Starting phenix.real_space_refine
on Thu Jul 24 08:49:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ej5_28176/07_2025/8ej5_28176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ej5_28176/07_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_28176/07_2025/8ej5_28176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ej5_28176/07_2025/8ej5_28176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ej5_28176/07_2025/8ej5_28176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ej5_28176/07_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-5711/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: 4.23, per 1000 atoms: 0.73
  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: 1.56
  Conformation dependent library (CDL) restraints added in 869.8 milliseconds
  

  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: 0.60
  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: 1.44

  Time building geometry restraints manager: 1.83 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:             25.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.720
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.760
-------------------------------------------------------------------------------
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= 0.905
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16173 (  309)
  hydrogen bonds       : angle       7.63068 (  906)
  covalent geometry    : bond        0.01199 ( 5966)
  covalent geometry    : angle       1.51889 ( 8100)

*********************** 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  : 0.628 
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: 0.1997
  time to fit residues: 83.3639
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  : 0.735 
-------------------------------------------------------------------------------
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 = 0.100094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.078757 restraints weight = 23679.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.081382 restraints weight = 14486.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.083155 restraints weight = 9879.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
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= 0.143
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  309)
  hydrogen bonds       : angle       5.61274 (  906)
  covalent geometry    : bond        0.00295 ( 5966)
  covalent geometry    : angle       0.64509 ( 8100)

*********************** 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  : 0.696 
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: 0.9261 (t80) cc_final: 0.9017 (t80)
REVERT: A  103 GLN cc_start: 0.8444 (tp40) cc_final: 0.7891 (tp40)
REVERT: A  137 ASN cc_start: 0.7553 (t0) cc_final: 0.7142 (t0)
REVERT: A  156 TRP cc_start: 0.7249 (m-90) cc_final: 0.6844 (m-90)
REVERT: A  235 LEU cc_start: 0.7980 (mm) cc_final: 0.7672 (mm)
REVERT: A  241 ASP cc_start: 0.8382 (m-30) cc_final: 0.8100 (p0)
REVERT: A  248 MET cc_start: 0.9379 (mpp) cc_final: 0.9072 (mpp)
REVERT: A  263 MET cc_start: 0.8581 (mtp) cc_final: 0.8232 (mtp)
REVERT: A  274 LEU cc_start: 0.9236 (mt) cc_final: 0.8935 (mt)
REVERT: A  322 LEU cc_start: 0.8584 (tp) cc_final: 0.8344 (tp)
REVERT: A  387 TYR cc_start: 0.9264 (m-80) cc_final: 0.9015 (m-10)
REVERT: A  394 VAL cc_start: 0.8744 (t) cc_final: 0.8459 (t)
REVERT: A  412 GLN cc_start: 0.9265 (mt0) cc_final: 0.8901 (mt0)
REVERT: A  428 PHE cc_start: 0.8456 (m-80) cc_final: 0.7891 (m-80)
REVERT: A  439 ASN cc_start: 0.9225 (t0) cc_final: 0.8684 (t0)
REVERT: A  467 MET cc_start: 0.6690 (tpp) cc_final: 0.6438 (tpp)
REVERT: A  468 PHE cc_start: 0.8621 (m-80) cc_final: 0.7914 (m-80)
REVERT: B   19 LEU cc_start: 0.9247 (mt) cc_final: 0.8952 (mt)
REVERT: B   24 ASP cc_start: 0.8394 (t0) cc_final: 0.8148 (t0)
REVERT: B   75 TRP cc_start: 0.9129 (t-100) cc_final: 0.8565 (t-100)
REVERT: B   88 HIS cc_start: 0.4915 (m170) cc_final: 0.4411 (m-70)
REVERT: C    4 GLU cc_start: 0.8924 (mp0) cc_final: 0.8216 (tm-30)
REVERT: C    9 TYR cc_start: 0.8401 (m-10) cc_final: 0.8048 (m-10)
REVERT: C   12 MET cc_start: 0.9252 (tpt) cc_final: 0.8521 (ptt)
REVERT: C   24 ASP cc_start: 0.8464 (t0) cc_final: 0.8159 (t0)
REVERT: C   27 THR cc_start: 0.7622 (m) cc_final: 0.7293 (m)
REVERT: C   52 PHE cc_start: 0.9332 (t80) cc_final: 0.9050 (t80)
REVERT: C   55 ASP cc_start: 0.8495 (t70) cc_final: 0.7836 (t0)
REVERT: C   75 TRP cc_start: 0.8495 (t60) cc_final: 0.7955 (t60)
REVERT: C   82 TYR cc_start: 0.8836 (t80) cc_final: 0.8198 (t80)
REVERT: C   89 ILE cc_start: 0.9323 (pt) cc_final: 0.9117 (mp)
REVERT: D   15 LEU cc_start: 0.9478 (tp) cc_final: 0.9221 (tp)
REVERT: D   19 LEU cc_start: 0.9563 (mt) cc_final: 0.9230 (mt)
REVERT: D   33 ASN cc_start: 0.8768 (m110) cc_final: 0.8398 (m-40)
REVERT: D   52 PHE cc_start: 0.9414 (t80) cc_final: 0.9206 (t80)
REVERT: D   55 ASP cc_start: 0.8395 (t0) cc_final: 0.7849 (t0)
REVERT: D   59 ASP cc_start: 0.9227 (m-30) cc_final: 0.8902 (m-30)
REVERT: D   63 LEU cc_start: 0.9468 (mt) cc_final: 0.9142 (mp)
REVERT: D   74 GLN cc_start: 0.8908 (mt0) cc_final: 0.7915 (mm110)
REVERT: D   89 ILE cc_start: 0.8596 (pt) cc_final: 0.8312 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1837
  time to fit residues: 59.7059
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  : 0.740 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
D  54 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.073989 restraints weight = 24487.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.076385 restraints weight = 14822.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.078024 restraints weight = 10010.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.5929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5966  Z= 0.163
  Angle     :  0.625   9.700   8100  Z= 0.332
  Chirality :  0.042   0.195    835
  Planarity :  0.004   0.058   1071
  Dihedral  :  5.480  68.405    784
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.95 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  1.38 (0.32), residues: 717
  helix:  1.44 (0.26), residues: 408
  sheet:  0.75 (0.74), residues: 44
  loop :  0.28 (0.41), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  22 
 HIS   0.005   0.002   HIS A 363 
 PHE   0.023   0.002   PHE C  25 
 TYR   0.018   0.002   TYR B   9 
 ARG   0.008   0.001   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04004 (  309)
  hydrogen bonds       : angle       5.27239 (  906)
  covalent geometry    : bond        0.00345 ( 5966)
  covalent geometry    : angle       0.62535 ( 8100)

