Starting phenix.real_space_refine
on Tue Feb 11 13:19:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ej5_28176/02_2025/8ej5_28176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ej5_28176/02_2025/8ej5_28176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ej5_28176/02_2025/8ej5_28176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ej5_28176/02_2025/8ej5_28176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ej5_28176/02_2025/8ej5_28176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ej5_28176/02_2025/8ej5_28176.cif"
  }
  resolution = 4.9
  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=   0.003
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      17      5.16       5
     C    3712      2.51       5
     N     981      2.21       5
     O    1108      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5818
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3556
          Classifications: {'peptide': 457}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 435}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 754
          Classifications: {'peptide': 90}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "C"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 754
          Classifications: {'peptide': 90}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "D"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 754
          Classifications: {'peptide': 90}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
  Time building chain proxies: 3.93, per 1000 atoms: 0.68
  Number of scatterers: 5818
  At special positions: 0
  Unit cell: (74.368, 95.616, 131.472, 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      17     16.00
     O    1108      8.00
     N     981      7.00
     C    3712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.53
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1328

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      59.3% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 12
    Processing helix  chain 'A' and resid 22 through 30
      removed outlier: 4.300A  pdb=" N   GLY A  28 " --> pdb=" O   ASP A  24 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LYS A  29 " --> pdb=" O   ASP A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 39
    Processing helix  chain 'A' and resid 43 through 58
    Processing helix  chain 'A' and resid 60 through 72
    Processing helix  chain 'A' and resid 88 through 106
    Processing helix  chain 'A' and resid 123 through 137
    Processing helix  chain 'A' and resid 142 through 148
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 161 through 164
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 176 through 189
    Processing helix  chain 'A' and resid 212 through 233
      removed outlier: 4.151A  pdb=" N   TRP A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 277
      removed outlier: 3.513A  pdb=" N   LEU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 329
    Processing helix  chain 'A' and resid 336 through 340
    Processing helix  chain 'A' and resid 353 through 367
    Processing helix  chain 'A' and resid 382 through 390
      removed outlier: 3.662A  pdb=" N   VAL A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 464
      No H-bonds generated for 'chain 'A' and resid 462 through 464'
    Processing helix  chain 'B' and resid 2 through 21
      removed outlier: 3.824A  pdb=" N   GLN B  21 " --> pdb=" O   ASN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 45
    Processing helix  chain 'B' and resid 45 through 55
    Processing helix  chain 'B' and resid 61 through 68
      removed outlier: 3.529A  pdb=" N   TYR B  65 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 86
    Processing helix  chain 'C' and resid 2 through 21
      removed outlier: 3.825A  pdb=" N   GLN C  21 " --> pdb=" O   ASN C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 45
    Processing helix  chain 'C' and resid 45 through 55
    Processing helix  chain 'C' and resid 61 through 68
      removed outlier: 3.526A  pdb=" N   TYR C  65 " --> pdb=" O   SER C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 86
    Processing helix  chain 'D' and resid 2 through 21
      removed outlier: 3.806A  pdb=" N   GLN D  21 " --> pdb=" O   ASN D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 27 through 45
    Processing helix  chain 'D' and resid 45 through 55
    Processing helix  chain 'D' and resid 61 through 68
      removed outlier: 3.527A  pdb=" N   TYR D  65 " --> pdb=" O   SER D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 86
    Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 255
      removed outlier: 6.199A  pdb=" N   THR A 258 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 317
      removed outlier: 5.139A  pdb=" N   GLY A 315 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LEU A 454 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU A 434 " --> pdb=" O   VAL A 425 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 422 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.57

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1171
        1.32 -     1.45: 1552
        1.45 -     1.57: 3214
        1.57 -     1.70: 0
        1.70 -     1.82: 29
  Bond restraints: 5966
  Sorted by residual:
  bond pdb=" N   VAL A 394 "
       pdb=" CA  VAL A 394 "
    ideal  model  delta    sigma   weight residual
    1.459  1.504 -0.045 1.25e-02 6.40e+03 1.29e+01
  bond pdb=" N   VAL A 440 "
       pdb=" CA  VAL A 440 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.031 8.70e-03 1.32e+04 1.23e+01
  bond pdb=" N   VAL A 425 "
       pdb=" CA  VAL A 425 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.08e-02 8.57e+03 1.22e+01
  bond pdb=" N   VAL A 427 "
       pdb=" CA  VAL A 427 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.14e-02 7.69e+03 1.22e+01
  bond pdb=" N   GLU D  47 "
       pdb=" CA  GLU D  47 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 9.20e-03 1.18e+04 1.07e+01
  ... (remaining 5961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 6245
        1.82 -     3.65: 1697
        3.65 -     5.47: 133
        5.47 -     7.29: 23
        7.29 -     9.12: 2
  Bond angle restraints: 8100
  Sorted by residual:
  angle pdb=" CA  GLY A 314 "
        pdb=" C   GLY A 314 "
        pdb=" N   GLY A 315 "
      ideal   model   delta    sigma   weight residual
     115.11  120.97   -5.86 9.50e-01 1.11e+00 3.81e+01
