Starting phenix.real_space_refine
on Thu Mar  6 05:46:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wop_32654/03_2025/7wop_32654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wop_32654/03_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_32654/03_2025/7wop_32654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_2025/7wop_32654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_2025/7wop_32654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_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-5624/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: 6.33, per 1000 atoms: 1.24
  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: 2.07
  Conformation dependent library (CDL) restraints added in 954.3 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: 0.76
  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: 2.08

  Time building geometry restraints manager: 2.16 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:             139.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     22.020
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.080
  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:5.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  167.870
-------------------------------------------------------------------------------
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   5235  Z= 0.133
  Angle     :  0.536   5.738   7116  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 

*********************** 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  : 0.483 
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: 0.1970
  time to fit residues: 50.1172
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  : 0.872 
-------------------------------------------------------------------------------
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   5235  Z= 0.186
  Angle     :  0.622   7.161   7116  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 

*********************** 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  : 0.765 
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: 0.2380
  time to fit residues: 52.0899
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  : 1.177 
-------------------------------------------------------------------------------
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:    0.0670
   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:    0.5920

-------------------------------------------------------------------------------
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 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 ASN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 GLN
B 207 GLN
B 209 ASN
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.162574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.146890 restraints weight = 8322.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.151316 restraints weight = 4106.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.154059 restraints weight = 2384.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5235  Z= 0.267
  Angle     :  0.659   6.834   7116  Z= 0.345
  Chirality :  0.047   0.186    753
  Planarity :  0.005   0.045    932
  Dihedral  :  7.001  46.213    775
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.72 %
    Favored  : 85.28 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 20.40 %
    Favored  : 73.10 %
  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: -4.11 (0.29), residues: 659
  helix: -3.45 (0.66), residues: 34
  sheet: -1.85 (0.39), residues: 165
  loop : -3.25 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 171 
 HIS   0.006   0.001   HIS B  41 
 PHE   0.030   0.002   PHE C 153 
 TYR   0.020   0.002   TYR C 236 
 ARG   0.005   0.001   ARG A 454 

*********************** 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
  196 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 160
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5940 (t80)
REVERT: A  375 PHE cc_start: 0.7715 (m-10) cc_final: 0.7424 (m-10)
REVERT: A  399 SER cc_start: 0.8137 (m) cc_final: 0.7566 (t)
REVERT: A  453 TYR cc_start: 0.7914 (p90) cc_final: 0.7245 (p90)
REVERT: A  458 LYS cc_start: 0.8090 (tppt) cc_final: 0.7775 (tppt)
REVERT: A  474 GLN cc_start: 0.7848 (tt0) cc_final: 0.7495 (tt0)
REVERT: A  493 ARG cc_start: 0.7200 (ttt180) cc_final: 0.6855 (ttt180)
REVERT: B   60 VAL cc_start: 0.6800 (OUTLIER) cc_final: 0.6573 (m)
REVERT: B   85 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.5015 (pm20)
REVERT: B  163 VAL cc_start: 0.8561 (m) cc_final: 0.8245 (p)
REVERT: B  193 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.6851 (m-80)
REVERT: B  195 ILE cc_start: 0.7248 (mt) cc_final: 0.6624 (tt)
REVERT: B  227 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6840 (tp-100)
REVERT: B  231 TYR cc_start: 0.6492 (t80) cc_final: 0.6179 (t80)
REVERT: C   29 ILE cc_start: 0.8746 (mt) cc_final: 0.8459 (tt)
REVERT: C   33 THR cc_start: 0.7729 (p) cc_final: 0.7477 (m)
REVERT: C   68 SER cc_start: 0.8718 (t) cc_final: 0.8467 (p)
REVERT: C  158 MET cc_start: 0.8270 (mmm) cc_final: 0.7869 (mmt)
REVERT: C  170 GLU cc_start: 0.7564 (pp20) cc_final: 0.6786 (pp20)
REVERT: C  171 TRP cc_start: 0.7287 (t60) cc_final: 0.6787 (t60)
REVERT: C  173 SER cc_start: 0.7726 (t) cc_final: 0.7407 (p)
REVERT: C  236 TYR cc_start: 0.8084 (p90) cc_final: 0.7692 (p90)
  outliers start: 36
  outliers final: 25
  residues processed: 185
  average time/residue: 0.2028
  time to fit residues: 48.7817
Evaluate side-chains
  186 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
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  388 ASN
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   60 VAL
Chi-restraints excluded: chain B residue   68 LYS
Chi-restraints excluded: chain B residue   85 GLU
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  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:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0040
   chunk 3 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 57 optimal weight:    0.4980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 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 = 0.4044 r_free = 0.4044 target = 0.163699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.147632 restraints weight = 8532.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152165 restraints weight = 4186.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.155033 restraints weight = 2417.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   5235  Z= 0.250
  Angle     :  0.656   7.387   7116  Z= 0.342
  Chirality :  0.047   0.226    753
  Planarity :  0.005   0.045    932
  Dihedral  :  6.966  45.955    774
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.17 %
    Favored  : 84.83 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 21.48 %
    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: -3.97 (0.30), residues: 659
  helix: -3.10 (0.75), residues: 34
  sheet: -1.74 (0.40), residues: 163
  loop : -3.18 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.031   0.002   PHE C 153 
 TYR   0.020   0.002   TYR C 236 
 ARG   0.005   0.000   ARG A 454 