*********************** 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
  229 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.097 
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   19 PHE cc_start: 0.8220 (m-80) cc_final: 0.7798 (m-80)
REVERT: A   64 PHE cc_start: 0.9192 (t80) cc_final: 0.8914 (t80)
REVERT: A  103 GLN cc_start: 0.8663 (tp40) cc_final: 0.8026 (tp40)
REVERT: A  137 ASN cc_start: 0.7531 (t0) cc_final: 0.6954 (t0)
REVERT: A  138 MET cc_start: 0.7377 (mmp) cc_final: 0.6953 (mmm)
REVERT: A  156 TRP cc_start: 0.7231 (m-90) cc_final: 0.6993 (m-90)
REVERT: A  185 ILE cc_start: 0.8645 (mt) cc_final: 0.8443 (mt)
REVERT: A  241 ASP cc_start: 0.8565 (m-30) cc_final: 0.8225 (p0)
REVERT: A  248 MET cc_start: 0.9369 (mpp) cc_final: 0.9134 (mpp)
REVERT: A  270 GLU cc_start: 0.9047 (tp30) cc_final: 0.8670 (tp30)
REVERT: A  274 LEU cc_start: 0.9559 (mt) cc_final: 0.9356 (mt)
REVERT: A  322 LEU cc_start: 0.8888 (tp) cc_final: 0.8650 (tp)
REVERT: A  330 ILE cc_start: 0.8216 (mt) cc_final: 0.7993 (mt)
REVERT: A  357 LEU cc_start: 0.9139 (tp) cc_final: 0.8842 (tp)
REVERT: A  384 TRP cc_start: 0.9409 (p-90) cc_final: 0.8834 (p-90)
REVERT: A  412 GLN cc_start: 0.9448 (mt0) cc_final: 0.9112 (mt0)
REVERT: A  428 PHE cc_start: 0.8197 (m-80) cc_final: 0.7977 (m-80)
REVERT: A  433 PHE cc_start: 0.9250 (p90) cc_final: 0.9028 (p90)
REVERT: A  434 LEU cc_start: 0.9290 (mt) cc_final: 0.8965 (mt)
REVERT: A  437 ASN cc_start: 0.8542 (p0) cc_final: 0.7416 (p0)
REVERT: A  439 ASN cc_start: 0.9376 (t0) cc_final: 0.8837 (t0)
REVERT: B   12 MET cc_start: 0.8804 (tmm) cc_final: 0.8054 (mtt)
REVERT: B   19 LEU cc_start: 0.9049 (mt) cc_final: 0.8211 (mt)
REVERT: B   24 ASP cc_start: 0.7782 (t0) cc_final: 0.6096 (t0)
REVERT: C    4 GLU cc_start: 0.9105 (mp0) cc_final: 0.8297 (tm-30)
REVERT: C   10 THR cc_start: 0.9292 (m) cc_final: 0.9087 (p)
REVERT: C   19 LEU cc_start: 0.9531 (mt) cc_final: 0.9220 (mt)
REVERT: C   24 ASP cc_start: 0.8910 (t0) cc_final: 0.8527 (t0)
REVERT: C   27 THR cc_start: 0.8081 (m) cc_final: 0.7439 (m)
REVERT: C   55 ASP cc_start: 0.8354 (t70) cc_final: 0.7945 (t0)
REVERT: C   57 ASN cc_start: 0.8775 (t0) cc_final: 0.8538 (t0)
REVERT: C   77 PHE cc_start: 0.8474 (t80) cc_final: 0.8093 (t80)
REVERT: C   82 TYR cc_start: 0.8962 (t80) cc_final: 0.8726 (t80)
REVERT: D   15 LEU cc_start: 0.9568 (tp) cc_final: 0.9353 (tp)
REVERT: D   18 LEU cc_start: 0.9663 (mm) cc_final: 0.9422 (mm)
REVERT: D   33 ASN cc_start: 0.8893 (m110) cc_final: 0.8611 (m110)
REVERT: D   52 PHE cc_start: 0.9455 (t80) cc_final: 0.9159 (t80)
REVERT: D   55 ASP cc_start: 0.8323 (t0) cc_final: 0.7575 (t0)
REVERT: D   59 ASP cc_start: 0.9332 (m-30) cc_final: 0.9114 (m-30)
REVERT: D   60 LYS cc_start: 0.9129 (pttt) cc_final: 0.8434 (ptmm)
REVERT: D   63 LEU cc_start: 0.9672 (mt) cc_final: 0.9353 (mt)
REVERT: D   66 LEU cc_start: 0.9455 (mt) cc_final: 0.9130 (mt)
REVERT: D   70 ASP cc_start: 0.8127 (t70) cc_final: 0.7422 (t0)
REVERT: D   74 GLN cc_start: 0.8995 (mt0) cc_final: 0.8089 (mm-40)
REVERT: D   79 LYS cc_start: 0.9068 (ptpt) cc_final: 0.8778 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1893
  time to fit residues: 57.8188
Evaluate side-chains
  172 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 26 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 236 HIS
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  14 GLN
B  20 GLN
C  21 GLN
** C  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.093673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.073375 restraints weight = 25221.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.075832 restraints weight = 15150.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.077532 restraints weight = 10185.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.6808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5966  Z= 0.144
  Angle     :  0.606   9.554   8100  Z= 0.317
  Chirality :  0.041   0.179    835
  Planarity :  0.003   0.033   1071
  Dihedral  :  6.083  83.272    784
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  2.37 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.62 %
    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:  1.25 (0.32), residues: 717
  helix:  1.37 (0.26), residues: 407
  sheet:  0.13 (0.72), residues: 50
  loop :  0.27 (0.41), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C  75 
 HIS   0.006   0.001   HIS A 363 
 PHE   0.015   0.002   PHE D  25 
 TYR   0.013   0.001   TYR C  45 
 ARG   0.002   0.000   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  309)
  hydrogen bonds       : angle       5.00719 (  906)
  covalent geometry    : bond        0.00298 ( 5966)
  covalent geometry    : angle       0.60649 ( 8100)

