Starting phenix.real_space_refine
on Fri Aug 22 13:17:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yvh_34127/08_2025/7yvh_34127.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yvh_34127/08_2025/7yvh_34127.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yvh_34127/08_2025/7yvh_34127.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yvh_34127/08_2025/7yvh_34127.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yvh_34127/08_2025/7yvh_34127.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yvh_34127/08_2025/7yvh_34127.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.027
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      16      5.16       5
     C    1988      2.51       5
     N     530      2.21       5
     O     590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3124
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 818
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 865
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 1441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1441
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 129
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'PHE:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 75
  Time building chain proxies: 0.83, per 1000 atoms: 0.27
  Number of scatterers: 3124
  At special positions: 0
  Unit cell: (60.68, 70.52, 100.86, 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      16     16.00
     O     590      8.00
     N     530      7.00
     C    1988      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.15
  Conformation dependent library (CDL) restraints added in 84.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  762

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      9.5% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 4.074A  pdb=" N   SER A  83 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 75
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 4.152A  pdb=" N   THR C  90 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 344
    Processing helix  chain 'B' and resid 383 through 390
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.910A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
      removed outlier: 3.817A  pdb=" N   GLU A  70 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13
      removed outlier: 6.579A  pdb=" N   LEU A  11 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A  84 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   TRP A  35 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.708A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12
      removed outlier: 5.827A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.589A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454

    97 hydrogen bonds defined for protein.
    243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.27

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 500
        1.30 -     1.43: 919
        1.43 -     1.56: 1763
        1.56 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 3202
  Sorted by residual:
  bond pdb=" CA  ARG C  97 "
       pdb=" C   ARG C  97 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.094 1.21e-02 6.83e+03 5.98e+01
  bond pdb=" C   ARG C  97 "
       pdb=" O   ARG C  97 "
    ideal  model  delta    sigma   weight residual
    1.236  1.170  0.066 1.14e-02 7.69e+03 3.35e+01
  bond pdb=" CB  TYR B 473 "
       pdb=" CG  TYR B 473 "
    ideal  model  delta    sigma   weight residual
    1.512  1.421  0.091 2.20e-02 2.07e+03 1.70e+01
  bond pdb=" CB  TYR A  98 "
       pdb=" CG  TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.512  1.425  0.087 2.20e-02 2.07e+03 1.56e+01
  bond pdb=" CA  TYR A  98 "
       pdb=" CB  TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.533  1.473  0.060 1.72e-02 3.38e+03 1.22e+01
  ... (remaining 3197 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.53: 4292
        3.53 -     7.05: 61
        7.05 -    10.58: 10
       10.58 -    14.11: 0
       14.11 -    17.63: 2
  Bond angle restraints: 4365
  Sorted by residual:
  angle pdb=" N   GLN B 474 "
        pdb=" CA  GLN B 474 "
        pdb=" C   GLN B 474 "
      ideal   model   delta    sigma   weight residual
     108.86  125.29  -16.43 1.41e+00 5.03e-01 1.36e+02
  angle pdb=" C   TYR A  98 "
        pdb=" CA  TYR A  98 "
        pdb=" CB  TYR A  98 "
      ideal   model   delta    sigma   weight residual
     110.43   92.80   17.63 1.68e+00 3.54e-01 1.10e+02
  angle pdb=" O   ILE B 472 "
        pdb=" C   ILE B 472 "
        pdb=" N   TYR B 473 "
      ideal   model   delta    sigma   weight residual
     122.99  117.70    5.29 1.07e+00 8.73e-01 2.45e+01
  angle pdb=" O   TYR A  98 "
        pdb=" C   TYR A  98 "
        pdb=" N   THR A  99 "
      ideal   model   delta    sigma   weight residual
     123.46  118.79    4.67 9.90e-01 1.02e+00 2.23e+01
  angle pdb=" CA  CYS B 391 "
        pdb=" CB  CYS B 391 "
        pdb=" SG  CYS B 391 "
      ideal   model   delta    sigma   weight residual
     114.40  124.75  -10.35 2.30e+00 1.89e-01 2.03e+01
  ... (remaining 4360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.23: 1763
       23.23 -    46.46: 93
       46.46 -    69.69: 13
       69.69 -    92.92: 1
       92.92 -   116.15: 1
  Dihedral angle restraints: 1871
    sinusoidal: 667
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CA  PRO A  95 "
           pdb=" C   PRO A  95 "
           pdb=" N   PRO A  96 "
           pdb=" CA  PRO A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -63.85 -116.15     0      5.00e+00 4.00e-02 5.40e+02
  dihedral pdb=" C   TYR A  98 "
           pdb=" N   TYR A  98 "
           pdb=" CA  TYR A  98 "
           pdb=" CB  TYR A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.20  -21.40     0      2.50e+00 1.60e-01 7.33e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.05   44.95     1      1.00e+01 1.00e-02 2.81e+01