*********************** 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
  188 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.6988 (ptp-110)
REVERT: A  365 TYR cc_start: 0.8451 (m-80) cc_final: 0.7768 (m-80)
REVERT: A  378 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7773 (ttmt)
REVERT: A  399 SER cc_start: 0.8135 (m) cc_final: 0.7540 (p)
REVERT: A  453 TYR cc_start: 0.7919 (p90) cc_final: 0.7304 (p90)
REVERT: A  454 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7924 (tpp80)
REVERT: A  458 LYS cc_start: 0.8015 (tppt) cc_final: 0.7590 (mmmt)
REVERT: A  493 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6883 (ttt180)
REVERT: B   60 VAL cc_start: 0.6481 (OUTLIER) cc_final: 0.6224 (m)
REVERT: B  102 PHE cc_start: 0.8656 (m-80) cc_final: 0.8344 (m-10)
REVERT: B  185 TYR cc_start: 0.7083 (m-80) cc_final: 0.6611 (m-80)
REVERT: B  193 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6953 (m-80)
REVERT: B  195 ILE cc_start: 0.7252 (mt) cc_final: 0.6898 (tt)
REVERT: B  227 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6755 (tp-100)
REVERT: B  230 TYR cc_start: 0.7383 (t80) cc_final: 0.7141 (t80)
REVERT: B  231 TYR cc_start: 0.6744 (t80) cc_final: 0.6397 (t80)
REVERT: C   29 ILE cc_start: 0.8730 (mt) cc_final: 0.8401 (tt)
REVERT: C   33 THR cc_start: 0.7627 (p) cc_final: 0.7271 (m)
REVERT: C   68 SER cc_start: 0.8723 (t) cc_final: 0.8500 (p)
REVERT: C  158 MET cc_start: 0.8225 (mmm) cc_final: 0.7732 (mmt)
REVERT: C  170 GLU cc_start: 0.7658 (pp20) cc_final: 0.6834 (pp20)
REVERT: C  171 TRP cc_start: 0.7438 (t60) cc_final: 0.6804 (t60)
REVERT: C  173 SER cc_start: 0.7740 (t) cc_final: 0.7426 (p)
REVERT: C  236 TYR cc_start: 0.8068 (p90) cc_final: 0.7462 (p90)
  outliers start: 37
  outliers final: 24
  residues processed: 181
  average time/residue: 0.2034
  time to fit residues: 47.4895
Evaluate side-chains
  179 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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  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   54 SER
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  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  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:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0020
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.4788

-------------------------------------------------------------------------------
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**
A 477 ASN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.162861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146939 restraints weight = 8410.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.151377 restraints weight = 4185.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.154230 restraints weight = 2431.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5235  Z= 0.234
  Angle     :  0.651   6.415   7116  Z= 0.340
  Chirality :  0.047   0.203    753
  Planarity :  0.005   0.045    932
  Dihedral  :  7.065  45.573    774
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.48 %
    Favored  : 84.52 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 20.76 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.30), residues: 659
  helix: -2.88 (0.79), residues: 34
  sheet: -1.87 (0.39), residues: 176
  loop : -2.97 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.032   0.002   PHE C 153 
 TYR   0.030   0.002   TYR B  93 
 ARG   0.003   0.000   ARG A 403 