*********************** 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
  230 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 0.744 
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: 0.8356 (m-80) cc_final: 0.7868 (m-80)
REVERT: A   64 PHE cc_start: 0.9203 (t80) cc_final: 0.8969 (t80)
REVERT: A  103 GLN cc_start: 0.8479 (tp40) cc_final: 0.7891 (tp40)
REVERT: A  137 ASN cc_start: 0.7316 (t0) cc_final: 0.6748 (t0)
REVERT: A  138 MET cc_start: 0.7412 (mmp) cc_final: 0.6866 (mmm)
REVERT: A  156 TRP cc_start: 0.7314 (m-90) cc_final: 0.7078 (m-90)
REVERT: A  241 ASP cc_start: 0.8459 (m-30) cc_final: 0.8127 (p0)
REVERT: A  244 PHE cc_start: 0.8601 (m-10) cc_final: 0.8345 (m-10)
REVERT: A  248 MET cc_start: 0.9258 (mpp) cc_final: 0.8955 (mpp)
REVERT: A  350 ASP cc_start: 0.8686 (m-30) cc_final: 0.8309 (m-30)
REVERT: A  357 LEU cc_start: 0.9247 (tp) cc_final: 0.8942 (tp)
REVERT: A  412 GLN cc_start: 0.9480 (mt0) cc_final: 0.9136 (mt0)
REVERT: A  428 PHE cc_start: 0.8320 (m-80) cc_final: 0.8090 (m-80)
REVERT: A  437 ASN cc_start: 0.8516 (p0) cc_final: 0.7168 (p0)
REVERT: A  439 ASN cc_start: 0.9418 (t0) cc_final: 0.8864 (t0)
REVERT: A  451 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: A  467 MET cc_start: 0.8604 (ttm) cc_final: 0.8274 (ttm)
REVERT: B   19 LEU cc_start: 0.9102 (mt) cc_final: 0.8665 (mt)
REVERT: B   24 ASP cc_start: 0.7612 (t0) cc_final: 0.5096 (t0)
REVERT: B   89 ILE cc_start: 0.7345 (pt) cc_final: 0.7033 (pt)
REVERT: C    4 GLU cc_start: 0.9106 (mp0) cc_final: 0.8333 (tm-30)
REVERT: C   16 PHE cc_start: 0.9421 (t80) cc_final: 0.9101 (t80)
REVERT: C   20 GLN cc_start: 0.9321 (mt0) cc_final: 0.8892 (mt0)
REVERT: C   24 ASP cc_start: 0.8855 (t0) cc_final: 0.8441 (t0)
REVERT: C   27 THR cc_start: 0.8233 (m) cc_final: 0.7506 (m)
REVERT: C   41 LEU cc_start: 0.9594 (mt) cc_final: 0.9353 (mt)
REVERT: C   42 LEU cc_start: 0.8824 (mt) cc_final: 0.8553 (mt)
REVERT: C   46 ASN cc_start: 0.8956 (p0) cc_final: 0.8552 (p0)
REVERT: C   55 ASP cc_start: 0.8537 (t70) cc_final: 0.8137 (t0)
REVERT: C   75 TRP cc_start: 0.8735 (t60) cc_final: 0.8042 (t60)
REVERT: C   78 TYR cc_start: 0.8782 (t80) cc_final: 0.8222 (t80)
REVERT: C   82 TYR cc_start: 0.9132 (t80) cc_final: 0.8910 (t80)
REVERT: D   18 LEU cc_start: 0.9664 (mm) cc_final: 0.9375 (mm)
REVERT: D   19 LEU cc_start: 0.9548 (mt) cc_final: 0.9331 (mt)
REVERT: D   33 ASN cc_start: 0.8806 (m110) cc_final: 0.8472 (m110)
REVERT: D   52 PHE cc_start: 0.9326 (t80) cc_final: 0.9008 (t80)
REVERT: D   55 ASP cc_start: 0.8633 (t0) cc_final: 0.7302 (t0)
REVERT: D   60 LYS cc_start: 0.9122 (pttt) cc_final: 0.7995 (pttt)
REVERT: D   66 LEU cc_start: 0.9368 (mt) cc_final: 0.9136 (mt)
REVERT: D   74 GLN cc_start: 0.8971 (mt0) cc_final: 0.7990 (mm-40)
REVERT: D   89 ILE cc_start: 0.9297 (pt) cc_final: 0.9070 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2912
  time to fit residues: 88.5877
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  : 1.329 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 37 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.2184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.091343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.072636 restraints weight = 25450.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.074805 restraints weight = 15618.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.076302 restraints weight = 10625.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.7558

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= 0.161
  Angle     :  0.638   8.704   8100  Z= 0.334
  Chirality :  0.042   0.169    835
  Planarity :  0.004   0.036   1071
  Dihedral  :  6.229  86.382    784
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  2.37 %
    Favored  : 97.35 %
  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:  1.01 (0.31), residues: 717
  helix:  1.22 (0.26), residues: 407
  sheet:  0.10 (0.72), residues: 50
  loop :  0.06 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B  75 
 HIS   0.006   0.001   HIS A 363 
 PHE   0.015   0.002   PHE D  16 
 TYR   0.016   0.002   TYR C   9 
 ARG   0.010   0.001   ARG A 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  309)
  hydrogen bonds       : angle       5.05810 (  906)
  covalent geometry    : bond        0.00343 ( 5966)
  covalent geometry    : angle       0.63846 ( 8100)