  ... (remaining 1868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 432
       0.094 -    0.187: 40
       0.187 -    0.280: 6
       0.280 -    0.374: 1
       0.374 -    0.467: 1
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  GLN B 474 "
            pdb=" N   GLN B 474 "
            pdb=" C   GLN B 474 "
            pdb=" CB  GLN B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CA  TRP A  94 "
            pdb=" N   TRP A  94 "
            pdb=" C   TRP A  94 "
            pdb=" CB  TRP A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CB  THR C 112 "
            pdb=" CA  THR C 112 "
            pdb=" OG1 THR C 112 "
            pdb=" CG2 THR C 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 477 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  94 "   -0.035 2.00e-02 2.50e+03   2.57e-02 1.65e+01
        pdb=" CG  TRP A  94 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  94 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  94 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  94 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  94 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  94 "    0.062 5.00e-02 4.00e+02   9.22e-02 1.36e+01
        pdb=" N   PRO A  95 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  98 "    0.006 2.00e-02 2.50e+03   1.83e-02 6.68e+00
        pdb=" CG  TYR A  98 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  98 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  98 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  98 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  98 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  98 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A  98 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 22
        2.53 -     3.12: 2487
        3.12 -     3.72: 4482
        3.72 -     4.31: 6260
        4.31 -     4.90: 10416
  Nonbonded interactions: 23667
  Sorted by model distance:
  nonbonded pdb=" CD  ARG B 403 "
            pdb=" OD1 ASN B 405 "
     model   vdw
     1.941 3.440
  nonbonded pdb=" O   ARG C  31 "
            pdb=" OH  TYR B 473 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OG  SER C  56 "
            pdb=" OG1 THR B 415 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NZ  LYS B 378 "
            pdb=" O   CYS B 379 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   TRP A  94 "
            pdb=" N   GLY A  97 "
     model   vdw
     2.322 3.120
  ... (remaining 23662 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             16.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.770
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
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      :  0.006   0.094   3208  Z= 0.347
  Angle     :  1.128  17.632   4377  Z= 0.656
  Chirality :  0.063   0.467    480
  Planarity :  0.006   0.092    566
  Dihedral  : 13.300 116.151   1091
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.94 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  6.94 %
    Favored  : 91.48 %
  Cbeta Deviations :  0.52 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.17 (0.34), residues: 414
  helix: -4.90 (0.26), residues: 21
  sheet: -1.77 (0.40), residues: 128
  loop : -3.30 (0.31), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.041   0.003   TYR A  98 
 PHE   0.019   0.002   PHE B 371 
 TRP   0.068   0.005   TRP A  94 
 HIS   0.002   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 ( 3202)
  covalent geometry    : angle       1.10913 ( 4365)
  SS BOND              : bond        0.00650 (    6)
  SS BOND              : angle       4.11340 (   12)
  hydrogen bonds       : bond        0.25978 (   97)
  hydrogen bonds       : angle       9.90095 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.7548 (mp) cc_final: 0.7306 (mp)
REVERT: A   79 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7337 (mt0)
REVERT: C    6 GLU cc_start: 0.8464 (mp0) cc_final: 0.8178 (mp0)
REVERT: C   59 TYR cc_start: 0.8453 (m-80) cc_final: 0.8251 (m-80)
  outliers start: 5
  outliers final: 2
  residues processed: 113
  average time/residue: 0.0641
  time to fit residues: 8.5055
Evaluate side-chains
  64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PRO
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   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  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN
B 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.120205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.100086 restraints weight = 8300.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.102770 restraints weight = 4456.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.104506 restraints weight = 3003.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.105644 restraints weight = 2321.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.106293 restraints weight = 1958.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3208  Z= 0.166
  Angle     :  0.824  18.873   4377  Z= 0.419
  Chirality :  0.050   0.334    480
  Planarity :  0.006   0.089    566
  Dihedral  :  5.309  54.209    463
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  3.62 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.09 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.66 (0.37), residues: 414
  helix: -3.67 (0.66), residues: 23
  sheet: -0.71 (0.44), residues: 122
  loop : -2.22 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  45 
 TYR   0.019   0.002   TYR A  98 
 PHE   0.011   0.001   PHE B 371 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3202)
  covalent geometry    : angle       0.79503 ( 4365)
  SS BOND              : bond        0.00768 (    6)
