Starting phenix.real_space_refine
on Fri Aug 22 14:59:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bvt_16271/08_2025/8bvt_16271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bvt_16271/08_2025/8bvt_16271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bvt_16271/08_2025/8bvt_16271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bvt_16271/08_2025/8bvt_16271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bvt_16271/08_2025/8bvt_16271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bvt_16271/08_2025/8bvt_16271.cif"
  }
  resolution = 3.94
  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=   0.002 sd=   0.042
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      33      5.16       5
     C    2907      2.51       5
     N     776      2.21       5
     O     801      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 4517
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 3933
          Classifications: {'peptide': 508}
          Link IDs: {'PTRANS': 28, 'TRANS': 479}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 565
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 353
          Unresolved non-hydrogen angles: 462
          Unresolved non-hydrogen dihedrals: 309
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 7, 'PHE:plan': 2, 'TRP:plan': 5, 'TYR:plan': 7, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 216
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'RTO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.09, per 1000 atoms: 0.24
  Number of scatterers: 4517
  At special positions: 0
  Unit cell: (115.648, 70.72, 82.368, 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      33     16.00
     O     801      8.00
     N     776      7.00
     C    2907      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 128 " 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: 0.43
  Conformation dependent library (CDL) restraints added in 182.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1146

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      64.0% alpha, 5.6% 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 2 through 11
      removed outlier: 3.611A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
      removed outlier: 4.283A  pdb=" N   VAL A  21 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 132 through 160
      removed outlier: 3.687A  pdb=" N   GLN A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 181
    Processing helix  chain 'A' and resid 184 through 214
      removed outlier: 3.746A  pdb=" N   SER A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   MET A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 218 through 244
    Processing helix  chain 'A' and resid 246 through 266
      Proline residue:  A 257  - end of helix
      removed outlier: 4.009A  pdb=" N   ILE A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR A 264 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 279
    Processing helix  chain 'A' and resid 281 through 296
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 4.255A  pdb=" N   LYS A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 311
      removed outlier: 3.508A  pdb=" N   LEU A 309 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 332
      removed outlier: 3.531A  pdb=" N   CYS A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 359
      removed outlier: 3.981A  pdb=" N   ASP A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 364
      removed outlier: 3.974A  pdb=" N   GLY A 364 " --> pdb=" O   GLN A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 392
      removed outlier: 3.733A  pdb=" N   ASP A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'A' and resid 420 through 449
    Processing helix  chain 'A' and resid 453 through 478
      Proline residue:  A 473  - end of helix
      removed outlier: 4.010A  pdb=" N   THR A 478 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 502
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 515 through 517
      No H-bonds generated for 'chain 'A' and resid 515 through 517'
    Processing helix  chain 'A' and resid 518 through 523
    Processing helix  chain 'B' and resid 53 through 56
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 4.101A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.802A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  83 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET B  83 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS B  22 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 59
      removed outlier: 3.607A  pdb=" N   ARG B  59 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    843 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: 0.47

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.01 -     1.17: 1
        1.17 -     1.33: 1150
        1.33 -     1.49: 1534
        1.49 -     1.66: 1875
        1.66 -     1.82: 53
  Bond restraints: 4613
  Sorted by residual:
  bond pdb=" CB  PRO A  88 "
       pdb=" CG  PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.492  1.011  0.481 5.00e-02 4.00e+02 9.25e+01
  bond pdb=" CG  PRO A  88 "
       pdb=" CD  PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.503  1.217  0.286 3.40e-02 8.65e+02 7.06e+01
  bond pdb=" N   PRO A  88 "
       pdb=" CA  PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.465  1.566 -0.101 2.03e-02 2.43e+03 2.49e+01