*********************** 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
  215 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.710 
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: 0.8364 (m-80) cc_final: 0.8019 (m-10)
REVERT: A   64 PHE cc_start: 0.9174 (t80) cc_final: 0.8938 (t80)
REVERT: A   77 TRP cc_start: 0.8684 (m-90) cc_final: 0.8476 (m-90)
REVERT: A  137 ASN cc_start: 0.7324 (t0) cc_final: 0.6686 (t0)
REVERT: A  138 MET cc_start: 0.7385 (mmp) cc_final: 0.6832 (mmm)
REVERT: A  156 TRP cc_start: 0.7287 (m-90) cc_final: 0.7052 (m-90)
REVERT: A  241 ASP cc_start: 0.8548 (m-30) cc_final: 0.8111 (p0)
REVERT: A  244 PHE cc_start: 0.8429 (m-10) cc_final: 0.8133 (m-10)
REVERT: A  248 MET cc_start: 0.9281 (mpp) cc_final: 0.9069 (mpp)
REVERT: A  270 GLU cc_start: 0.8888 (tp30) cc_final: 0.8640 (tp30)
REVERT: A  274 LEU cc_start: 0.9531 (mt) cc_final: 0.9301 (mt)
REVERT: A  322 LEU cc_start: 0.8948 (tp) cc_final: 0.8697 (tp)
REVERT: A  357 LEU cc_start: 0.9268 (tp) cc_final: 0.8926 (tp)
REVERT: A  412 GLN cc_start: 0.9490 (mt0) cc_final: 0.9182 (mt0)
REVERT: A  437 ASN cc_start: 0.8501 (p0) cc_final: 0.7322 (p0)
REVERT: A  439 ASN cc_start: 0.9443 (t0) cc_final: 0.8890 (t0)
REVERT: A  451 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7882 (mt-10)
REVERT: A  467 MET cc_start: 0.8636 (ttm) cc_final: 0.8174 (ttm)
REVERT: B   12 MET cc_start: 0.8870 (tmm) cc_final: 0.8192 (mtt)
REVERT: B   19 LEU cc_start: 0.9098 (mt) cc_final: 0.8662 (mt)
REVERT: B   24 ASP cc_start: 0.7672 (t0) cc_final: 0.6067 (t0)
REVERT: B   75 TRP cc_start: 0.9331 (t-100) cc_final: 0.8736 (t-100)
REVERT: B   89 ILE cc_start: 0.7559 (pt) cc_final: 0.7270 (pt)
REVERT: C    4 GLU cc_start: 0.9148 (mp0) cc_final: 0.8507 (tm-30)
REVERT: C   16 PHE cc_start: 0.9594 (t80) cc_final: 0.9299 (t80)
REVERT: C   20 GLN cc_start: 0.9239 (mt0) cc_final: 0.9007 (mt0)
REVERT: C   27 THR cc_start: 0.8096 (m) cc_final: 0.6437 (m)
REVERT: C   30 ASN cc_start: 0.9308 (m-40) cc_final: 0.8891 (m-40)
REVERT: C   41 LEU cc_start: 0.9627 (mt) cc_final: 0.9424 (mt)
REVERT: C   55 ASP cc_start: 0.8631 (t70) cc_final: 0.8206 (t0)
REVERT: C   90 PHE cc_start: 0.7546 (m-80) cc_final: 0.7034 (m-10)
REVERT: D   17 ASN cc_start: 0.9353 (t0) cc_final: 0.9114 (m110)
REVERT: D   19 LEU cc_start: 0.9573 (mt) cc_final: 0.9299 (mt)
REVERT: D   42 LEU cc_start: 0.9081 (mt) cc_final: 0.8785 (mt)
REVERT: D   55 ASP cc_start: 0.8522 (t0) cc_final: 0.7263 (t0)
REVERT: D   60 LYS cc_start: 0.9173 (pttt) cc_final: 0.8244 (pttt)
REVERT: D   66 LEU cc_start: 0.9500 (mt) cc_final: 0.9245 (mt)
REVERT: D   74 GLN cc_start: 0.9054 (mt0) cc_final: 0.8048 (mm110)
REVERT: D   81 PHE cc_start: 0.8260 (t80) cc_final: 0.7867 (t80)
REVERT: D   84 ASN cc_start: 0.8610 (t0) cc_final: 0.8343 (t0)
REVERT: D   89 ILE cc_start: 0.9455 (pt) cc_final: 0.9173 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1957
  time to fit residues: 56.7180
Evaluate side-chains
  183 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 70 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0670
   chunk 28 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    2.0124

-------------------------------------------------------------------------------
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
C  21 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.090381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.071312 restraints weight = 25192.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.073570 restraints weight = 15088.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.075081 restraints weight = 10173.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.8025

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= 0.150
  Angle     :  0.616   8.837   8100  Z= 0.321
  Chirality :  0.042   0.175    835
  Planarity :  0.004   0.058   1071
  Dihedral  :  6.148  87.107    784
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.07 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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:  0.93 (0.31), residues: 717
  helix:  1.22 (0.25), residues: 407
  sheet: -0.08 (0.71), residues: 52
  loop : -0.06 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C  22 
 HIS   0.004   0.001   HIS C  88 
 PHE   0.013   0.002   PHE D  16 
 TYR   0.015   0.001   TYR D   9 
 ARG   0.003   0.001   ARG A 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  309)
  hydrogen bonds       : angle       4.96154 (  906)
  covalent geometry    : bond        0.00320 ( 5966)
  covalent geometry    : angle       0.61567 ( 8100)