  SS BOND              : angle       4.24691 (   12)
  hydrogen bonds       : bond        0.04170 (   97)
  hydrogen bonds       : angle       6.83676 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8609 (m-80) cc_final: 0.8395 (m-80)
REVERT: B  390 LEU cc_start: 0.7825 (mt) cc_final: 0.7467 (mt)
REVERT: B  474 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6505 (pp30)
  outliers start: 13
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0482
  time to fit residues: 4.4293
Evaluate side-chains
  67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.115679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.095763 restraints weight = 8328.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.098461 restraints weight = 4467.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.100277 restraints weight = 2978.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.101463 restraints weight = 2273.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.102136 restraints weight = 1894.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3208  Z= 0.195
  Angle     :  0.808  18.206   4377  Z= 0.413
  Chirality :  0.049   0.311    480
  Planarity :  0.006   0.082    566
  Dihedral  :  5.663  57.091    460
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.56 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 20.50 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.40), residues: 414
  helix: -2.83 (0.86), residues: 23
  sheet: -0.59 (0.42), residues: 145
  loop : -1.76 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  24 
 TYR   0.018   0.002   TYR A  49 
 PHE   0.019   0.002   PHE B 371 
 TRP   0.014   0.003   TRP B 436 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3202)
  covalent geometry    : angle       0.78103 ( 4365)
  SS BOND              : bond        0.01033 (    6)
  SS BOND              : angle       4.06328 (   12)
  hydrogen bonds       : bond        0.03757 (   97)
  hydrogen bonds       : angle       6.51112 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8673 (m-80) cc_final: 0.8444 (m-80)
REVERT: B  356 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8045 (tptp)
REVERT: B  386 LYS cc_start: 0.9007 (tptt) cc_final: 0.8472 (tppt)
REVERT: B  390 LEU cc_start: 0.7721 (mt) cc_final: 0.6935 (mt)
  outliers start: 20
  outliers final: 13
  residues processed: 76
  average time/residue: 0.0657
  time to fit residues: 6.3009
Evaluate side-chains
  68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 6 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.117039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.096457 restraints weight = 8265.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.099123 restraints weight = 4411.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.100948 restraints weight = 2960.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.102114 restraints weight = 2285.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.102747 restraints weight = 1924.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3208  Z= 0.135
  Angle     :  0.762  19.872   4377  Z= 0.386
  Chirality :  0.048   0.315    480
  Planarity :  0.005   0.071    566
  Dihedral  :  5.113  53.907    460
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 23.97 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.41), residues: 414
  helix: -2.45 (0.91), residues: 23
  sheet: -0.15 (0.44), residues: 139
  loop : -1.59 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  24 
 TYR   0.016   0.001   TYR A  49 
 PHE   0.016   0.001   PHE B 371 
 TRP   0.011   0.002   TRP A  94 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3202)
  covalent geometry    : angle       0.73285 ( 4365)
  SS BOND              : bond        0.00755 (    6)
  SS BOND              : angle       4.07135 (   12)
  hydrogen bonds       : bond        0.03527 (   97)
  hydrogen bonds       : angle       6.05479 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8611 (m-80) cc_final: 0.8395 (m-80)
REVERT: B  356 LYS cc_start: 0.8273 (mmmt) cc_final: 0.8032 (tptp)
REVERT: B  386 LYS cc_start: 0.8986 (tptt) cc_final: 0.8394 (tppt)
REVERT: B  390 LEU cc_start: 0.7694 (mt) cc_final: 0.6761 (mt)
REVERT: B  474 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7231 (pp30)
  outliers start: 13
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0647
  time to fit residues: 5.5594
Evaluate side-chains
  69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 25 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.116965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.096347 restraints weight = 8137.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.099029 restraints weight = 4402.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.100800 restraints weight = 2974.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.101980 restraints weight = 2295.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.102729 restraints weight = 1929.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3208  Z= 0.131
  Angle     :  0.775  23.122   4377  Z= 0.389
  Chirality :  0.047   0.293    480
  Planarity :  0.005   0.066    566
  Dihedral  :  4.953  52.308    460
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 22.08 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.40), residues: 414
  helix: -2.13 (0.97), residues: 23
  sheet:  0.11 (0.45), residues: 126
  loop : -1.61 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  24 
 TYR   0.015   0.001   TYR A  49 
 PHE   0.013   0.001   PHE B 371 
 TRP   0.008   0.001   TRP A  94 
 HIS   0.001   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3202)
  covalent geometry    : angle       0.74419 ( 4365)
  SS BOND              : bond        0.00942 (    6)
  SS BOND              : angle       4.18471 (   12)