  angle pdb=" N   GLY A 315 "
        pdb=" CA  GLY A 315 "
        pdb=" C   GLY A 315 "
      ideal   model   delta    sigma   weight residual
     110.56  118.63   -8.07 1.36e+00 5.41e-01 3.52e+01
  angle pdb=" N   ASN A 284 "
        pdb=" CA  ASN A 284 "
        pdb=" C   ASN A 284 "
      ideal   model   delta    sigma   weight residual
     111.54  104.26    7.28 1.36e+00 5.41e-01 2.87e+01
  angle pdb=" N   LYS A 272 "
        pdb=" CA  LYS A 272 "
        pdb=" C   LYS A 272 "
      ideal   model   delta    sigma   weight residual
     111.28  105.48    5.80 1.09e+00 8.42e-01 2.83e+01
  angle pdb=" CA  LYS A 242 "
        pdb=" C   LYS A 242 "
        pdb=" O   LYS A 242 "
      ideal   model   delta    sigma   weight residual
     120.63  114.92    5.71 1.08e+00 8.57e-01 2.80e+01
  ... (remaining 8095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 3161
       16.49 -    32.97: 214
       32.97 -    49.46: 63
       49.46 -    65.95: 11
       65.95 -    82.44: 3
  Dihedral angle restraints: 3452
    sinusoidal: 1360
      harmonic: 2092
  Sorted by residual:
  dihedral pdb=" C   ASN A 316 "
           pdb=" N   ASN A 316 "
           pdb=" CA  ASN A 316 "
           pdb=" CB  ASN A 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.15   10.55     0      2.50e+00 1.60e-01 1.78e+01
  dihedral pdb=" N   ASN A 465 "
           pdb=" CA  ASN A 465 "
           pdb=" CB  ASN A 465 "
           pdb=" CG  ASN A 465 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.56  -54.44     3      1.50e+01 4.44e-03 9.28e+00
  dihedral pdb=" CA  ILE A 275 "
           pdb=" CB  ILE A 275 "
           pdb=" CG1 ILE A 275 "
           pdb=" CD1 ILE A 275 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.13  -52.87     3      1.50e+01 4.44e-03 9.15e+00
  ... (remaining 3449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 366
       0.067 -    0.135: 376
       0.135 -    0.202: 85
       0.202 -    0.270: 6
       0.270 -    0.337: 2
  Chirality restraints: 835
  Sorted by residual:
  chirality pdb=" CA  ILE A 251 "
            pdb=" N   ILE A 251 "
            pdb=" C   ILE A 251 "
            pdb=" CB  ILE A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" CA  ILE A 238 "
            pdb=" N   ILE A 238 "
            pdb=" C   ILE A 238 "
            pdb=" CB  ILE A 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  ASN A 316 "
            pdb=" N   ASN A 316 "
            pdb=" C   ASN A 316 "
            pdb=" CB  ASN A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 832 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  84 "   -0.019 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   SER A  84 "    0.064 2.00e-02 2.50e+03
        pdb=" O   SER A  84 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PRO A  85 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  78 "    0.045 2.00e-02 2.50e+03   2.29e-02 1.05e+01
        pdb=" CG  TYR D  78 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  78 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  78 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  78 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR D  78 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  78 "    0.042 2.00e-02 2.50e+03   2.19e-02 9.62e+00
        pdb=" CG  TYR B  78 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  78 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  78 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  78 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  78 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  78 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 2740
        2.96 -     3.44: 6379
        3.44 -     3.93: 10549
        3.93 -     4.41: 11549
        4.41 -     4.90: 18520
  Nonbonded interactions: 49737
  Sorted by model distance:
  nonbonded pdb=" O   SER A  84 "
            pdb=" OE1 GLU B  58 "
     model   vdw
     2.472 3.040
  nonbonded pdb=" O   ARG A 311 "
            pdb=" N   ASP A 456 "
     model   vdw
     2.478 3.120
  nonbonded pdb=" N   PHE A 244 "
            pdb=" O   ILE A 251 "
     model   vdw
     2.487 3.120
  nonbonded pdb=" O   GLY A 281 "
            pdb=" OD1 ASP A 464 "
     model   vdw
     2.488 3.040
  nonbonded pdb=" N   THR A 318 "
            pdb=" OD1 ASN A 321 "
     model   vdw
     2.490 3.120
  ... (remaining 49732 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             1.330
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.170
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
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      :  0.012   0.047   5966  Z= 0.776
  Angle     :  1.519   9.118   8100  Z= 1.153
  Chirality :  0.090   0.337    835
  Planarity :  0.010   0.109   1071
  Dihedral  : 12.691  82.437   2124
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  1.95 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  4.91 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 717
  helix:  1.44 (0.25), residues: 397
  sheet:  0.11 (0.71), residues: 42
  loop :  0.49 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.006   TRP A  79 
 HIS   0.019   0.004   HIS C  88 
 PHE   0.024   0.004   PHE B  77 
 TYR   0.045   0.005   TYR D  78 
 ARG   0.008   0.002   ARG A 382 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 328
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7439 (ttm) cc_final: 0.6453 (ttm)
REVERT: A   33 ILE cc_start: 0.6295 (mt) cc_final: 0.6059 (mt)
REVERT: A   74 ASN cc_start: 0.6556 (t0) cc_final: 0.4873 (t0)
REVERT: A   80 LEU cc_start: 0.8388 (tp) cc_final: 0.8181 (tp)
REVERT: A  176 ASN cc_start: 0.9194 (t0) cc_final: 0.8478 (p0)
REVERT: A  179 LEU cc_start: 0.8689 (tp) cc_final: 0.7989 (tp)
REVERT: A  229 ASP cc_start: 0.8564 (m-30) cc_final: 0.8296 (m-30)
REVERT: A  234 ASP cc_start: 0.8173 (m-30) cc_final: 0.7842 (t0)
REVERT: A  241 ASP cc_start: 0.8580 (m-30) cc_final: 0.8082 (p0)
REVERT: A  322 LEU cc_start: 0.8657 (tp) cc_final: 0.8281 (tp)
REVERT: A  335 PHE cc_start: 0.7934 (t80) cc_final: 0.7420 (t80)
REVERT: A  350 ASP cc_start: 0.8412 (m-30) cc_final: 0.7843 (m-30)
REVERT: A  357 LEU cc_start: 0.9093 (tp) cc_final: 0.8798 (tp)
REVERT: A  361 TYR cc_start: 0.8506 (t80) cc_final: 0.8182 (t80)
REVERT: A  362 MET cc_start: 0.9093 (mmm) cc_final: 0.8638 (mmt)
REVERT: A  363 HIS cc_start: 0.8420 (t-170) cc_final: 0.8072 (t70)