*********************** 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
  191 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 149
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7240 (ptp-110) cc_final: 0.6899 (ptp-110)
REVERT: A  378 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7850 (ttmt)
REVERT: A  453 TYR cc_start: 0.7943 (p90) cc_final: 0.7393 (p90)
REVERT: B   85 GLU cc_start: 0.5522 (OUTLIER) cc_final: 0.5031 (pm20)
REVERT: B  102 PHE cc_start: 0.8519 (m-80) cc_final: 0.8195 (m-10)
REVERT: B  185 TYR cc_start: 0.6852 (m-80) cc_final: 0.6446 (m-80)
REVERT: B  193 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7015 (m-80)
REVERT: B  195 ILE cc_start: 0.7232 (mt) cc_final: 0.6901 (tt)
REVERT: B  227 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6593 (tp-100)
REVERT: B  230 TYR cc_start: 0.7398 (t80) cc_final: 0.7160 (t80)
REVERT: B  231 TYR cc_start: 0.6902 (t80) cc_final: 0.6487 (t80)
REVERT: C   29 ILE cc_start: 0.8683 (mt) cc_final: 0.8443 (tt)
REVERT: C   33 THR cc_start: 0.7670 (p) cc_final: 0.7261 (m)
REVERT: C   68 SER cc_start: 0.8580 (t) cc_final: 0.8336 (p)
REVERT: C  158 MET cc_start: 0.8185 (mmm) cc_final: 0.7592 (mmt)
REVERT: C  170 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7218 (pp20)
REVERT: C  171 TRP cc_start: 0.7504 (t60) cc_final: 0.7214 (t60)
REVERT: C  184 TYR cc_start: 0.8048 (m-10) cc_final: 0.7728 (m-10)
REVERT: C  236 TYR cc_start: 0.8036 (p90) cc_final: 0.7420 (p90)
  outliers start: 42
  outliers final: 29
  residues processed: 179
  average time/residue: 0.2337
  time to fit residues: 54.4760
Evaluate side-chains
  178 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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  371 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
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   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  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    5 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  170 GLU
Chi-restraints excluded: chain C residue  174 VAL
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:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 4 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN
C  32 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.161514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.145215 restraints weight = 8417.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.149741 restraints weight = 4182.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.152720 restraints weight = 2426.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5235  Z= 0.255
  Angle     :  0.681   7.456   7116  Z= 0.357
  Chirality :  0.047   0.198    753
  Planarity :  0.005   0.046    932
  Dihedral  :  7.039  45.564    773
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.54 %
    Favored  : 83.46 %
  Rotamer:
    Outliers :  7.94 %
    Allowed  : 21.84 %
    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: -3.78 (0.30), residues: 659
  helix: -2.76 (0.82), residues: 34
  sheet: -1.57 (0.40), residues: 170
  loop : -3.09 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.033   0.002   PHE C 153 
 TYR   0.046   0.002   TYR B  93 
 ARG   0.012   0.001   ARG A 346 

*********************** 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
  186 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7238 (ptp-110) cc_final: 0.6849 (ptp-110)
REVERT: A  365 TYR cc_start: 0.8438 (m-80) cc_final: 0.7507 (m-80)
REVERT: A  378 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7870 (ttmt)
REVERT: A  388 ASN cc_start: 0.8256 (m-40) cc_final: 0.7816 (m110)
REVERT: A  453 TYR cc_start: 0.7949 (p90) cc_final: 0.7378 (p90)
REVERT: A  474 GLN cc_start: 0.7692 (tt0) cc_final: 0.6615 (tt0)
REVERT: B   25 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6921 (p)
REVERT: B   85 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5024 (pm20)
REVERT: B  102 PHE cc_start: 0.8500 (m-80) cc_final: 0.8211 (m-10)
REVERT: B  185 TYR cc_start: 0.6808 (m-80) cc_final: 0.6432 (m-80)
REVERT: B  193 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7002 (m-80)
REVERT: B  195 ILE cc_start: 0.7249 (mt) cc_final: 0.6898 (tt)
REVERT: B  227 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6405 (tp-100)
REVERT: B  230 TYR cc_start: 0.7413 (t80) cc_final: 0.7162 (t80)
REVERT: C   33 THR cc_start: 0.7682 (p) cc_final: 0.7228 (m)
REVERT: C   68 SER cc_start: 0.8612 (t) cc_final: 0.8357 (p)
REVERT: C  170 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7157 (pp20)
REVERT: C  184 TYR cc_start: 0.8120 (m-10) cc_final: 0.7795 (m-10)
REVERT: C  192 PHE cc_start: 0.7405 (m-80) cc_final: 0.6909 (m-80)
REVERT: C  236 TYR cc_start: 0.7875 (p90) cc_final: 0.7442 (p90)
  outliers start: 44
  outliers final: 31
  residues processed: 172
  average time/residue: 0.1741
  time to fit residues: 38.0410
Evaluate side-chains
  180 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 143
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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  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   54 SER
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  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 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   71 SER
Chi-restraints excluded: chain C residue  170 GLU
Chi-restraints excluded: chain C residue  182 THR
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:    0.3980
   chunk 43 optimal weight:    0.2980
   chunk 21 optimal weight:    0.1980
   chunk 16 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.3378