*********************** 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
  209 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 2.153 
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: 0.8406 (m-80) cc_final: 0.8090 (m-80)
REVERT: A   64 PHE cc_start: 0.9173 (t80) cc_final: 0.8926 (t80)
REVERT: A  137 ASN cc_start: 0.7328 (t0) cc_final: 0.6588 (t0)
REVERT: A  138 MET cc_start: 0.7478 (mmp) cc_final: 0.6925 (mmm)
REVERT: A  241 ASP cc_start: 0.8681 (m-30) cc_final: 0.8385 (p0)
REVERT: A  242 LYS cc_start: 0.9117 (mmpt) cc_final: 0.8915 (mmmt)
REVERT: A  244 PHE cc_start: 0.8442 (m-10) cc_final: 0.8105 (m-10)
REVERT: A  248 MET cc_start: 0.9278 (mpp) cc_final: 0.9065 (mpp)
REVERT: A  270 GLU cc_start: 0.8821 (tp30) cc_final: 0.8559 (tp30)
REVERT: A  322 LEU cc_start: 0.8899 (tp) cc_final: 0.8636 (tp)
REVERT: A  412 GLN cc_start: 0.9461 (mt0) cc_final: 0.9185 (mt0)
REVERT: A  437 ASN cc_start: 0.8627 (p0) cc_final: 0.7613 (p0)
REVERT: A  439 ASN cc_start: 0.9443 (t0) cc_final: 0.8863 (t0)
REVERT: A  467 MET cc_start: 0.8743 (ttm) cc_final: 0.8226 (ttm)
REVERT: B   12 MET cc_start: 0.8811 (tmm) cc_final: 0.8207 (mtt)
REVERT: B   19 LEU cc_start: 0.9072 (mt) cc_final: 0.8739 (mt)
REVERT: B   24 ASP cc_start: 0.7816 (t0) cc_final: 0.6573 (t0)
REVERT: B   75 TRP cc_start: 0.9326 (t-100) cc_final: 0.8932 (t-100)
REVERT: C    4 GLU cc_start: 0.9048 (mp0) cc_final: 0.8509 (tm-30)
REVERT: C   13 LEU cc_start: 0.9350 (tp) cc_final: 0.8889 (tp)
REVERT: C   27 THR cc_start: 0.8412 (m) cc_final: 0.6919 (m)
REVERT: C   30 ASN cc_start: 0.9336 (m-40) cc_final: 0.9003 (m-40)
REVERT: C   41 LEU cc_start: 0.9627 (mt) cc_final: 0.9410 (mt)
REVERT: C   47 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: C   55 ASP cc_start: 0.8427 (t70) cc_final: 0.7982 (t0)
REVERT: C   75 TRP cc_start: 0.8907 (t60) cc_final: 0.8561 (t60)
REVERT: C   82 TYR cc_start: 0.9065 (t80) cc_final: 0.8497 (t80)
REVERT: D   17 ASN cc_start: 0.9312 (t0) cc_final: 0.9086 (m110)
REVERT: D   19 LEU cc_start: 0.9568 (mt) cc_final: 0.9189 (mt)
REVERT: D   42 LEU cc_start: 0.9141 (mt) cc_final: 0.8895 (mt)
REVERT: D   52 PHE cc_start: 0.9527 (t80) cc_final: 0.8938 (t80)
REVERT: D   55 ASP cc_start: 0.8213 (t0) cc_final: 0.7176 (t0)
REVERT: D   60 LYS cc_start: 0.9198 (pttt) cc_final: 0.8239 (pttt)
REVERT: D   66 LEU cc_start: 0.9594 (mt) cc_final: 0.9140 (mt)
REVERT: D   74 GLN cc_start: 0.9116 (mt0) cc_final: 0.8294 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.2719
  time to fit residues: 78.6276
Evaluate side-chains
  175 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 ASN
C  88 HIS
D  33 ASN
D  54 ASN
D  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.091161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.072681 restraints weight = 25087.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.074850 restraints weight = 15403.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.076365 restraints weight = 10446.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.8348

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= 0.130
  Angle     :  0.636   8.936   8100  Z= 0.331
  Chirality :  0.043   0.194    835
  Planarity :  0.004   0.060   1071
  Dihedral  :  6.163  86.392    784
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.21 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  0.70 (0.31), residues: 717
  helix:  1.03 (0.26), residues: 401
  sheet: -0.04 (0.71), residues: 52
  loop : -0.15 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP A 156 
 HIS   0.005   0.001   HIS A  12 
 PHE   0.011   0.001   PHE D  25 
 TYR   0.029   0.001   TYR D   9 
 ARG   0.002   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  309)
  hydrogen bonds       : angle       4.96887 (  906)
  covalent geometry    : bond        0.00278 ( 5966)
  covalent geometry    : angle       0.63624 ( 8100)

*********************** 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  : 0.784 
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: 0.8415 (m-80) cc_final: 0.8131 (m-10)
REVERT: A   64 PHE cc_start: 0.9198 (t80) cc_final: 0.8965 (t80)
REVERT: A   77 TRP cc_start: 0.8485 (m-90) cc_final: 0.8260 (m-90)
REVERT: A  137 ASN cc_start: 0.7303 (t0) cc_final: 0.6633 (t0)
REVERT: A  138 MET cc_start: 0.7553 (mmp) cc_final: 0.7022 (mmm)
REVERT: A  241 ASP cc_start: 0.8761 (m-30) cc_final: 0.8348 (p0)
REVERT: A  242 LYS cc_start: 0.9099 (mmpt) cc_final: 0.8866 (mmmt)
REVERT: A  244 PHE cc_start: 0.8415 (m-10) cc_final: 0.8083 (m-80)
REVERT: A  257 ASN cc_start: 0.8643 (t0) cc_final: 0.8372 (t0)
REVERT: A  270 GLU cc_start: 0.8729 (tp30) cc_final: 0.8437 (tp30)
REVERT: A  274 LEU cc_start: 0.9529 (mt) cc_final: 0.9088 (mt)
REVERT: A  322 LEU cc_start: 0.8918 (tp) cc_final: 0.8634 (tp)
REVERT: A  412 GLN cc_start: 0.9444 (mt0) cc_final: 0.9240 (mt0)
REVERT: A  437 ASN cc_start: 0.8615 (p0) cc_final: 0.7757 (p0)
REVERT: A  467 MET cc_start: 0.8733 (ttm) cc_final: 0.8235 (ttm)
REVERT: B   19 LEU cc_start: 0.9151 (mt) cc_final: 0.8756 (mt)
REVERT: B   24 ASP cc_start: 0.7639 (t0) cc_final: 0.6526 (t0)
REVERT: B   75 TRP cc_start: 0.9317 (t-100) cc_final: 0.8900 (t-100)
REVERT: B   89 ILE cc_start: 0.7291 (pt) cc_final: 0.6903 (pt)
REVERT: C    4 GLU cc_start: 0.9133 (mp0) cc_final: 0.8585 (tm-30)
REVERT: C   20 GLN cc_start: 0.9153 (mt0) cc_final: 0.8926 (mt0)
REVERT: C   30 ASN cc_start: 0.9359 (m-40) cc_final: 0.9010 (m-40)
REVERT: C   32 ASN cc_start: 0.9025 (m-40) cc_final: 0.8775 (m110)
REVERT: C   57 ASN cc_start: 0.8919 (t0) cc_final: 0.8645 (t0)
REVERT: C   82 TYR cc_start: 0.9196 (t80) cc_final: 0.8746 (t80)
REVERT: D   11 GLU cc_start: 0.9461 (pp20) cc_final: 0.8982 (pp20)
REVERT: D   19 LEU cc_start: 0.9624 (mt) cc_final: 0.9115 (mt)
REVERT: D   33 ASN cc_start: 0.9157 (m110) cc_final: 0.8694 (m110)
REVERT: D   42 LEU cc_start: 0.9144 (mt) cc_final: 0.7846 (mt)
REVERT: D   55 ASP cc_start: 0.8479 (t0) cc_final: 0.7503 (t0)
REVERT: D   60 LYS cc_start: 0.9155 (pttt) cc_final: 0.8404 (pttt)
REVERT: D   78 TYR cc_start: 0.8408 (t80) cc_final: 0.7525 (t80)
REVERT: D   82 TYR cc_start: 0.8687 (t80) cc_final: 0.8485 (t80)
REVERT: D   88 HIS cc_start: 0.8923 (m90) cc_final: 0.8074 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2263
  time to fit residues: 65.2000
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  : 0.830 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 40 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.091329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.072554 restraints weight = 24753.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.074836 restraints weight = 14746.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.076387 restraints weight = 9919.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.8753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   5966  Z= 0.136
  Angle     :  0.648   9.492   8100  Z= 0.333
  Chirality :  0.043   0.184    835
  Planarity :  0.004   0.047   1071
  Dihedral  :  6.222  88.982    784
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.49 %
    Favored  : 96.23 %
  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:  0.60 (0.32), residues: 717
  helix:  0.90 (0.26), residues: 401
  sheet:  0.04 (0.72), residues: 52
  loop : -0.15 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 156 
 HIS   0.003   0.001   HIS A  12 
 PHE   0.016   0.001   PHE D  77 
 TYR   0.018   0.002   TYR D   9 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  309)
  hydrogen bonds       : angle       5.12529 (  906)
  covalent geometry    : bond        0.00295 ( 5966)
  covalent geometry    : angle       0.64817 ( 8100)