REVERT: A  366 TRP cc_start: 0.7592 (m100) cc_final: 0.7165 (m100)
REVERT: A  412 GLN cc_start: 0.8505 (mt0) cc_final: 0.8260 (mt0)
REVERT: A  438 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6783 (m-10)
REVERT: A  439 ASN cc_start: 0.8977 (t0) cc_final: 0.8442 (t0)
REVERT: A  455 ILE cc_start: 0.8795 (mm) cc_final: 0.8249 (mp)
REVERT: A  469 PHE cc_start: 0.8974 (p90) cc_final: 0.8695 (p90)
REVERT: B   19 LEU cc_start: 0.8990 (mt) cc_final: 0.8728 (mt)
REVERT: B   89 ILE cc_start: 0.5995 (pt) cc_final: 0.5415 (pt)
REVERT: C   12 MET cc_start: 0.8845 (tpt) cc_final: 0.8053 (tpt)
REVERT: C   19 LEU cc_start: 0.9480 (mt) cc_final: 0.9270 (mt)
REVERT: C   36 VAL cc_start: 0.9385 (t) cc_final: 0.9032 (m)
REVERT: C   38 CYS cc_start: 0.9134 (m) cc_final: 0.7947 (t)
REVERT: C   42 LEU cc_start: 0.8909 (mt) cc_final: 0.6001 (mt)
REVERT: C   62 LEU cc_start: 0.9434 (tp) cc_final: 0.9090 (tp)
REVERT: C   77 PHE cc_start: 0.8051 (t80) cc_final: 0.7832 (t80)
REVERT: C   82 TYR cc_start: 0.8394 (t80) cc_final: 0.7898 (t80)
REVERT: D   15 LEU cc_start: 0.9449 (tp) cc_final: 0.9114 (tp)
REVERT: D   17 ASN cc_start: 0.8021 (m-40) cc_final: 0.7456 (m110)
REVERT: D   19 LEU cc_start: 0.9459 (mt) cc_final: 0.9172 (mt)
REVERT: D   66 LEU cc_start: 0.8729 (mt) cc_final: 0.8485 (mt)
REVERT: D   74 GLN cc_start: 0.8940 (mt0) cc_final: 0.8290 (mm-40)
  outliers start: 20
  outliers final: 5
  residues processed: 333
  average time/residue: 0.1919
  time to fit residues: 80.5910
Evaluate side-chains
  197 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 191
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    0.1980
   chunk 56 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 HIS
C  32 ASN
D  33 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.100076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.078768 restraints weight = 23716.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.081380 restraints weight = 14460.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.083173 restraints weight = 9899.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5966  Z= 0.184
  Angle     :  0.645   9.858   8100  Z= 0.342
  Chirality :  0.044   0.258    835
  Planarity :  0.006   0.143   1071
  Dihedral  :  5.728  87.919    784
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  1.81 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.32), residues: 717
  helix:  1.82 (0.26), residues: 403
  sheet:  0.43 (0.75), residues: 44
  loop :  0.30 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 156 
 HIS   0.004   0.001   HIS A 396 
 PHE   0.023   0.003   PHE D  25 
 TYR   0.019   0.002   TYR D  78 
 ARG   0.008   0.001   ARG A 382 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.9258 (t80) cc_final: 0.9011 (t80)
REVERT: A  103 GLN cc_start: 0.8443 (tp40) cc_final: 0.7892 (tp40)
REVERT: A  137 ASN cc_start: 0.7557 (t0) cc_final: 0.7145 (t0)
REVERT: A  156 TRP cc_start: 0.7252 (m-90) cc_final: 0.6847 (m-90)
REVERT: A  235 LEU cc_start: 0.7989 (mm) cc_final: 0.7690 (mm)
REVERT: A  241 ASP cc_start: 0.8390 (m-30) cc_final: 0.8106 (p0)
REVERT: A  248 MET cc_start: 0.9387 (mpp) cc_final: 0.9075 (mpp)
REVERT: A  263 MET cc_start: 0.8574 (mtp) cc_final: 0.8230 (mtp)
REVERT: A  274 LEU cc_start: 0.9237 (mt) cc_final: 0.8936 (mt)
REVERT: A  322 LEU cc_start: 0.8584 (tp) cc_final: 0.8345 (tp)
REVERT: A  387 TYR cc_start: 0.9258 (m-80) cc_final: 0.9009 (m-10)
REVERT: A  394 VAL cc_start: 0.8749 (t) cc_final: 0.8468 (t)
REVERT: A  412 GLN cc_start: 0.9264 (mt0) cc_final: 0.8901 (mt0)
REVERT: A  428 PHE cc_start: 0.8459 (m-80) cc_final: 0.7907 (m-80)
REVERT: A  439 ASN cc_start: 0.9227 (t0) cc_final: 0.8674 (t0)
REVERT: A  467 MET cc_start: 0.6694 (tpp) cc_final: 0.6442 (tpp)
REVERT: A  468 PHE cc_start: 0.8611 (m-80) cc_final: 0.7911 (m-80)
REVERT: B   19 LEU cc_start: 0.9243 (mt) cc_final: 0.8947 (mt)
REVERT: B   24 ASP cc_start: 0.8396 (t0) cc_final: 0.8156 (t0)
REVERT: B   75 TRP cc_start: 0.9125 (t-100) cc_final: 0.8567 (t-100)
REVERT: B   88 HIS cc_start: 0.4897 (m170) cc_final: 0.4396 (m-70)
REVERT: C    4 GLU cc_start: 0.8916 (mp0) cc_final: 0.8213 (tm-30)
REVERT: C    9 TYR cc_start: 0.8395 (m-10) cc_final: 0.8040 (m-10)
REVERT: C   12 MET cc_start: 0.9250 (tpt) cc_final: 0.8520 (ptt)
REVERT: C   24 ASP cc_start: 0.8451 (t0) cc_final: 0.8154 (t0)
REVERT: C   27 THR cc_start: 0.7635 (m) cc_final: 0.7308 (m)
REVERT: C   52 PHE cc_start: 0.9329 (t80) cc_final: 0.9044 (t80)
REVERT: C   55 ASP cc_start: 0.8494 (t70) cc_final: 0.7836 (t0)
REVERT: C   75 TRP cc_start: 0.8486 (t60) cc_final: 0.7949 (t60)
REVERT: C   82 TYR cc_start: 0.8835 (t80) cc_final: 0.8196 (t80)
REVERT: C   89 ILE cc_start: 0.9317 (pt) cc_final: 0.9111 (mp)
REVERT: D   15 LEU cc_start: 0.9476 (tp) cc_final: 0.9216 (tp)
REVERT: D   19 LEU cc_start: 0.9557 (mt) cc_final: 0.9222 (mt)
REVERT: D   33 ASN cc_start: 0.8772 (m110) cc_final: 0.8400 (m-40)
REVERT: D   52 PHE cc_start: 0.9413 (t80) cc_final: 0.9207 (t80)
REVERT: D   55 ASP cc_start: 0.8387 (t0) cc_final: 0.7843 (t0)
REVERT: D   59 ASP cc_start: 0.9231 (m-30) cc_final: 0.8904 (m-30)
REVERT: D   63 LEU cc_start: 0.9470 (mt) cc_final: 0.9145 (mp)
REVERT: D   74 GLN cc_start: 0.8916 (mt0) cc_final: 0.7921 (mm110)
REVERT: D   89 ILE cc_start: 0.8591 (pt) cc_final: 0.8311 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1595
  time to fit residues: 51.5912
Evaluate side-chains
  190 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0000
   chunk 22 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
D  14 GLN
D  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.094652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.073769 restraints weight = 24272.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.076242 restraints weight = 14437.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.077825 restraints weight = 9712.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.6032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5966  Z= 0.205
  Angle     :  0.624   9.652   8100  Z= 0.332
  Chirality :  0.042   0.196    835
  Planarity :  0.004   0.047   1071
  Dihedral  :  5.516  68.650    784
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.09 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.32), residues: 717
  helix:  1.38 (0.26), residues: 408
  sheet:  0.09 (0.73), residues: 50
  loop :  0.36 (0.41), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  22 
 HIS   0.005   0.002   HIS A 363 