  bond pdb=" N04 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.625  1.711 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C11 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.776  1.817 -0.041 2.00e-02 2.50e+03 4.10e+00
  ... (remaining 4608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.67: 6278
        8.67 -    17.35: 10
       17.35 -    26.02: 1
       26.02 -    34.69: 1
       34.69 -    43.37: 2
  Bond angle restraints: 6292
  Sorted by residual:
  angle pdb=" CA  PRO A  88 "
        pdb=" CB  PRO A  88 "
        pdb=" CG  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     104.50   66.53   37.97 1.90e+00 2.77e-01 3.99e+02
  angle pdb=" N   PRO A  88 "
        pdb=" CD  PRO A  88 "
        pdb=" CG  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     103.20   74.08   29.12 1.50e+00 4.44e-01 3.77e+02
  angle pdb=" CB  PRO A  88 "
        pdb=" CG  PRO A  88 "
        pdb=" CD  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     106.10  149.47  -43.37 3.20e+00 9.77e-02 1.84e+02
  angle pdb=" CA  PRO A  88 "
        pdb=" N   PRO A  88 "
        pdb=" CD  PRO A  88 "
      ideal   model   delta    sigma   weight residual
     112.00   99.99   12.01 1.40e+00 5.10e-01 7.36e+01
  angle pdb=" CA  PRO A 494 "
        pdb=" N   PRO A 494 "
        pdb=" CD  PRO A 494 "
      ideal   model   delta    sigma   weight residual
     112.00  102.70    9.30 1.40e+00 5.10e-01 4.41e+01
  ... (remaining 6287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 2318
       17.69 -    35.37: 314
       35.37 -    53.06: 74
       53.06 -    70.75: 12
       70.75 -    88.44: 10
  Dihedral angle restraints: 2728
    sinusoidal: 944
      harmonic: 1784
  Sorted by residual:
  dihedral pdb=" CB  CYS A  78 "
           pdb=" SG  CYS A  78 "
           pdb=" SG  CYS A 128 "
           pdb=" CB  CYS A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.55   65.45     1      1.00e+01 1.00e-02 5.61e+01
  dihedral pdb=" N   PRO A  88 "
           pdb=" CG  PRO A  88 "
           pdb=" CD  PRO A  88 "
           pdb=" CB  PRO A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  107.54  -77.54     1      1.50e+01 4.44e-03 3.35e+01
  dihedral pdb=" CA  PRO A  88 "
           pdb=" CB  PRO A  88 "
           pdb=" CG  PRO A  88 "
           pdb=" CD  PRO A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      38.00  123.96  -85.96     1      2.00e+01 2.50e-03 2.23e+01
  ... (remaining 2725 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 564
       0.048 -    0.095: 138
       0.095 -    0.143: 31
       0.143 -    0.190: 6
       0.190 -    0.238: 3
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CA  PRO A 494 "
            pdb=" N   PRO A 494 "
            pdb=" C   PRO A 494 "
            pdb=" CB  PRO A 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  PRO A  88 "
            pdb=" N   PRO A  88 "
            pdb=" C   PRO A  88 "
            pdb=" CB  PRO A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.93   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  PRO A 257 "
            pdb=" N   PRO A 257 "
            pdb=" C   PRO A 257 "
            pdb=" CB  PRO A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.11e-01
  ... (remaining 739 not shown)

  Planarity restraints: 799
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 114 "    0.052 2.00e-02 2.50e+03   9.66e-02 9.34e+01
        pdb=" C   SER B 114 "   -0.167 2.00e-02 2.50e+03
        pdb=" O   SER B 114 "    0.061 2.00e-02 2.50e+03
        pdb=" N   ALA B 115 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 493 "    0.070 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO A 494 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO A 494 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 494 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  87 "    0.046 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO A  88 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.035 5.00e-02 4.00e+02
  ... (remaining 796 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 164
        2.71 -     3.25: 4839
        3.25 -     3.80: 7722
        3.80 -     4.35: 8493
        4.35 -     4.90: 14395
  Nonbonded interactions: 35613
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 172 "
            pdb=" OG  SER A 198 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP A  70 "
            pdb=" N   GLN A  74 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OG  SER A 401 "
            pdb=" O   CYS A 433 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NH1 ARG A 394 "
            pdb=" OG1 THR A 507 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" ND2 ASN A  39 "
            pdb=" O   MET A 358 "
     model   vdw
     2.285 3.120
  ... (remaining 35608 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:             1.940
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.200
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
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      :  0.009   0.481   4615  Z= 0.268
  Angle     :  1.221  43.365   6296  Z= 0.576
  Chirality :  0.046   0.238    742
  Planarity :  0.007   0.100    799
  Dihedral  : 17.639  88.436   1576
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 44.99 %
    Favored  : 54.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.33 (0.34), residues: 615
  helix:  1.09 (0.27), residues: 357