*********************** 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
  209 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.207 
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: 0.8467 (m-80) cc_final: 0.8197 (m-10)
REVERT: A   77 TRP cc_start: 0.8488 (m-90) cc_final: 0.8204 (m-90)
REVERT: A  112 TRP cc_start: 0.3912 (m100) cc_final: 0.3470 (m100)
REVERT: A  137 ASN cc_start: 0.7371 (t0) cc_final: 0.6624 (t0)
REVERT: A  138 MET cc_start: 0.7669 (mmp) cc_final: 0.7158 (mmm)
REVERT: A  176 ASN cc_start: 0.9199 (t0) cc_final: 0.8767 (p0)
REVERT: A  241 ASP cc_start: 0.8827 (m-30) cc_final: 0.8486 (p0)
REVERT: A  242 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8745 (mmmt)
REVERT: A  244 PHE cc_start: 0.8397 (m-10) cc_final: 0.7973 (m-80)
REVERT: A  257 ASN cc_start: 0.8571 (t0) cc_final: 0.8289 (t0)
REVERT: A  322 LEU cc_start: 0.8827 (tp) cc_final: 0.8540 (tp)
REVERT: A  325 LYS cc_start: 0.9289 (ptmm) cc_final: 0.9072 (ptmm)
REVERT: A  412 GLN cc_start: 0.9369 (mt0) cc_final: 0.9153 (mt0)
REVERT: A  437 ASN cc_start: 0.8636 (p0) cc_final: 0.7826 (p0)
REVERT: A  439 ASN cc_start: 0.9321 (t0) cc_final: 0.9115 (m-40)
REVERT: A  467 MET cc_start: 0.8780 (ttm) cc_final: 0.8269 (ttm)
REVERT: B   16 PHE cc_start: 0.9253 (t80) cc_final: 0.8935 (t80)
REVERT: B   20 GLN cc_start: 0.7817 (tp-100) cc_final: 0.7190 (tp40)
REVERT: B   24 ASP cc_start: 0.7619 (t0) cc_final: 0.7298 (t0)
REVERT: B   34 LEU cc_start: 0.8897 (tp) cc_final: 0.8674 (tp)
REVERT: B   89 ILE cc_start: 0.6931 (pt) cc_final: 0.6381 (pt)
REVERT: C    4 GLU cc_start: 0.9110 (mp0) cc_final: 0.8568 (tm-30)
REVERT: C   30 ASN cc_start: 0.9222 (m-40) cc_final: 0.8919 (m-40)
REVERT: C   32 ASN cc_start: 0.8940 (m-40) cc_final: 0.8715 (m110)
REVERT: C   33 ASN cc_start: 0.9264 (m-40) cc_final: 0.9043 (m-40)
REVERT: C   41 LEU cc_start: 0.9584 (mt) cc_final: 0.9372 (mt)
REVERT: C   57 ASN cc_start: 0.8984 (t0) cc_final: 0.8774 (t0)
REVERT: C   82 TYR cc_start: 0.9222 (t80) cc_final: 0.8692 (t80)
REVERT: D   17 ASN cc_start: 0.9141 (m110) cc_final: 0.8691 (m110)
REVERT: D   19 LEU cc_start: 0.9500 (mt) cc_final: 0.9023 (mt)
REVERT: D   24 ASP cc_start: 0.6433 (m-30) cc_final: 0.5773 (p0)
REVERT: D   29 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9194 (mp0)
REVERT: D   55 ASP cc_start: 0.8115 (t0) cc_final: 0.7220 (t0)
REVERT: D   60 LYS cc_start: 0.9053 (pttt) cc_final: 0.8456 (pttt)
REVERT: D   79 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8716 (mtmt)
REVERT: D   81 PHE cc_start: 0.8379 (t80) cc_final: 0.7727 (t80)
REVERT: D   82 TYR cc_start: 0.8595 (t80) cc_final: 0.7646 (t80)
REVERT: D   88 HIS cc_start: 0.9148 (m90) cc_final: 0.8105 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.2845
  time to fit residues: 81.2413
Evaluate side-chains
  178 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 HIS
D  33 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.090265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.071628 restraints weight = 25526.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.073882 restraints weight = 15032.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.075445 restraints weight = 10076.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.9006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5966  Z= 0.138
  Angle     :  0.621   7.597   8100  Z= 0.326
  Chirality :  0.042   0.182    835
  Planarity :  0.004   0.040   1071
  Dihedral  :  6.057  85.443    784
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.07 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  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 (0.32), residues: 717
  helix:  0.83 (0.26), residues: 395
  sheet:  0.01 (0.72), residues: 52
  loop : -0.05 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 156 
 HIS   0.006   0.001   HIS B  88 
 PHE   0.022   0.002   PHE B  25 
 TYR   0.030   0.002   TYR D   9 
 ARG   0.002   0.001   ARG A 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  309)
  hydrogen bonds       : angle       5.13900 (  906)
  covalent geometry    : bond        0.00300 ( 5966)
  covalent geometry    : angle       0.62113 ( 8100)