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.163963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.147958 restraints weight = 8209.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.152396 restraints weight = 4085.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.155215 restraints weight = 2382.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5235  Z= 0.200
  Angle     :  0.653   6.383   7116  Z= 0.342
  Chirality :  0.046   0.153    753
  Planarity :  0.005   0.046    932
  Dihedral  :  6.944  45.701    773
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.57 %
    Favored  : 85.43 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 24.19 %
    Favored  : 68.77 %
  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: -3.61 (0.31), residues: 659
  helix: -2.58 (0.83), residues: 34
  sheet: -1.51 (0.40), residues: 182
  loop : -2.97 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  98 
 HIS   0.002   0.001   HIS B  41 
 PHE   0.035   0.002   PHE C 153 
 TYR   0.046   0.002   TYR B  93 
 ARG   0.006   0.000   ARG A 346 

*********************** 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
  173 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7236 (ptp-110) cc_final: 0.6795 (ptp-110)
REVERT: A  378 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7776 (ttmt)
REVERT: A  453 TYR cc_start: 0.7859 (p90) cc_final: 0.7408 (p90)
REVERT: B   25 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6916 (p)
REVERT: B   85 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.5067 (pm20)
REVERT: B  102 PHE cc_start: 0.8430 (m-80) cc_final: 0.8126 (m-10)
REVERT: B  111 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.4123 (tm)
REVERT: B  185 TYR cc_start: 0.6636 (m-80) cc_final: 0.6399 (m-80)
REVERT: B  193 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6746 (m-80)
REVERT: B  195 ILE cc_start: 0.7269 (mt) cc_final: 0.6884 (tt)
REVERT: B  227 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6310 (tp-100)
REVERT: C   33 THR cc_start: 0.7641 (p) cc_final: 0.7177 (m)
REVERT: C   68 SER cc_start: 0.8589 (t) cc_final: 0.8338 (p)
REVERT: C  158 MET cc_start: 0.8109 (mmm) cc_final: 0.7686 (mmt)
REVERT: C  170 GLU cc_start: 0.7670 (pp20) cc_final: 0.7164 (pp20)
REVERT: C  171 TRP cc_start: 0.7392 (t60) cc_final: 0.7146 (t60)
REVERT: C  184 TYR cc_start: 0.8146 (m-10) cc_final: 0.7888 (m-80)
REVERT: C  192 PHE cc_start: 0.7491 (m-80) cc_final: 0.6727 (m-80)
REVERT: C  207 MET cc_start: 0.6491 (mtm) cc_final: 0.6059 (mtm)
REVERT: C  236 TYR cc_start: 0.7805 (p90) cc_final: 0.7360 (p90)
  outliers start: 39
  outliers final: 25
  residues processed: 162
  average time/residue: 0.2709
  time to fit residues: 57.1246
Evaluate side-chains
  164 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  395 VAL
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 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  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 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   71 SER
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:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0000
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4462

-------------------------------------------------------------------------------
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 = 0.4038 r_free = 0.4038 target = 0.162385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146353 restraints weight = 8293.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.150718 restraints weight = 4178.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.153600 restraints weight = 2459.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6660
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5235  Z= 0.231
  Angle     :  0.679   7.445   7116  Z= 0.354
  Chirality :  0.047   0.195    753
  Planarity :  0.005   0.046    932
  Dihedral  :  7.024  45.147    772
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.48 %
    Favored  : 84.52 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 25.27 %
    Favored  : 68.77 %
  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: -3.51 (0.31), residues: 659
  helix: -2.44 (0.84), residues: 34
  sheet: -1.30 (0.42), residues: 169
  loop : -2.95 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  98 
 HIS   0.002   0.001   HIS B  41 
 PHE   0.035   0.002   PHE C 153 
 TYR   0.045   0.002   TYR B  93 
 ARG   0.005   0.000   ARG A 454 