  sheet:  0.48 (0.82), residues: 48
  loop : -1.34 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.016   0.001   TYR A 482 
 PHE   0.025   0.002   PHE A 262 
 TRP   0.017   0.001   TRP A 109 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00929 ( 4613)
  covalent geometry    : angle       1.22064 ( 6292)
  SS BOND              : bond        0.00474 (    2)
  SS BOND              : angle       1.43776 (    4)
  hydrogen bonds       : bond        0.13470 (  289)
  hydrogen bonds       : angle       5.71807 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 TYR cc_start: 0.7709 (t80) cc_final: 0.7377 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0338
  time to fit residues: 4.6426
Evaluate side-chains
  92 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.0070
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0000
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    0.4802

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.127738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.106821 restraints weight = 12460.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.109904 restraints weight = 6273.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.111883 restraints weight = 3968.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113323 restraints weight = 2930.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.114170 restraints weight = 2358.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.0745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4615  Z= 0.134
  Angle     :  0.743  14.004   6296  Z= 0.347
  Chirality :  0.041   0.148    742
  Planarity :  0.004   0.036    799
  Dihedral  :  5.033  29.318    686
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 39.86 %
    Favored  : 57.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.61 (0.35), residues: 615
  helix:  1.27 (0.28), residues: 362
  sheet:  0.90 (0.82), residues: 49
  loop : -1.29 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.017   0.001   TYR A 354 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.011   0.001   TRP A 109 
 HIS   0.001   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4613)
  covalent geometry    : angle       0.74153 ( 6292)
  SS BOND              : bond        0.00480 (    2)
  SS BOND              : angle       1.97069 (    4)
  hydrogen bonds       : bond        0.04393 (  289)
  hydrogen bonds       : angle       4.81141 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8698 (tpt) cc_final: 0.8238 (tpt)
REVERT: A  142 MET cc_start: 0.9586 (tpp) cc_final: 0.9218 (tpp)
REVERT: A  168 ASN cc_start: 0.7917 (m-40) cc_final: 0.7502 (m110)
REVERT: A  399 MET cc_start: 0.7734 (mpp) cc_final: 0.7478 (mpp)
REVERT: A  482 TYR cc_start: 0.7558 (t80) cc_final: 0.7151 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0362
  time to fit residues: 5.8221
Evaluate side-chains
  103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.124781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.103141 restraints weight = 12541.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.106097 restraints weight = 6439.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.108154 restraints weight = 4178.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.109375 restraints weight = 3111.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.110380 restraints weight = 2577.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4615  Z= 0.154
  Angle     :  0.692   9.765   6296  Z= 0.323
  Chirality :  0.041   0.159    742
  Planarity :  0.004   0.044    799
  Dihedral  :  4.956  29.976    686
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 39.63 %
    Favored  : 55.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.68 (0.35), residues: 615
  helix:  1.35 (0.27), residues: 362
  sheet:  0.90 (0.82), residues: 49
  loop : -1.29 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 273 
 TYR   0.012   0.001   TYR A 354 
 PHE   0.014   0.001   PHE A   3 
 TRP   0.009   0.001   TRP A 274 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4613)
  covalent geometry    : angle       0.69034 ( 6292)
  SS BOND              : bond        0.00424 (    2)
  SS BOND              : angle       2.01231 (    4)
  hydrogen bonds       : bond        0.04207 (  289)
  hydrogen bonds       : angle       4.67745 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8752 (tpt) cc_final: 0.8330 (tpt)
REVERT: A   76 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7935 (mm-30)
REVERT: A  122 THR cc_start: 0.9413 (p) cc_final: 0.9107 (t)
REVERT: A  361 GLN cc_start: 0.7556 (mm110) cc_final: 0.7354 (mm110)
REVERT: A  394 ARG cc_start: 0.7714 (mtm180) cc_final: 0.6914 (mtm180)
REVERT: A  482 TYR cc_start: 0.7561 (t80) cc_final: 0.7022 (t80)
REVERT: A  485 MET cc_start: 0.9132 (tmm) cc_final: 0.8742 (tpt)
  outliers start: 19
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0387
  time to fit residues: 5.9291
Evaluate side-chains
  113 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  339 PHE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 35 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0470
   chunk 59 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.7482