*********************** 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
  217 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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: 0.8428 (m-90) cc_final: 0.8186 (m-90)
REVERT: A  137 ASN cc_start: 0.7357 (t0) cc_final: 0.6628 (t0)
REVERT: A  138 MET cc_start: 0.7714 (mmp) cc_final: 0.7150 (mmm)
REVERT: A  176 ASN cc_start: 0.9236 (t0) cc_final: 0.8783 (p0)
REVERT: A  241 ASP cc_start: 0.8747 (m-30) cc_final: 0.8398 (p0)
REVERT: A  242 LYS cc_start: 0.9090 (mmpt) cc_final: 0.8714 (mmmt)
REVERT: A  244 PHE cc_start: 0.8370 (m-10) cc_final: 0.7999 (m-80)
REVERT: A  257 ASN cc_start: 0.8595 (t0) cc_final: 0.8310 (t0)
REVERT: A  270 GLU cc_start: 0.8647 (tp30) cc_final: 0.8402 (tp30)
REVERT: A  274 LEU cc_start: 0.9484 (mt) cc_final: 0.9085 (mt)
REVERT: A  278 ILE cc_start: 0.8810 (tp) cc_final: 0.8600 (tp)
REVERT: A  292 ASP cc_start: 0.7816 (m-30) cc_final: 0.7428 (p0)
REVERT: A  322 LEU cc_start: 0.8812 (tp) cc_final: 0.8521 (tp)
REVERT: A  362 MET cc_start: 0.9463 (mmm) cc_final: 0.9162 (mmt)
REVERT: A  412 GLN cc_start: 0.9380 (mt0) cc_final: 0.9056 (mt0)
REVERT: A  428 PHE cc_start: 0.8272 (m-80) cc_final: 0.7840 (m-80)
REVERT: A  437 ASN cc_start: 0.8522 (p0) cc_final: 0.7671 (p0)
REVERT: A  467 MET cc_start: 0.8788 (ttm) cc_final: 0.8246 (ttm)
REVERT: B   12 MET cc_start: 0.8930 (tmm) cc_final: 0.8346 (mtt)
REVERT: B   13 LEU cc_start: 0.9327 (tp) cc_final: 0.8903 (tp)
REVERT: B   16 PHE cc_start: 0.9226 (t80) cc_final: 0.9007 (t80)
REVERT: B   24 ASP cc_start: 0.7482 (t0) cc_final: 0.7016 (t0)
REVERT: B   34 LEU cc_start: 0.8992 (tp) cc_final: 0.8743 (tp)
REVERT: B   75 TRP cc_start: 0.9017 (t-100) cc_final: 0.8695 (t-100)
REVERT: B   89 ILE cc_start: 0.7123 (pt) cc_final: 0.6843 (pt)
REVERT: C    4 GLU cc_start: 0.9127 (mp0) cc_final: 0.8580 (tm-30)
REVERT: C   10 THR cc_start: 0.9388 (m) cc_final: 0.9170 (m)
REVERT: C   12 MET cc_start: 0.8794 (ptp) cc_final: 0.8565 (ptp)
REVERT: C   30 ASN cc_start: 0.9388 (m-40) cc_final: 0.9101 (m-40)
REVERT: C   57 ASN cc_start: 0.8948 (t0) cc_final: 0.8701 (t0)
REVERT: C   82 TYR cc_start: 0.9323 (t80) cc_final: 0.8870 (t80)
REVERT: D   11 GLU cc_start: 0.9550 (pp20) cc_final: 0.9338 (pp20)
REVERT: D   12 MET cc_start: 0.8755 (mmm) cc_final: 0.7990 (tpp)
REVERT: D   17 ASN cc_start: 0.9137 (m110) cc_final: 0.8653 (m110)
REVERT: D   19 LEU cc_start: 0.9548 (mt) cc_final: 0.9044 (mt)
REVERT: D   22 TRP cc_start: 0.8860 (m-10) cc_final: 0.8469 (m-10)
REVERT: D   55 ASP cc_start: 0.8344 (t0) cc_final: 0.7134 (t0)
REVERT: D   60 LYS cc_start: 0.9152 (pttt) cc_final: 0.8296 (pttt)
REVERT: D   79 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8554 (mtmt)
REVERT: D   81 PHE cc_start: 0.8428 (t80) cc_final: 0.7897 (t80)
REVERT: D   82 TYR cc_start: 0.8689 (t80) cc_final: 0.8185 (t80)
REVERT: D   88 HIS cc_start: 0.9206 (m90) cc_final: 0.8089 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1775
  time to fit residues: 51.4446
Evaluate side-chains
  189 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   chunk 42 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0980
   chunk 20 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
** C  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 HIS
D  33 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.092461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073758 restraints weight = 24916.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.076073 restraints weight = 14802.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.077684 restraints weight = 9855.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.9224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5966  Z= 0.127
  Angle     :  0.649   8.926   8100  Z= 0.334
  Chirality :  0.044   0.201    835
  Planarity :  0.004   0.045   1071
  Dihedral  :  5.987  89.109    784
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.49 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.53 (0.31), residues: 717
  helix:  0.79 (0.26), residues: 396
  sheet:  0.06 (0.71), residues: 52
  loop : -0.07 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A  12 
 PHE   0.021   0.002   PHE C  52 
 TYR   0.025   0.001   TYR D   9 
 ARG   0.002   0.001   ARG A 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (  309)
  hydrogen bonds       : angle       5.14069 (  906)
  covalent geometry    : bond        0.00272 ( 5966)
  covalent geometry    : angle       0.64898 ( 8100)