*********************** 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
  176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7208 (ptp-110) cc_final: 0.6777 (ptp-110)
REVERT: A  369 TYR cc_start: 0.7257 (m-80) cc_final: 0.7049 (m-80)
REVERT: A  378 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7904 (ttmt)
REVERT: A  453 TYR cc_start: 0.7922 (p90) cc_final: 0.7434 (p90)
REVERT: B   25 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6866 (p)
REVERT: B   85 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.5095 (pm20)
REVERT: B  102 PHE cc_start: 0.8412 (m-80) cc_final: 0.8135 (m-10)
REVERT: B  111 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.4191 (tm)
REVERT: B  193 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7324 (m-80)
REVERT: B  195 ILE cc_start: 0.7237 (mt) cc_final: 0.6810 (tt)
REVERT: B  227 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6338 (tp-100)
REVERT: C   33 THR cc_start: 0.7627 (p) cc_final: 0.7241 (m)
REVERT: C   68 SER cc_start: 0.8648 (t) cc_final: 0.8364 (p)
REVERT: C  158 MET cc_start: 0.8131 (mmm) cc_final: 0.7683 (mmt)
REVERT: C  170 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7402 (pp20)
REVERT: C  184 TYR cc_start: 0.8174 (m-10) cc_final: 0.7890 (m-80)
REVERT: C  192 PHE cc_start: 0.7602 (m-80) cc_final: 0.7005 (m-80)
REVERT: C  236 TYR cc_start: 0.7816 (p90) cc_final: 0.7324 (p90)
  outliers start: 33
  outliers final: 24
  residues processed: 166
  average time/residue: 0.1707
  time to fit residues: 36.1139
Evaluate side-chains
  173 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
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  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 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   71 SER
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  170 GLU
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:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0770
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4023 r_free = 0.4023 target = 0.161538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.145638 restraints weight = 8244.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.149977 restraints weight = 4157.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.152838 restraints weight = 2447.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5235  Z= 0.270
  Angle     :  0.713   7.643   7116  Z= 0.374
  Chirality :  0.048   0.184    753
  Planarity :  0.005   0.046    932
  Dihedral  :  7.089  45.057    770
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.08 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 25.27 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.31), residues: 659
  helix: -3.29 (0.78), residues: 28
  sheet: -1.48 (0.40), residues: 175
  loop : -2.86 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  98 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.036   0.002   PHE C 153 
 TYR   0.046   0.002   TYR B  93 
 ARG   0.005   0.001   ARG A 454 

*********************** 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
  175 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.7143 (ptp-110) cc_final: 0.6717 (ptp-110)
REVERT: A  378 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7887 (ttmt)
REVERT: A  453 TYR cc_start: 0.7968 (p90) cc_final: 0.7538 (p90)
REVERT: B   25 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6878 (p)
REVERT: B   85 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.5094 (pm20)
REVERT: B  102 PHE cc_start: 0.8413 (m-80) cc_final: 0.8164 (m-10)
REVERT: B  111 LEU cc_start: 0.4542 (OUTLIER) cc_final: 0.4335 (tm)
REVERT: B  185 TYR cc_start: 0.7073 (m-80) cc_final: 0.6629 (m-80)
REVERT: B  227 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6434 (tp-100)
REVERT: C   33 THR cc_start: 0.7628 (p) cc_final: 0.7206 (m)
REVERT: C   68 SER cc_start: 0.8698 (t) cc_final: 0.8431 (p)
REVERT: C  158 MET cc_start: 0.8165 (mmm) cc_final: 0.7626 (mmt)
REVERT: C  170 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7325 (pp20)
REVERT: C  171 TRP cc_start: 0.8071 (t60) cc_final: 0.7681 (t60)
REVERT: C  184 TYR cc_start: 0.8280 (m-10) cc_final: 0.7941 (m-80)
REVERT: C  192 PHE cc_start: 0.7629 (m-80) cc_final: 0.7019 (m-80)
REVERT: C  236 TYR cc_start: 0.7795 (p90) cc_final: 0.7415 (p90)
  outliers start: 34
  outliers final: 25
  residues processed: 162
  average time/residue: 0.1950
  time to fit residues: 39.9017
Evaluate side-chains
  170 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
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   88 TYR
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  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   71 SER
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  170 GLU
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:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0970
   chunk 64 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:    0.3980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4029 r_free = 0.4029 target = 0.161792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.145746 restraints weight = 8286.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150150 restraints weight = 4172.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.153042 restraints weight = 2452.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5235  Z= 0.263
  Angle     :  0.719   8.116   7116  Z= 0.378
  Chirality :  0.048   0.190    753
  Planarity :  0.005   0.046    932
  Dihedral  :  7.065  45.098    770
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.08 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 25.99 %
    Favored  : 68.05 %
  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: -3.48 (0.31), residues: 659
  helix: -3.19 (0.79), residues: 28
  sheet: -1.45 (0.42), residues: 163
  loop : -2.78 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  98 
 HIS   0.002   0.001   HIS B  41 
 PHE   0.036   0.002   PHE C 153 
 TYR   0.046   0.002   TYR B  93 
 ARG   0.007   0.001   ARG C  17 