  hydrogen bonds       : bond        0.03446 (   97)
  hydrogen bonds       : angle       5.78141 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8238 (mmmt) cc_final: 0.8029 (tptp)
REVERT: B  474 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7599 (pp30)
  outliers start: 20
  outliers final: 14
  residues processed: 74
  average time/residue: 0.0675
  time to fit residues: 6.1806
Evaluate side-chains
  70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.114910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094411 restraints weight = 8172.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.097082 restraints weight = 4371.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.098798 restraints weight = 2907.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.100025 restraints weight = 2237.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.100800 restraints weight = 1853.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.4903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3208  Z= 0.181
  Angle     :  0.869  25.110   4377  Z= 0.439
  Chirality :  0.051   0.384    480
  Planarity :  0.005   0.066    566
  Dihedral  :  5.224  50.930    460
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 24.92 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.40), residues: 414
  helix: -2.12 (0.97), residues: 23
  sheet: -0.07 (0.43), residues: 139
  loop : -1.59 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  24 
 TYR   0.015   0.002   TYR A  49 
 PHE   0.015   0.002   PHE A  71 
 TRP   0.013   0.002   TRP A  94 
 HIS   0.008   0.003   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3202)
  covalent geometry    : angle       0.82735 ( 4365)
  SS BOND              : bond        0.01161 (    6)
  SS BOND              : angle       5.14833 (   12)
  hydrogen bonds       : bond        0.03756 (   97)
  hydrogen bonds       : angle       5.77544 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8592 (m-80) cc_final: 0.8368 (m-80)
REVERT: B  356 LYS cc_start: 0.8216 (mmmt) cc_final: 0.8000 (tptp)
REVERT: B  474 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7707 (pp30)
  outliers start: 18
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0757
  time to fit residues: 6.8948
Evaluate side-chains
  71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
B 422 ASN
B 519 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.115531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.095070 restraints weight = 8218.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.097775 restraints weight = 4373.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.099559 restraints weight = 2905.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.100571 restraints weight = 2214.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.101386 restraints weight = 1879.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3208  Z= 0.148
  Angle     :  0.861  24.976   4377  Z= 0.432
  Chirality :  0.050   0.373    480
  Planarity :  0.005   0.063    566
  Dihedral  :  5.149  50.445    460
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 25.55 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.57 (0.40), residues: 414
  helix: -2.09 (0.99), residues: 23
  sheet:  0.16 (0.44), residues: 133
  loop : -1.69 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  24 
 TYR   0.015   0.002   TYR A  49 
 PHE   0.014   0.001   PHE A  71 
 TRP   0.012   0.002   TRP A  94 
 HIS   0.010   0.004   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3202)
  covalent geometry    : angle       0.81581 ( 4365)
  SS BOND              : bond        0.01069 (    6)
  SS BOND              : angle       5.32189 (   12)
  hydrogen bonds       : bond        0.03773 (   97)
  hydrogen bonds       : angle       5.50919 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7720 (mtp-110)
REVERT: C   59 TYR cc_start: 0.8615 (m-80) cc_final: 0.8388 (m-80)
REVERT: C   79 TYR cc_start: 0.7267 (m-80) cc_final: 0.6942 (m-80)
REVERT: B  371 PHE cc_start: 0.5007 (OUTLIER) cc_final: 0.4091 (t80)
REVERT: B  474 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7723 (pp30)
  outliers start: 20
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0764
  time to fit residues: 6.9629
Evaluate side-chains
  74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
B 519 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.115459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.095041 restraints weight = 8330.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097802 restraints weight = 4404.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.099608 restraints weight = 2909.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.100783 restraints weight = 2216.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.101447 restraints weight = 1846.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3208  Z= 0.142
  Angle     :  0.863  24.580   4377  Z= 0.431
  Chirality :  0.050   0.369    480
  Planarity :  0.005   0.062    566
  Dihedral  :  5.107  49.474    460
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 24.92 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.40), residues: 414
  helix: -2.11 (1.00), residues: 23
  sheet:  0.31 (0.45), residues: 130
  loop : -1.69 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  24 
 TYR   0.011   0.001   TYR A  98 
 PHE   0.022   0.001   PHE A  71 
 TRP   0.012   0.002   TRP A  94 
 HIS   0.007   0.003   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3202)
  covalent geometry    : angle       0.81707 ( 4365)
  SS BOND              : bond        0.01034 (    6)
  SS BOND              : angle       5.35011 (   12)
  hydrogen bonds       : bond        0.03805 (   97)