********************** 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
  216 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8060 (m-80) cc_final: 0.7810 (m-10)
REVERT: A   77 TRP cc_start: 0.8395 (m-90) cc_final: 0.8148 (m-90)
REVERT: A  102 SER cc_start: 0.7982 (t) cc_final: 0.7691 (m)
REVERT: A  103 GLN cc_start: 0.8610 (mp10) cc_final: 0.8060 (mp10)
REVERT: A  132 TYR cc_start: 0.7028 (t80) cc_final: 0.6726 (t80)
REVERT: A  137 ASN cc_start: 0.7319 (t0) cc_final: 0.6580 (t0)
REVERT: A  138 MET cc_start: 0.7788 (mmp) cc_final: 0.7253 (mmm)
REVERT: A  176 ASN cc_start: 0.9217 (t0) cc_final: 0.8686 (p0)
REVERT: A  238 ILE cc_start: 0.9079 (mm) cc_final: 0.8845 (mm)
REVERT: A  241 ASP cc_start: 0.8727 (m-30) cc_final: 0.8422 (p0)
REVERT: A  242 LYS cc_start: 0.9067 (mmpt) cc_final: 0.8699 (mmmt)
REVERT: A  244 PHE cc_start: 0.8584 (m-10) cc_final: 0.8189 (m-80)
REVERT: A  257 ASN cc_start: 0.8570 (t0) cc_final: 0.8278 (t0)
REVERT: A  270 GLU cc_start: 0.8695 (tp30) cc_final: 0.8371 (tp30)
REVERT: A  274 LEU cc_start: 0.9380 (mt) cc_final: 0.9150 (mt)
REVERT: A  292 ASP cc_start: 0.7730 (m-30) cc_final: 0.7364 (p0)
REVERT: A  322 LEU cc_start: 0.8765 (tp) cc_final: 0.8486 (tp)
REVERT: A  412 GLN cc_start: 0.9207 (mt0) cc_final: 0.8934 (mt0)
REVERT: A  437 ASN cc_start: 0.8767 (p0) cc_final: 0.7506 (p0)
REVERT: A  440 VAL cc_start: 0.8798 (m) cc_final: 0.7798 (m)
REVERT: A  467 MET cc_start: 0.8711 (ttm) cc_final: 0.8281 (ttm)
REVERT: B   12 MET cc_start: 0.8874 (tmm) cc_final: 0.8411 (mtt)
REVERT: B   13 LEU cc_start: 0.9370 (tp) cc_final: 0.8985 (tp)
REVERT: B   34 LEU cc_start: 0.8892 (tp) cc_final: 0.8677 (tp)
REVERT: B   75 TRP cc_start: 0.9029 (t-100) cc_final: 0.8674 (t-100)
REVERT: B   89 ILE cc_start: 0.7162 (pt) cc_final: 0.6648 (pt)
REVERT: C    4 GLU cc_start: 0.9151 (mp0) cc_final: 0.8568 (tm-30)
REVERT: C   10 THR cc_start: 0.9328 (m) cc_final: 0.9093 (p)
REVERT: C   13 LEU cc_start: 0.9081 (mm) cc_final: 0.8841 (mm)
REVERT: C   32 ASN cc_start: 0.9014 (m110) cc_final: 0.8716 (m110)
REVERT: C   55 ASP cc_start: 0.8614 (t70) cc_final: 0.8144 (t0)
REVERT: C   57 ASN cc_start: 0.8981 (t0) cc_final: 0.8780 (t0)
REVERT: C   82 TYR cc_start: 0.9349 (t80) cc_final: 0.8993 (t80)
REVERT: D   13 LEU cc_start: 0.8767 (tt) cc_final: 0.8512 (tt)
REVERT: D   17 ASN cc_start: 0.9023 (m110) cc_final: 0.8428 (m110)
REVERT: D   19 LEU cc_start: 0.9546 (mt) cc_final: 0.9121 (mt)
REVERT: D   22 TRP cc_start: 0.8642 (m-10) cc_final: 0.8260 (m-10)
REVERT: D   24 ASP cc_start: 0.6140 (m-30) cc_final: 0.5341 (p0)
REVERT: D   55 ASP cc_start: 0.8102 (t0) cc_final: 0.6745 (t0)
REVERT: D   60 LYS cc_start: 0.9046 (pttt) cc_final: 0.8212 (pttt)
REVERT: D   78 TYR cc_start: 0.8080 (t80) cc_final: 0.7200 (t80)
REVERT: D   79 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8497 (mtmt)
REVERT: D   82 TYR cc_start: 0.8805 (t80) cc_final: 0.8504 (t80)
REVERT: D   88 HIS cc_start: 0.9242 (m90) cc_final: 0.8198 (m90)
REVERT: D   90 PHE cc_start: 0.8251 (m-10) cc_final: 0.7903 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2012
  time to fit residues: 57.3787
Evaluate side-chains
  184 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:   30.0000
   chunk 57 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  33 ASN
D  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.090829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.072546 restraints weight = 25702.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.074748 restraints weight = 15394.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.076213 restraints weight = 10285.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.9501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5966  Z= 0.146
  Angle     :  0.651   9.201   8100  Z= 0.344
  Chirality :  0.043   0.183    835
  Planarity :  0.004   0.055   1071
  Dihedral  :  6.053  83.899    784
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.35 %
    Favored  : 96.37 %
  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:  0.42 (0.31), residues: 717
  helix:  0.73 (0.26), residues: 402
  sheet:  0.21 (0.73), residues: 50
  loop : -0.25 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 156 
 HIS   0.005   0.001   HIS C  88 
 PHE   0.021   0.002   PHE B  25 
 TYR   0.022   0.002   TYR D   9 
 ARG   0.009   0.001   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  309)
  hydrogen bonds       : angle       5.23025 (  906)
  covalent geometry    : bond        0.00318 ( 5966)
  covalent geometry    : angle       0.65077 ( 8100)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2763.52 seconds
wall clock time: 52 minutes 17.01 seconds (3137.01 seconds total)