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.125850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.104218 restraints weight = 12439.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107280 restraints weight = 6368.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.109318 restraints weight = 4098.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.110695 restraints weight = 3047.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.111472 restraints weight = 2495.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4615  Z= 0.127
  Angle     :  0.687  11.919   6296  Z= 0.313
  Chirality :  0.041   0.160    742
  Planarity :  0.004   0.046    799
  Dihedral  :  4.778  30.514    686
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 39.16 %
    Favored  : 55.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.74 (0.35), residues: 615
  helix:  1.40 (0.27), residues: 362
  sheet:  1.03 (0.83), residues: 49
  loop : -1.32 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.010   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4613)
  covalent geometry    : angle       0.68606 ( 6292)
  SS BOND              : bond        0.00542 (    2)
  SS BOND              : angle       1.66142 (    4)
  hydrogen bonds       : bond        0.04025 (  289)
  hydrogen bonds       : angle       4.54945 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8747 (tpt) cc_final: 0.8338 (tpt)
REVERT: A   76 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7883 (mm-30)
REVERT: A  361 GLN cc_start: 0.7556 (mm110) cc_final: 0.7342 (mm110)
REVERT: A  482 TYR cc_start: 0.7581 (t80) cc_final: 0.6969 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0321
  time to fit residues: 5.0508
Evaluate side-chains
  105 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:   50.0000
   chunk 32 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.127046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.105494 restraints weight = 12524.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.108555 restraints weight = 6301.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.110593 restraints weight = 4030.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.111791 restraints weight = 2997.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.112815 restraints weight = 2483.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4615  Z= 0.132
  Angle     :  0.714  15.676   6296  Z= 0.322
  Chirality :  0.041   0.158    742
  Planarity :  0.004   0.049    799
  Dihedral  :  4.707  31.630    686
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 40.33 %
    Favored  : 54.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.70 (0.35), residues: 615
  helix:  1.38 (0.27), residues: 361
  sheet:  0.81 (0.82), residues: 50
  loop : -1.30 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.009   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4613)
  covalent geometry    : angle       0.71327 ( 6292)
  SS BOND              : bond        0.00502 (    2)
  SS BOND              : angle       1.66222 (    4)
  hydrogen bonds       : bond        0.03990 (  289)
  hydrogen bonds       : angle       4.53792 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8825 (tpt) cc_final: 0.8431 (tpt)
REVERT: A   76 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7864 (mm-30)
REVERT: A  122 THR cc_start: 0.9425 (p) cc_final: 0.9154 (t)
REVERT: A  482 TYR cc_start: 0.7585 (t80) cc_final: 0.6936 (t80)
REVERT: A  485 MET cc_start: 0.9126 (tmm) cc_final: 0.8711 (tpt)
  outliers start: 23
  outliers final: 19
  residues processed: 110
  average time/residue: 0.0329
  time to fit residues: 5.3732
Evaluate side-chains
  111 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:   50.0000
   chunk 52 optimal weight:   40.0000
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.126695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.105087 restraints weight = 12649.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.108050 restraints weight = 6394.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.110039 restraints weight = 4119.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.111491 restraints weight = 3074.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.112346 restraints weight = 2508.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4615  Z= 0.140
  Angle     :  0.726  14.811   6296  Z= 0.328
  Chirality :  0.041   0.144    742
  Planarity :  0.004   0.049    799
  Dihedral  :  4.633  32.765    686
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 39.39 %
    Favored  : 54.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.78 (0.35), residues: 615
  helix:  1.47 (0.27), residues: 359
  sheet:  0.88 (0.83), residues: 50
  loop : -1.29 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.009   0.001   TYR A 354 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.006   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4613)
  covalent geometry    : angle       0.72458 ( 6292)
  SS BOND              : bond        0.00490 (    2)
  SS BOND              : angle       1.65313 (    4)
  hydrogen bonds       : bond        0.04037 (  289)
  hydrogen bonds       : angle       4.49820 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A    7 LEU cc_start: 0.9502 (tp) cc_final: 0.9294 (tp)
REVERT: A   23 MET cc_start: 0.8835 (tpt) cc_final: 0.8448 (tpt)
REVERT: A   76 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7897 (mm-30)
REVERT: A  122 THR cc_start: 0.9426 (p) cc_final: 0.9157 (t)
REVERT: A  234 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7608 (tm-30)
