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2657.73 seconds
wall clock time: 48 minutes 17.48 seconds (2897.48 seconds total)