 PHE   0.022   0.002   PHE C  25 
 TYR   0.022   0.002   TYR B   9 
 ARG   0.008   0.001   ARG A  98 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8188 (m-80) cc_final: 0.7757 (m-80)
REVERT: A   64 PHE cc_start: 0.9210 (t80) cc_final: 0.8915 (t80)
REVERT: A  103 GLN cc_start: 0.8672 (tp40) cc_final: 0.8032 (tp40)
REVERT: A  137 ASN cc_start: 0.7538 (t0) cc_final: 0.6927 (t0)
REVERT: A  138 MET cc_start: 0.7379 (mmp) cc_final: 0.6923 (mmm)
REVERT: A  156 TRP cc_start: 0.7177 (m-90) cc_final: 0.6934 (m-90)
REVERT: A  185 ILE cc_start: 0.8556 (mt) cc_final: 0.8343 (mt)
REVERT: A  229 ASP cc_start: 0.8755 (m-30) cc_final: 0.8515 (m-30)
REVERT: A  241 ASP cc_start: 0.8647 (m-30) cc_final: 0.8320 (p0)
REVERT: A  248 MET cc_start: 0.9360 (mpp) cc_final: 0.9132 (mpp)
REVERT: A  270 GLU cc_start: 0.9027 (tp30) cc_final: 0.8694 (tp30)
REVERT: A  274 LEU cc_start: 0.9578 (mt) cc_final: 0.9359 (mt)
REVERT: A  322 LEU cc_start: 0.8897 (tp) cc_final: 0.8655 (tp)
REVERT: A  330 ILE cc_start: 0.8263 (mt) cc_final: 0.8043 (mt)
REVERT: A  357 LEU cc_start: 0.9181 (tp) cc_final: 0.8887 (tp)
REVERT: A  384 TRP cc_start: 0.9412 (p-90) cc_final: 0.8900 (p-90)
REVERT: A  412 GLN cc_start: 0.9483 (mt0) cc_final: 0.9237 (mt0)
REVERT: A  433 PHE cc_start: 0.9221 (p90) cc_final: 0.8975 (p90)
REVERT: A  434 LEU cc_start: 0.9253 (mt) cc_final: 0.8998 (mt)
REVERT: A  437 ASN cc_start: 0.8571 (p0) cc_final: 0.7609 (p0)
REVERT: A  439 ASN cc_start: 0.9364 (t0) cc_final: 0.8850 (t0)
REVERT: A  469 PHE cc_start: 0.9037 (p90) cc_final: 0.8742 (p90)
REVERT: B    9 TYR cc_start: 0.7948 (m-80) cc_final: 0.7728 (m-80)
REVERT: B   12 MET cc_start: 0.8831 (tmm) cc_final: 0.8089 (mtt)
REVERT: B   19 LEU cc_start: 0.9061 (mt) cc_final: 0.8220 (mt)
REVERT: B   24 ASP cc_start: 0.7777 (t0) cc_final: 0.6067 (t0)
REVERT: C    4 GLU cc_start: 0.9134 (mp0) cc_final: 0.8335 (tm-30)
REVERT: C   16 PHE cc_start: 0.9543 (t80) cc_final: 0.9321 (t80)
REVERT: C   19 LEU cc_start: 0.9530 (mt) cc_final: 0.9196 (mt)
REVERT: C   24 ASP cc_start: 0.8915 (t0) cc_final: 0.8507 (t0)
REVERT: C   27 THR cc_start: 0.8086 (m) cc_final: 0.7410 (m)
REVERT: C   46 ASN cc_start: 0.8887 (p0) cc_final: 0.8678 (p0)
REVERT: C   55 ASP cc_start: 0.8368 (t70) cc_final: 0.7917 (t0)
REVERT: C   57 ASN cc_start: 0.8784 (t0) cc_final: 0.8549 (t0)
REVERT: C   75 TRP cc_start: 0.8713 (t60) cc_final: 0.8115 (t60)
REVERT: C   77 PHE cc_start: 0.8475 (t80) cc_final: 0.8077 (t80)
REVERT: C   82 TYR cc_start: 0.8979 (t80) cc_final: 0.8732 (t80)
REVERT: C   85 TYR cc_start: 0.9040 (m-10) cc_final: 0.8824 (m-80)
REVERT: C   89 ILE cc_start: 0.9423 (pt) cc_final: 0.9213 (mp)
REVERT: D   18 LEU cc_start: 0.9647 (mm) cc_final: 0.9378 (mm)
REVERT: D   33 ASN cc_start: 0.8790 (m110) cc_final: 0.8511 (m110)
REVERT: D   52 PHE cc_start: 0.9461 (t80) cc_final: 0.9181 (t80)
REVERT: D   55 ASP cc_start: 0.8340 (t0) cc_final: 0.7561 (t0)
REVERT: D   59 ASP cc_start: 0.9337 (m-30) cc_final: 0.9102 (m-30)
REVERT: D   60 LYS cc_start: 0.9140 (pttt) cc_final: 0.8448 (ptmm)
REVERT: D   63 LEU cc_start: 0.9668 (mt) cc_final: 0.9349 (mt)
REVERT: D   66 LEU cc_start: 0.9496 (mt) cc_final: 0.9174 (mt)
REVERT: D   70 ASP cc_start: 0.8069 (t70) cc_final: 0.7258 (t0)
REVERT: D   74 GLN cc_start: 0.8986 (mt0) cc_final: 0.8103 (mm-40)
REVERT: D   79 LYS cc_start: 0.9081 (ptpt) cc_final: 0.8777 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1576
  time to fit residues: 48.8629
Evaluate side-chains
  177 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 236 HIS
A 461 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  14 GLN
B  20 GLN
C  21 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.093106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.072888 restraints weight = 25085.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.075307 restraints weight = 14962.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.076969 restraints weight = 10041.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.6881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5966  Z= 0.199
  Angle     :  0.605   9.173   8100  Z= 0.316
  Chirality :  0.041   0.193    835
  Planarity :  0.003   0.034   1071
  Dihedral  :  6.275  89.622    784
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  2.51 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.32), residues: 717
  helix:  1.37 (0.26), residues: 407
  sheet:  0.10 (0.71), residues: 50
  loop :  0.28 (0.41), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  75 
 HIS   0.006   0.001   HIS A 363 
 PHE   0.022   0.002   PHE C  52 
 TYR   0.013   0.001   TYR C  45 
 ARG   0.003   0.001   ARG A  98 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8413 (m-80) cc_final: 0.7926 (m-80)
REVERT: A   64 PHE cc_start: 0.9215 (t80) cc_final: 0.8953 (t80)
REVERT: A  103 GLN cc_start: 0.8482 (tp40) cc_final: 0.7888 (tp40)
REVERT: A  137 ASN cc_start: 0.7446 (t0) cc_final: 0.6836 (t0)
REVERT: A  138 MET cc_start: 0.7423 (mmp) cc_final: 0.6935 (mmm)
REVERT: A  241 ASP cc_start: 0.8494 (m-30) cc_final: 0.8232 (p0)
REVERT: A  244 PHE cc_start: 0.8613 (m-10) cc_final: 0.8387 (m-10)
REVERT: A  248 MET cc_start: 0.9253 (mpp) cc_final: 0.8934 (mpp)
REVERT: A  270 GLU cc_start: 0.8930 (tp30) cc_final: 0.8518 (tp30)
REVERT: A  273 ASP cc_start: 0.8829 (m-30) cc_final: 0.8350 (m-30)
REVERT: A  322 LEU cc_start: 0.8910 (tp) cc_final: 0.8683 (tp)
REVERT: A  350 ASP cc_start: 0.8553 (m-30) cc_final: 0.8133 (m-30)
REVERT: A  357 LEU cc_start: 0.9222 (tp) cc_final: 0.8927 (tp)
REVERT: A  412 GLN cc_start: 0.9527 (mt0) cc_final: 0.9209 (mt0)
REVERT: A  433 PHE cc_start: 0.9139 (p90) cc_final: 0.8928 (p90)
REVERT: A  437 ASN cc_start: 0.8444 (p0) cc_final: 0.7123 (p0)
REVERT: A  439 ASN cc_start: 0.9433 (t0) cc_final: 0.8890 (t0)
REVERT: A  451 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: A  467 MET cc_start: 0.8576 (ttm) cc_final: 0.8097 (ttm)
REVERT: B   19 LEU cc_start: 0.9086 (mt) cc_final: 0.8661 (mt)
REVERT: B   24 ASP cc_start: 0.7633 (t0) cc_final: 0.4913 (t0)
REVERT: B   89 ILE cc_start: 0.7500 (pt) cc_final: 0.7287 (pt)
REVERT: C    4 GLU cc_start: 0.9115 (mp0) cc_final: 0.8372 (tm-30)
REVERT: C   16 PHE cc_start: 0.9449 (t80) cc_final: 0.9186 (t80)
REVERT: C   20 GLN cc_start: 0.9295 (mt0) cc_final: 0.8931 (mt0)
REVERT: C   24 ASP cc_start: 0.8857 (t0) cc_final: 0.8467 (t0)
REVERT: C   27 THR cc_start: 0.8158 (m) cc_final: 0.6329 (m)