REVERT: A  361 GLN cc_start: 0.7452 (mm110) cc_final: 0.6897 (mm110)
REVERT: A  399 MET cc_start: 0.7936 (mpp) cc_final: 0.7683 (mpp)
REVERT: A  482 TYR cc_start: 0.7586 (t80) cc_final: 0.6945 (t80)
  outliers start: 27
  outliers final: 22
  residues processed: 113
  average time/residue: 0.0353
  time to fit residues: 5.8317
Evaluate side-chains
  114 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 58 optimal weight:   30.0000
   chunk 44 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.127376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.105697 restraints weight = 12555.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108732 restraints weight = 6431.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.110817 restraints weight = 4143.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112049 restraints weight = 3068.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113054 restraints weight = 2528.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4615  Z= 0.131
  Angle     :  0.753  15.868   6296  Z= 0.332
  Chirality :  0.041   0.177    742
  Planarity :  0.004   0.049    799
  Dihedral  :  4.595  33.046    686
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 38.93 %
    Favored  : 54.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.83 (0.35), residues: 615
  helix:  1.51 (0.27), residues: 358
  sheet:  1.19 (0.85), residues: 49
  loop : -1.35 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.010   0.001   TYR A 354 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4613)
  covalent geometry    : angle       0.75202 ( 6292)
  SS BOND              : bond        0.00432 (    2)
  SS BOND              : angle       1.59880 (    4)
  hydrogen bonds       : bond        0.03987 (  289)
  hydrogen bonds       : angle       4.46902 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8832 (tpt) cc_final: 0.8448 (tpt)
REVERT: A   76 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7892 (mm-30)
REVERT: A  234 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: A  359 ASP cc_start: 0.8848 (t0) cc_final: 0.8627 (t0)
REVERT: A  464 MET cc_start: 0.7956 (ttt) cc_final: 0.7505 (ttp)
REVERT: A  482 TYR cc_start: 0.7600 (t80) cc_final: 0.6950 (t80)
REVERT: A  485 MET cc_start: 0.9086 (tmm) cc_final: 0.8652 (tpt)
  outliers start: 28
  outliers final: 19
  residues processed: 118
  average time/residue: 0.0388
  time to fit residues: 6.5786
Evaluate side-chains
  114 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 50 optimal weight:   50.0000
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.127680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.105715 restraints weight = 12659.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.108836 restraints weight = 6501.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.110892 restraints weight = 4179.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.112186 restraints weight = 3123.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.113118 restraints weight = 2568.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4615  Z= 0.139
  Angle     :  0.828  15.580   6296  Z= 0.360
  Chirality :  0.042   0.219    742
  Planarity :  0.004   0.047    799
  Dihedral  :  4.587  33.517    686
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 39.39 %
    Favored  : 55.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.73 (0.35), residues: 615
  helix:  1.41 (0.27), residues: 358
  sheet:  1.21 (0.85), residues: 49
  loop : -1.35 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 162 
 TYR   0.020   0.001   TYR A 354 
 PHE   0.017   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 109 
 HIS   0.002   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4613)
  covalent geometry    : angle       0.82697 ( 6292)
  SS BOND              : bond        0.00764 (    2)
  SS BOND              : angle       1.71633 (    4)
  hydrogen bonds       : bond        0.04103 (  289)
  hydrogen bonds       : angle       4.53038 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8829 (tpt) cc_final: 0.8439 (tpt)
REVERT: A   76 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7873 (mm-30)
REVERT: A  234 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: A  359 ASP cc_start: 0.8928 (t0) cc_final: 0.8714 (t0)
REVERT: A  482 TYR cc_start: 0.7591 (t80) cc_final: 0.6920 (t80)
REVERT: A  485 MET cc_start: 0.9122 (tmm) cc_final: 0.8655 (tpt)
  outliers start: 23
  outliers final: 20
  residues processed: 114
  average time/residue: 0.0380
  time to fit residues: 6.3028
Evaluate side-chains
  113 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 57 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 45 optimal weight:    0.6980
   chunk 0 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   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  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.131888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.107440 restraints weight = 12716.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.110679 restraints weight = 6435.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.112688 restraints weight = 4129.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.114239 restraints weight = 3094.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.115036 restraints weight = 2522.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4615  Z= 0.137