********************** 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
  174 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6851 (tmt90)
REVERT: A  357 ARG cc_start: 0.7172 (ptp-110) cc_final: 0.6777 (ptp-110)
REVERT: A  378 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7938 (ttmt)
REVERT: A  453 TYR cc_start: 0.7950 (p90) cc_final: 0.7467 (p90)
REVERT: B   25 THR cc_start: 0.7179 (OUTLIER) cc_final: 0.6853 (p)
REVERT: B   85 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.5087 (pm20)
REVERT: B  102 PHE cc_start: 0.8388 (m-80) cc_final: 0.8129 (m-10)
REVERT: B  185 TYR cc_start: 0.7214 (m-80) cc_final: 0.6769 (m-80)
REVERT: B  195 ILE cc_start: 0.7557 (tp) cc_final: 0.7237 (tt)
REVERT: B  227 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6477 (tp-100)
REVERT: C   33 THR cc_start: 0.7624 (p) cc_final: 0.7177 (m)
REVERT: C   68 SER cc_start: 0.8693 (t) cc_final: 0.8433 (p)
REVERT: C  158 MET cc_start: 0.8148 (mmm) cc_final: 0.7613 (mmt)
REVERT: C  170 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7337 (pp20)
REVERT: C  171 TRP cc_start: 0.7928 (t60) cc_final: 0.7658 (t60)
REVERT: C  184 TYR cc_start: 0.8262 (m-10) cc_final: 0.7934 (m-80)
REVERT: C  192 PHE cc_start: 0.7632 (m-80) cc_final: 0.7032 (m-80)
REVERT: C  225 SER cc_start: 0.8536 (t) cc_final: 0.8146 (p)
REVERT: C  236 TYR cc_start: 0.7817 (p90) cc_final: 0.7402 (p90)
  outliers start: 33
  outliers final: 26
  residues processed: 164
  average time/residue: 0.2333
  time to fit residues: 49.5032
Evaluate side-chains
  172 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ARG
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   88 TYR
Chi-restraints excluded: chain B residue   90 CYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  109 THR
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  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   34 VAL
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  170 GLU
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:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 12 optimal weight:    0.3980
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0970
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.162445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.146578 restraints weight = 8389.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.151011 restraints weight = 4160.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.153831 restraints weight = 2420.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.4614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5235  Z= 0.222
  Angle     :  0.706   8.156   7116  Z= 0.365
  Chirality :  0.047   0.177    753
  Planarity :  0.005   0.046    932
  Dihedral  :  6.814  45.195    768
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.17 %
    Favored  : 84.83 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 26.71 %
    Favored  : 67.51 %
  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: -3.37 (0.31), residues: 659
  helix: -3.00 (0.83), residues: 28
  sheet: -1.42 (0.43), residues: 163
  loop : -2.69 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C  98 
 HIS   0.002   0.001   HIS B  41 
 PHE   0.036   0.002   PHE C 153 
 TYR   0.042   0.002   TYR B  93 
 ARG   0.007   0.000   ARG C  17 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2902.49 seconds
wall clock time: 53 minutes 59.61 seconds (3239.61 seconds total)