REVERT: C   30 ASN cc_start: 0.9220 (m-40) cc_final: 0.8898 (m-40)
REVERT: C   41 LEU cc_start: 0.9609 (mt) cc_final: 0.9372 (mt)
REVERT: C   42 LEU cc_start: 0.8908 (mt) cc_final: 0.8683 (mt)
REVERT: C   46 ASN cc_start: 0.8926 (p0) cc_final: 0.8662 (p0)
REVERT: C   55 ASP cc_start: 0.8540 (t70) cc_final: 0.8130 (t0)
REVERT: C   75 TRP cc_start: 0.8978 (t60) cc_final: 0.8396 (t-100)
REVERT: C   79 LYS cc_start: 0.9311 (pttp) cc_final: 0.8993 (pttm)
REVERT: C   82 TYR cc_start: 0.9130 (t80) cc_final: 0.8895 (t80)
REVERT: C   89 ILE cc_start: 0.9510 (pt) cc_final: 0.9306 (mp)
REVERT: D   18 LEU cc_start: 0.9673 (mm) cc_final: 0.9388 (mm)
REVERT: D   19 LEU cc_start: 0.9553 (mt) cc_final: 0.9286 (mt)
REVERT: D   33 ASN cc_start: 0.8810 (m110) cc_final: 0.8568 (m110)
REVERT: D   52 PHE cc_start: 0.9383 (t80) cc_final: 0.9065 (t80)
REVERT: D   55 ASP cc_start: 0.8215 (t0) cc_final: 0.6836 (t0)
REVERT: D   60 LYS cc_start: 0.9106 (pttt) cc_final: 0.7975 (pttt)
REVERT: D   63 LEU cc_start: 0.9724 (mt) cc_final: 0.9492 (mt)
REVERT: D   66 LEU cc_start: 0.9371 (mt) cc_final: 0.9143 (mt)
REVERT: D   74 GLN cc_start: 0.8962 (mt0) cc_final: 0.7918 (mm-40)
REVERT: D   89 ILE cc_start: 0.9374 (pt) cc_final: 0.9147 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1683
  time to fit residues: 50.1046
Evaluate side-chains
  182 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5742

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

Flipped N/Q/H residues before XYZ refinement:
** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 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 = 0.3510 r_free = 0.3510 target = 0.092706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.073826 restraints weight = 25195.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.076026 restraints weight = 15446.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.077547 restraints weight = 10493.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.7472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5966  Z= 0.184
  Angle     :  0.602   8.639   8100  Z= 0.314
  Chirality :  0.041   0.188    835
  Planarity :  0.003   0.034   1071
  Dihedral  :  6.179  88.021    784
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  2.51 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.31), residues: 717
  helix:  1.29 (0.26), residues: 407
  sheet:  0.11 (0.71), residues: 50
  loop :  0.07 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 156 
 HIS   0.005   0.001   HIS A 363 
 PHE   0.019   0.002   PHE D  16 
 TYR   0.012   0.001   TYR C  78 
 ARG   0.012   0.001   ARG A 277 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7208 (m-40) cc_final: 0.7003 (t0)
REVERT: A   19 PHE cc_start: 0.8437 (m-80) cc_final: 0.8050 (m-10)
REVERT: A   64 PHE cc_start: 0.9215 (t80) cc_final: 0.8972 (t80)
REVERT: A  103 GLN cc_start: 0.8501 (tp40) cc_final: 0.7884 (tm-30)
REVERT: A  137 ASN cc_start: 0.7380 (t0) cc_final: 0.6752 (t0)
REVERT: A  138 MET cc_start: 0.7376 (mmp) cc_final: 0.6910 (mmm)
REVERT: A  241 ASP cc_start: 0.8561 (m-30) cc_final: 0.8114 (p0)
REVERT: A  244 PHE cc_start: 0.8605 (m-10) cc_final: 0.8332 (m-10)
REVERT: A  248 MET cc_start: 0.9281 (mpp) cc_final: 0.9053 (mpp)
REVERT: A  270 GLU cc_start: 0.8898 (tp30) cc_final: 0.8658 (tp30)
REVERT: A  274 LEU cc_start: 0.9452 (mt) cc_final: 0.9235 (mt)
REVERT: A  322 LEU cc_start: 0.8942 (tp) cc_final: 0.8698 (tp)
REVERT: A  357 LEU cc_start: 0.9271 (tp) cc_final: 0.8901 (tp)
REVERT: A  412 GLN cc_start: 0.9495 (mt0) cc_final: 0.9140 (mt0)
REVERT: A  433 PHE cc_start: 0.9047 (p90) cc_final: 0.8818 (p90)
REVERT: A  437 ASN cc_start: 0.8480 (p0) cc_final: 0.7203 (p0)
REVERT: A  439 ASN cc_start: 0.9409 (t0) cc_final: 0.8851 (t0)
REVERT: A  451 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: A  467 MET cc_start: 0.8560 (ttm) cc_final: 0.8100 (ttm)
REVERT: B   12 MET cc_start: 0.8892 (tmm) cc_final: 0.8234 (mtt)
REVERT: B   19 LEU cc_start: 0.9076 (mt) cc_final: 0.8766 (mt)
REVERT: B   20 GLN cc_start: 0.8399 (tp40) cc_final: 0.7456 (tp-100)
REVERT: B   24 ASP cc_start: 0.7575 (t0) cc_final: 0.6175 (t0)
REVERT: B   89 ILE cc_start: 0.7564 (pt) cc_final: 0.7224 (pt)
REVERT: C    4 GLU cc_start: 0.9172 (mp0) cc_final: 0.8404 (tm-30)
REVERT: C   20 GLN cc_start: 0.9239 (mt0) cc_final: 0.8970 (mt0)
REVERT: C   27 THR cc_start: 0.8013 (m) cc_final: 0.6383 (m)
REVERT: C   30 ASN cc_start: 0.9295 (m-40) cc_final: 0.8938 (m-40)
REVERT: C   55 ASP cc_start: 0.8580 (t70) cc_final: 0.8131 (t0)
REVERT: C   75 TRP cc_start: 0.8904 (t60) cc_final: 0.8559 (t-100)
REVERT: C   78 TYR cc_start: 0.8829 (t80) cc_final: 0.8537 (t80)
REVERT: C   79 LYS cc_start: 0.9295 (pttp) cc_final: 0.9013 (pttm)
REVERT: D   16 PHE cc_start: 0.9446 (t80) cc_final: 0.9179 (t80)
REVERT: D   17 ASN cc_start: 0.9328 (t0) cc_final: 0.9111 (m110)
REVERT: D   19 LEU cc_start: 0.9604 (mt) cc_final: 0.9298 (mt)
REVERT: D   52 PHE cc_start: 0.9372 (t80) cc_final: 0.9095 (t80)
REVERT: D   55 ASP cc_start: 0.8277 (t0) cc_final: 0.7032 (t0)
REVERT: D   60 LYS cc_start: 0.9104 (pttt) cc_final: 0.8211 (pttt)
REVERT: D   66 LEU cc_start: 0.9536 (mt) cc_final: 0.9186 (mt)
REVERT: D   74 GLN cc_start: 0.9070 (mt0) cc_final: 0.8142 (mm110)
REVERT: D   81 PHE cc_start: 0.8127 (t80) cc_final: 0.7700 (t80)
REVERT: D   89 ILE cc_start: 0.9419 (pt) cc_final: 0.9117 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1673
  time to fit residues: 48.2400
Evaluate side-chains
  181 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 46 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0020
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    2.9996

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
D  40 GLN
D  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.088104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.068928 restraints weight = 25428.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.071089 restraints weight = 15186.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072589 restraints weight = 10292.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.8276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5966  Z= 0.255
  Angle     :  0.690   9.294   8100  Z= 0.360
  Chirality :  0.043   0.186    835
  Planarity :  0.004   0.035   1071
  Dihedral  :  6.359  88.341    784
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.49 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.69 (0.31), residues: 717