  Angle     :  0.841  15.700   6296  Z= 0.368
  Chirality :  0.043   0.208    742
  Planarity :  0.005   0.047    799
  Dihedral  :  4.490  33.587    686
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 39.16 %
    Favored  : 55.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.63 (0.35), residues: 615
  helix:  1.30 (0.27), residues: 363
  sheet:  1.18 (0.84), residues: 50
  loop : -1.42 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.008   0.001   TYR A 354 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 109 
 HIS   0.003   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4613)
  covalent geometry    : angle       0.83856 ( 6292)
  SS BOND              : bond        0.00545 (    2)
  SS BOND              : angle       2.83626 (    4)
  hydrogen bonds       : bond        0.04037 (  289)
  hydrogen bonds       : angle       4.52251 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8818 (tpt) cc_final: 0.8432 (tpt)
REVERT: A   76 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7905 (mm-30)
REVERT: A  109 TRP cc_start: 0.8709 (m-90) cc_final: 0.8364 (m-90)
REVERT: A  234 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: A  464 MET cc_start: 0.8019 (ttt) cc_final: 0.7631 (ttp)
REVERT: A  482 TYR cc_start: 0.7605 (t80) cc_final: 0.6923 (t80)
REVERT: A  485 MET cc_start: 0.9109 (tmm) cc_final: 0.8674 (tpt)
  outliers start: 21
  outliers final: 19
  residues processed: 109
  average time/residue: 0.0286
  time to fit residues: 4.6343
Evaluate side-chains
  111 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.126801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.105325 restraints weight = 12411.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108373 restraints weight = 6438.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.110391 restraints weight = 4176.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.111790 restraints weight = 3129.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.112583 restraints weight = 2563.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4615  Z= 0.140
  Angle     :  0.860  16.329   6296  Z= 0.376
  Chirality :  0.043   0.207    742
  Planarity :  0.005   0.047    799
  Dihedral  :  4.487  33.391    686
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 38.69 %
    Favored  : 55.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.65 (0.35), residues: 615
  helix:  1.32 (0.27), residues: 363
  sheet:  1.18 (0.84), residues: 50
  loop : -1.42 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 273 
 TYR   0.008   0.001   TYR A 444 
 PHE   0.015   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 109 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4613)
  covalent geometry    : angle       0.85808 ( 6292)
  SS BOND              : bond        0.00553 (    2)
  SS BOND              : angle       2.28301 (    4)
  hydrogen bonds       : bond        0.04013 (  289)
  hydrogen bonds       : angle       4.54772 (  843)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   76 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8068 (mm-30)
REVERT: A  109 TRP cc_start: 0.8703 (m-90) cc_final: 0.8308 (m-90)
REVERT: A  234 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: A  464 MET cc_start: 0.7974 (ttt) cc_final: 0.7618 (ttp)
REVERT: A  482 TYR cc_start: 0.7688 (t80) cc_final: 0.6985 (t80)
REVERT: A  485 MET cc_start: 0.9116 (tmm) cc_final: 0.8719 (tpt)
  outliers start: 23
  outliers final: 21
  residues processed: 109
  average time/residue: 0.0376
  time to fit residues: 6.0613
Evaluate side-chains
  114 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  493 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0270
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0270
   chunk 60 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 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 = 0.3960 r_free = 0.3960 target = 0.131625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.107144 restraints weight = 12911.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110333 restraints weight = 6506.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.112534 restraints weight = 4187.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113853 restraints weight = 3111.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.114871 restraints weight = 2568.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4615  Z= 0.138
  Angle     :  0.845  16.348   6296  Z= 0.369
  Chirality :  0.043   0.207    742
  Planarity :  0.005   0.047    799
  Dihedral  :  4.339  31.011    686
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 39.39 %
    Favored  : 55.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  0.64 (0.35), residues: 615
  helix:  1.30 (0.27), residues: 363
  sheet:  1.19 (0.84), residues: 50
  loop : -1.39 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.007   0.001   TYR A 169 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 274 
 HIS   0.001   0.000   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4613)
  covalent geometry    : angle       0.84386 ( 6292)
  SS BOND              : bond        0.00596 (    2)
  SS BOND              : angle       1.99351 (    4)
  hydrogen bonds       : bond        0.03969 (  289)
  hydrogen bonds       : angle       4.54471 (  843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 747.27 seconds
wall clock time: 13 minutes 34.51 seconds (814.51 seconds total)