  hydrogen bonds       : angle       5.44133 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   59 TYR cc_start: 0.8607 (m-80) cc_final: 0.8405 (m-80)
REVERT: C   79 TYR cc_start: 0.7286 (m-80) cc_final: 0.6985 (m-80)
REVERT: B  371 PHE cc_start: 0.5034 (OUTLIER) cc_final: 0.4138 (t80)
REVERT: B  386 LYS cc_start: 0.8969 (tptp) cc_final: 0.8604 (tppt)
REVERT: B  474 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7736 (pp30)
  outliers start: 18
  outliers final: 13
  residues processed: 68
  average time/residue: 0.0724
  time to fit residues: 5.9773
Evaluate side-chains
  71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0970
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
B 417 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.116338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.096110 restraints weight = 8255.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.098898 restraints weight = 4356.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.100710 restraints weight = 2873.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.101894 restraints weight = 2190.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.102543 restraints weight = 1821.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3208  Z= 0.127
  Angle     :  0.818  23.272   4377  Z= 0.410
  Chirality :  0.049   0.345    480
  Planarity :  0.005   0.057    566
  Dihedral  :  4.907  45.813    460
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 24.92 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.40), residues: 414
  helix: -1.97 (1.04), residues: 23
  sheet:  0.35 (0.48), residues: 122
  loop : -1.62 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  24 
 TYR   0.014   0.001   TYR A  49 
 PHE   0.013   0.001   PHE A  71 
 TRP   0.012   0.002   TRP A  94 
 HIS   0.001   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3202)
  covalent geometry    : angle       0.77496 ( 4365)
  SS BOND              : bond        0.00901 (    6)
  SS BOND              : angle       5.06610 (   12)
  hydrogen bonds       : bond        0.03766 (   97)
  hydrogen bonds       : angle       5.24329 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  371 PHE cc_start: 0.4940 (OUTLIER) cc_final: 0.3977 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 73
  average time/residue: 0.0894
  time to fit residues: 7.5815
Evaluate side-chains
  71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.115522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.095752 restraints weight = 8067.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.098384 restraints weight = 4403.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.100136 restraints weight = 2951.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.101250 restraints weight = 2259.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.101727 restraints weight = 1900.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3208  Z= 0.145
  Angle     :  0.861  23.170   4377  Z= 0.433
  Chirality :  0.049   0.347    480
  Planarity :  0.005   0.062    566
  Dihedral  :  4.956  46.407    459
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 25.87 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.40), residues: 414
  helix: -2.03 (1.01), residues: 23
  sheet:  0.60 (0.48), residues: 120
  loop : -1.59 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  86 
 TYR   0.045   0.002   TYR C  79 
 PHE   0.014   0.001   PHE A  71 
 TRP   0.010   0.002   TRP A  94 
 HIS   0.001   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3202)
  covalent geometry    : angle       0.81947 ( 4365)
  SS BOND              : bond        0.00945 (    6)
  SS BOND              : angle       5.10465 (   12)
  hydrogen bonds       : bond        0.03798 (   97)
  hydrogen bonds       : angle       5.50247 (  243)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.8297 (mp10) cc_final: 0.7955 (mt0)
REVERT: C   59 TYR cc_start: 0.8514 (m-80) cc_final: 0.8095 (m-80)
REVERT: B  371 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.4029 (t80)
REVERT: B  386 LYS cc_start: 0.8976 (tptp) cc_final: 0.8748 (tppt)
  outliers start: 14
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0730
  time to fit residues: 5.6851
Evaluate side-chains
  69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  436 TRP
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.113764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.093387 restraints weight = 8332.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.096098 restraints weight = 4441.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.097889 restraints weight = 2949.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.099040 restraints weight = 2241.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.099710 restraints weight = 1871.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3208  Z= 0.176
  Angle     :  0.882  23.156   4377  Z= 0.445
  Chirality :  0.050   0.349    480
  Planarity :  0.005   0.060    566
  Dihedral  :  5.223  48.696    459
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 26.18 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.40), residues: 414
  helix: -2.11 (1.01), residues: 23
  sheet:  0.38 (0.45), residues: 134
  loop : -1.52 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  86 
 TYR   0.020   0.002   TYR C 107 
 PHE   0.013   0.001   PHE A  71 
 TRP   0.014   0.002   TRP A  35 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3202)
  covalent geometry    : angle       0.84131 ( 4365)
  SS BOND              : bond        0.00976 (    6)
  SS BOND              : angle       5.14272 (   12)
  hydrogen bonds       : bond        0.03881 (   97)
  hydrogen bonds       : angle       5.76190 (  243)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1021.72 seconds
wall clock time: 18 minutes 22.57 seconds (1102.57 seconds total)