  helix:  0.94 (0.26), residues: 408
  sheet:  0.10 (0.72), residues: 50
  loop : -0.07 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 156 
 HIS   0.004   0.001   HIS D  88 
 PHE   0.022   0.002   PHE A 468 
 TYR   0.019   0.002   TYR A 387 
 ARG   0.005   0.001   ARG A 277 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8354 (m-80) cc_final: 0.8108 (m-80)
REVERT: A   77 TRP cc_start: 0.8495 (m-90) cc_final: 0.8281 (m-90)
REVERT: A  137 ASN cc_start: 0.7485 (t0) cc_final: 0.6686 (t0)
REVERT: A  138 MET cc_start: 0.7560 (mmp) cc_final: 0.7102 (mmm)
REVERT: A  241 ASP cc_start: 0.8743 (m-30) cc_final: 0.8427 (p0)
REVERT: A  242 LYS cc_start: 0.9168 (mmpt) cc_final: 0.8746 (mmmt)
REVERT: A  244 PHE cc_start: 0.8446 (m-10) cc_final: 0.8169 (m-10)
REVERT: A  248 MET cc_start: 0.9300 (mpp) cc_final: 0.9094 (mpp)
REVERT: A  270 GLU cc_start: 0.8974 (tp30) cc_final: 0.8723 (tp30)
REVERT: A  322 LEU cc_start: 0.8832 (tp) cc_final: 0.8557 (tp)
REVERT: A  357 LEU cc_start: 0.9391 (tp) cc_final: 0.8979 (tp)
REVERT: A  412 GLN cc_start: 0.9490 (mt0) cc_final: 0.9152 (mt0)
REVERT: A  437 ASN cc_start: 0.8572 (p0) cc_final: 0.7484 (p0)
REVERT: A  439 ASN cc_start: 0.9428 (t0) cc_final: 0.8876 (t0)
REVERT: A  467 MET cc_start: 0.8569 (ttm) cc_final: 0.7998 (ttm)
REVERT: B   12 MET cc_start: 0.8821 (tmm) cc_final: 0.8291 (mtt)
REVERT: B   16 PHE cc_start: 0.9219 (t80) cc_final: 0.8914 (t80)
REVERT: B   20 GLN cc_start: 0.7711 (tp-100) cc_final: 0.6917 (tp-100)
REVERT: B   24 ASP cc_start: 0.7612 (t0) cc_final: 0.6997 (t0)
REVERT: B   34 LEU cc_start: 0.8892 (tp) cc_final: 0.8621 (tp)
REVERT: C    4 GLU cc_start: 0.8996 (mp0) cc_final: 0.8437 (tm-30)
REVERT: C    9 TYR cc_start: 0.8669 (m-10) cc_final: 0.8036 (m-10)
REVERT: C   41 LEU cc_start: 0.9631 (mt) cc_final: 0.9424 (mt)
REVERT: C   57 ASN cc_start: 0.8996 (t0) cc_final: 0.8757 (t0)
REVERT: C   78 TYR cc_start: 0.8877 (t80) cc_final: 0.8572 (t80)
REVERT: D   16 PHE cc_start: 0.9436 (t80) cc_final: 0.9100 (t80)
REVERT: D   17 ASN cc_start: 0.9287 (t0) cc_final: 0.9064 (m110)
REVERT: D   19 LEU cc_start: 0.9541 (mt) cc_final: 0.9186 (mt)
REVERT: D   29 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9105 (mp0)
REVERT: D   39 GLN cc_start: 0.9332 (tp40) cc_final: 0.8859 (tm-30)
REVERT: D   42 LEU cc_start: 0.9198 (mt) cc_final: 0.8975 (mt)
REVERT: D   52 PHE cc_start: 0.9473 (t80) cc_final: 0.9202 (t80)
REVERT: D   55 ASP cc_start: 0.7989 (t0) cc_final: 0.6679 (t0)
REVERT: D   60 LYS cc_start: 0.9239 (pttt) cc_final: 0.8190 (pttt)
REVERT: D   63 LEU cc_start: 0.9732 (mt) cc_final: 0.9326 (mt)
REVERT: D   74 GLN cc_start: 0.9021 (mt0) cc_final: 0.8186 (mm110)
REVERT: D   88 HIS cc_start: 0.8949 (m-70) cc_final: 0.8294 (m90)
REVERT: D   89 ILE cc_start: 0.9513 (pt) cc_final: 0.9094 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1696
  time to fit residues: 46.9257
Evaluate side-chains
  166 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 63 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
B  20 GLN
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 ASN
C  46 ASN
C  64 GLN
** C  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.089512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.070181 restraints weight = 25501.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.072392 restraints weight = 15081.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.073896 restraints weight = 10059.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.8607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5966  Z= 0.193
  Angle     :  0.641  10.642   8100  Z= 0.336
  Chirality :  0.043   0.191    835
  Planarity :  0.004   0.079   1071
  Dihedral  :  6.231  86.530    784
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.21 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.57 (0.31), residues: 717
  helix:  0.92 (0.26), residues: 401
  sheet: -0.10 (0.70), residues: 52
  loop : -0.20 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 156 
 HIS   0.003   0.001   HIS B  88 
 PHE   0.027   0.002   PHE C  52 
 TYR   0.027   0.002   TYR D   9 
 ARG   0.005   0.001   ARG A  98 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8474 (m-80) cc_final: 0.8266 (m-80)
REVERT: A   64 PHE cc_start: 0.9257 (t80) cc_final: 0.9032 (t80)
REVERT: A   77 TRP cc_start: 0.8472 (m-90) cc_final: 0.8264 (m-90)
REVERT: A  137 ASN cc_start: 0.7420 (t0) cc_final: 0.6666 (t0)
REVERT: A  138 MET cc_start: 0.7610 (mmp) cc_final: 0.7088 (mmm)
REVERT: A  241 ASP cc_start: 0.8803 (m-30) cc_final: 0.8400 (p0)
REVERT: A  242 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8546 (mmmt)
REVERT: A  244 PHE cc_start: 0.8452 (m-10) cc_final: 0.8120 (m-80)
REVERT: A  248 MET cc_start: 0.9255 (mpp) cc_final: 0.9025 (mpp)
REVERT: A  257 ASN cc_start: 0.8643 (t0) cc_final: 0.8380 (t0)
REVERT: A  270 GLU cc_start: 0.8940 (tp30) cc_final: 0.8702 (tp30)
REVERT: A  274 LEU cc_start: 0.9554 (mt) cc_final: 0.9327 (mt)
REVERT: A  277 ARG cc_start: 0.7381 (mpp-170) cc_final: 0.6785 (mpp80)
REVERT: A  322 LEU cc_start: 0.8847 (tp) cc_final: 0.8597 (tp)
REVERT: A  325 LYS cc_start: 0.9396 (ptmm) cc_final: 0.9162 (ptmm)
REVERT: A  357 LEU cc_start: 0.9412 (tp) cc_final: 0.9023 (tp)
REVERT: A  412 GLN cc_start: 0.9462 (mt0) cc_final: 0.9154 (mt0)
REVERT: A  437 ASN cc_start: 0.8643 (p0) cc_final: 0.7565 (p0)
REVERT: A  467 MET cc_start: 0.8566 (ttm) cc_final: 0.8124 (ttm)
REVERT: B   12 MET cc_start: 0.8876 (tmm) cc_final: 0.8394 (mtt)
REVERT: B   16 PHE cc_start: 0.9357 (t80) cc_final: 0.8984 (t80)
REVERT: B   19 LEU cc_start: 0.9242 (mt) cc_final: 0.8968 (mt)
REVERT: B   20 GLN cc_start: 0.7790 (tp40) cc_final: 0.7353 (tp-100)
REVERT: B   24 ASP cc_start: 0.7536 (t0) cc_final: 0.6989 (t0)
REVERT: B   34 LEU cc_start: 0.8881 (tp) cc_final: 0.8535 (tp)
REVERT: B   89 ILE cc_start: 0.7431 (pt) cc_final: 0.6957 (pt)
REVERT: C    4 GLU cc_start: 0.8965 (mp0) cc_final: 0.8399 (tm-30)
REVERT: C    9 TYR cc_start: 0.8745 (m-10) cc_final: 0.8168 (m-10)
REVERT: C   30 ASN cc_start: 0.9361 (m-40) cc_final: 0.9045 (m-40)
REVERT: C   41 LEU cc_start: 0.9607 (mt) cc_final: 0.9402 (mt)
REVERT: C   57 ASN cc_start: 0.9015 (t0) cc_final: 0.8781 (t0)
REVERT: C   75 TRP cc_start: 0.8987 (t60) cc_final: 0.8608 (t-100)
REVERT: C   79 LYS cc_start: 0.9294 (pttp) cc_final: 0.8996 (pttm)
REVERT: C   82 TYR cc_start: 0.9222 (t80) cc_final: 0.8582 (t80)
REVERT: C   90 PHE cc_start: 0.7983 (m-10) cc_final: 0.7611 (m-10)
REVERT: D   16 PHE cc_start: 0.9439 (t80) cc_final: 0.9172 (t80)
REVERT: D   19 LEU cc_start: 0.9582 (mt) cc_final: 0.9261 (mt)
REVERT: D   29 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9103 (mp0)
REVERT: D   39 GLN cc_start: 0.9354 (tp40) cc_final: 0.8803 (tm-30)
REVERT: D   60 LYS cc_start: 0.9260 (pttt) cc_final: 0.8922 (pttt)
REVERT: D   74 GLN cc_start: 0.9032 (mt0) cc_final: 0.8204 (mm110)
REVERT: D   82 TYR cc_start: 0.8642 (t80) cc_final: 0.8343 (t80)
REVERT: D   88 HIS cc_start: 0.9129 (m-70) cc_final: 0.8394 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1832
  time to fit residues: 51.0800
Evaluate side-chains
  166 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   chunk 56 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  21 GLN
C  33 ASN
** C  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.090153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.071086 restraints weight = 24934.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.073339 restraints weight = 14619.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.074859 restraints weight = 9696.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.8887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5966  Z= 0.189
  Angle     :  0.664  10.912   8100  Z= 0.348
  Chirality :  0.044   0.199    835
  Planarity :  0.004   0.040   1071
  Dihedral  :  6.195  84.479    784
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.35 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.43 (0.31), residues: 717
  helix:  0.79 (0.26), residues: 401
  sheet: -0.00 (0.72), residues: 52
  loop : -0.27 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C  22 
 HIS   0.003   0.001   HIS B  88 
 PHE   0.023   0.002   PHE C  52 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.013   0.001   ARG A  98 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ASN cc_start: 0.7465 (t0) cc_final: 0.6626 (t0)
REVERT: A  138 MET cc_start: 0.7747 (mmp) cc_final: 0.7201 (mmm)
REVERT: A  241 ASP cc_start: 0.8777 (m-30) cc_final: 0.8406 (p0)
REVERT: A  242 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8521 (mmmt)
REVERT: A  244 PHE cc_start: 0.8411 (m-10) cc_final: 0.8038 (m-80)
REVERT: A  248 MET cc_start: 0.9251 (mpp) cc_final: 0.9030 (mpp)
REVERT: A  257 ASN cc_start: 0.8611 (t0) cc_final: 0.8351 (t0)
REVERT: A  270 GLU cc_start: 0.8901 (tp30) cc_final: 0.8681 (tp30)
REVERT: A  271 MET cc_start: 0.9160 (mmp) cc_final: 0.8894 (mmm)
REVERT: A  277 ARG cc_start: 0.7578 (mpp-170) cc_final: 0.6881 (mpp80)
REVERT: A  322 LEU cc_start: 0.8818 (tp) cc_final: 0.8599 (tp)
REVERT: A  357 LEU cc_start: 0.9458 (tp) cc_final: 0.9073 (tp)
REVERT: A  412 GLN cc_start: 0.9442 (mt0) cc_final: 0.9085 (mt0)
REVERT: A  437 ASN cc_start: 0.8640 (p0) cc_final: 0.7545 (p0)
REVERT: A  467 MET cc_start: 0.8620 (ttm) cc_final: 0.8154 (ttm)
REVERT: B   16 PHE cc_start: 0.9301 (t80) cc_final: 0.8924 (t80)
REVERT: B   19 LEU cc_start: 0.9178 (mt) cc_final: 0.8932 (mt)
REVERT: B   24 ASP cc_start: 0.7595 (t0) cc_final: 0.7246 (t0)
REVERT: B   34 LEU cc_start: 0.8903 (tp) cc_final: 0.8547 (tp)
REVERT: B   89 ILE cc_start: 0.7335 (pt) cc_final: 0.6793 (pt)
REVERT: C    4 GLU cc_start: 0.8942 (mp0) cc_final: 0.8419 (tm-30)
REVERT: C   30 ASN cc_start: 0.9398 (m-40) cc_final: 0.9150 (m-40)
REVERT: C   41 LEU cc_start: 0.9578 (mt) cc_final: 0.9375 (mt)
REVERT: C   57 ASN cc_start: 0.9006 (t0) cc_final: 0.8766 (t0)
REVERT: C   75 TRP cc_start: 0.9048 (t60) cc_final: 0.8819 (t-100)
REVERT: C   78 TYR cc_start: 0.8677 (t80) cc_final: 0.8444 (t80)
REVERT: C   79 LYS cc_start: 0.9286 (pttp) cc_final: 0.8951 (pttm)
REVERT: C   82 TYR cc_start: 0.9240 (t80) cc_final: 0.8681 (t80)
REVERT: D   16 PHE cc_start: 0.9344 (t80) cc_final: 0.9135 (t80)
REVERT: D   17 ASN cc_start: 0.8956 (m110) cc_final: 0.8504 (m110)
REVERT: D   19 LEU cc_start: 0.9548 (mt) cc_final: 0.9022 (mt)
REVERT: D   29 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9150 (mp0)
REVERT: D   55 ASP cc_start: 0.7939 (t0) cc_final: 0.6717 (t0)
REVERT: D   60 LYS cc_start: 0.9235 (pttt) cc_final: 0.8063 (pttt)
REVERT: D   74 GLN cc_start: 0.9081 (mt0) cc_final: 0.8672 (mp10)
REVERT: D   82 TYR cc_start: 0.8658 (t80) cc_final: 0.8248 (t80)
REVERT: D   88 HIS cc_start: 0.9206 (m-70) cc_final: 0.8417 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1637
  time to fit residues: 43.1706
Evaluate side-chains
  165 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:   20.0000
   chunk 60 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  40 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 = 0.3411 r_free = 0.3411 target = 0.087255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.068140 restraints weight = 26746.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.070344 restraints weight = 15529.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.071832 restraints weight = 10299.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.9465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5966  Z= 0.242
  Angle     :  0.692  11.497   8100  Z= 0.364
  Chirality :  0.044   0.215    835
  Planarity :  0.004   0.040   1071
  Dihedral  :  6.319  86.790    784
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.63 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.01 (0.31), residues: 717
  helix:  0.47 (0.25), residues: 407
  sheet: -0.16 (0.72), residues: 52
  loop : -0.54 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  22 
 HIS   0.004   0.001   HIS B  88 
 PHE   0.023   0.002   PHE C  52 
 TYR   0.021   0.002   TYR A 387 
 ARG   0.009   0.001   ARG A  98 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8504 (m-80) cc_final: 0.8190 (m-10)
REVERT: A  103 GLN cc_start: 0.8709 (mp10) cc_final: 0.8453 (mp10)
REVERT: A  137 ASN cc_start: 0.7348 (t0) cc_final: 0.6707 (t0)
REVERT: A  138 MET cc_start: 0.8029 (mmp) cc_final: 0.7483 (mmm)
REVERT: A  241 ASP cc_start: 0.8750 (m-30) cc_final: 0.8356 (p0)
REVERT: A  242 LYS cc_start: 0.9046 (mmpt) cc_final: 0.8544 (mmmt)
REVERT: A  244 PHE cc_start: 0.8432 (m-10) cc_final: 0.8093 (m-80)
REVERT: A  248 MET cc_start: 0.9238 (mpp) cc_final: 0.9019 (mpp)
REVERT: A  257 ASN cc_start: 0.8627 (t0) cc_final: 0.8393 (t0)
REVERT: A  277 ARG cc_start: 0.7739 (mpp-170) cc_final: 0.7071 (mpp80)
REVERT: A  322 LEU cc_start: 0.8823 (tp) cc_final: 0.8593 (tp)
REVERT: A  357 LEU cc_start: 0.9519 (tp) cc_final: 0.9101 (tp)
REVERT: A  362 MET cc_start: 0.9486 (mmm) cc_final: 0.9276 (mmt)
REVERT: A  412 GLN cc_start: 0.9387 (mt0) cc_final: 0.9014 (mt0)
REVERT: A  437 ASN cc_start: 0.8529 (p0) cc_final: 0.7329 (p0)
REVERT: B   12 MET cc_start: 0.8986 (tmm) cc_final: 0.8515 (mtt)
REVERT: B   19 LEU cc_start: 0.9241 (mt) cc_final: 0.8893 (mt)
REVERT: B   20 GLN cc_start: 0.8401 (tp40) cc_final: 0.7960 (tp-100)
REVERT: B   59 ASP cc_start: 0.8783 (m-30) cc_final: 0.8189 (t70)
REVERT: B   89 ILE cc_start: 0.7553 (pt) cc_final: 0.7159 (pt)
REVERT: C    2 THR cc_start: 0.8579 (m) cc_final: 0.8263 (m)
REVERT: C   20 GLN cc_start: 0.9244 (mt0) cc_final: 0.8930 (mt0)
REVERT: C   30 ASN cc_start: 0.9427 (m-40) cc_final: 0.9219 (m110)
REVERT: C   41 LEU cc_start: 0.9598 (mt) cc_final: 0.9393 (mt)
REVERT: C   57 ASN cc_start: 0.9114 (t0) cc_final: 0.8882 (t0)
REVERT: C   78 TYR cc_start: 0.8812 (t80) cc_final: 0.8495 (t80)
REVERT: D    9 TYR cc_start: 0.9038 (m-10) cc_final: 0.8676 (m-80)
REVERT: D   17 ASN cc_start: 0.9019 (m110) cc_final: 0.8599 (m110)
REVERT: D   19 LEU cc_start: 0.9531 (mt) cc_final: 0.9074 (mt)
REVERT: D   22 TRP cc_start: 0.8832 (m-10) cc_final: 0.8585 (m-10)
REVERT: D   55 ASP cc_start: 0.7905 (t0) cc_final: 0.6816 (t0)
REVERT: D   60 LYS cc_start: 0.9312 (pttt) cc_final: 0.8037 (pttt)
REVERT: D   82 TYR cc_start: 0.8646 (t80) cc_final: 0.8071 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1735
  time to fit residues: 47.7458
Evaluate side-chains
  165 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0000
   chunk 58 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 412 GLN
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.090125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.071205 restraints weight = 26363.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.073451 restraints weight = 15456.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.074977 restraints weight = 10205.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.9688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   5966  Z= 0.199
  Angle     :  0.712  11.202   8100  Z= 0.377
  Chirality :  0.046   0.217    835
  Planarity :  0.004   0.039   1071
  Dihedral  :  6.114  89.198    784
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.91 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.07 (0.30), residues: 717
  helix:  0.35 (0.25), residues: 407
  sheet:  0.17 (0.71), residues: 48
  loop : -0.53 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP A 156 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.020   0.002   PHE C  52 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.011   0.001   ARG A  98 

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

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

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1434 Ramachandran restraints generated.
    717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 TRP cc_start: 0.8397 (m100) cc_final: 0.8167 (m100)
REVERT: A  103 GLN cc_start: 0.8693 (mp10) cc_final: 0.8449 (mp10)
REVERT: A  137 ASN cc_start: 0.7358 (t0) cc_final: 0.6672 (t0)
REVERT: A  138 MET cc_start: 0.7975 (mmp) cc_final: 0.7584 (mmm)
REVERT: A  238 ILE cc_start: 0.9098 (mm) cc_final: 0.8861 (mm)
REVERT: A  241 ASP cc_start: 0.8732 (m-30) cc_final: 0.8339 (p0)
REVERT: A  242 LYS cc_start: 0.9087 (mmpt) cc_final: 0.8463 (mmmt)
REVERT: A  244 PHE cc_start: 0.8485 (m-10) cc_final: 0.8135 (m-80)
REVERT: A  248 MET cc_start: 0.9234 (mpp) cc_final: 0.9015 (mpp)
REVERT: A  257 ASN cc_start: 0.8491 (t0) cc_final: 0.8269 (t0)
REVERT: A  270 GLU cc_start: 0.8883 (tp30) cc_final: 0.8634 (tp30)
REVERT: A  274 LEU cc_start: 0.9554 (mt) cc_final: 0.9343 (mt)
REVERT: A  322 LEU cc_start: 0.8825 (tp) cc_final: 0.8591 (tp)
REVERT: A  357 LEU cc_start: 0.9508 (tp) cc_final: 0.9193 (tp)
REVERT: A  412 GLN cc_start: 0.9323 (mt0) cc_final: 0.9025 (mt0)
REVERT: A  437 ASN cc_start: 0.8705 (p0) cc_final: 0.7637 (p0)
REVERT: A  440 VAL cc_start: 0.9097 (m) cc_final: 0.8387 (m)
REVERT: B   12 MET cc_start: 0.9027 (tmm) cc_final: 0.8576 (mtt)
REVERT: B   13 LEU cc_start: 0.9378 (tp) cc_final: 0.9012 (tp)
REVERT: B   59 ASP cc_start: 0.8695 (m-30) cc_final: 0.8262 (t0)
REVERT: C   47 GLU cc_start: 0.9171 (pm20) cc_final: 0.8969 (pm20)
REVERT: C   51 LYS cc_start: 0.9671 (mtmm) cc_final: 0.9359 (ptpt)
REVERT: C   57 ASN cc_start: 0.9041 (t0) cc_final: 0.8795 (t0)
REVERT: C   78 TYR cc_start: 0.8780 (t80) cc_final: 0.8315 (t80)
REVERT: C   82 TYR cc_start: 0.9339 (t80) cc_final: 0.8903 (t80)
REVERT: D   17 ASN cc_start: 0.8963 (m110) cc_final: 0.8507 (m110)
REVERT: D   19 LEU cc_start: 0.9553 (mt) cc_final: 0.9194 (mt)
REVERT: D   22 TRP cc_start: 0.8841 (m-10) cc_final: 0.8624 (m-10)
REVERT: D   55 ASP cc_start: 0.8068 (t0) cc_final: 0.7575 (t0)
REVERT: D   60 LYS cc_start: 0.9295 (pttt) cc_final: 0.9014 (pttt)
REVERT: D   78 TYR cc_start: 0.8297 (t80) cc_final: 0.8009 (t80)
REVERT: D   82 TYR cc_start: 0.8896 (t80) cc_final: 0.8414 (t80)
REVERT: D   88 HIS cc_start: 0.9155 (m-70) cc_final: 0.8823 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1709
  time to fit residues: 48.3758
Evaluate side-chains
  174 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 32 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  20 GLN
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  33 ASN
** D  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.072554 restraints weight = 25781.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.074788 restraints weight = 15456.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.076312 restraints weight = 10332.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.9876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   5966  Z= 0.199
  Angle     :  0.725  10.464   8100  Z= 0.378
  Chirality :  0.046   0.211    835
  Planarity :  0.004   0.055   1071
  Dihedral  :  5.878  86.813    784
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.49 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.13 (0.31), residues: 717
  helix:  0.28 (0.25), residues: 407
  sheet: -0.14 (0.68), residues: 52
  loop : -0.46 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP A 156 
 HIS   0.003   0.001   HIS D  88 
 PHE   0.023   0.002   PHE A  19 
 TYR   0.022   0.001   TYR C  78 
 ARG   0.014   0.001   ARG A  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2055.45 seconds
wall clock time: 37 minutes 48.69 seconds (2268.69 seconds total)