Starting phenix.real_space_refine
on Fri Aug 22 19:46:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ofz_16864/08_2025/8ofz_16864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ofz_16864/08_2025/8ofz_16864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ofz_16864/08_2025/8ofz_16864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ofz_16864/08_2025/8ofz_16864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ofz_16864/08_2025/8ofz_16864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ofz_16864/08_2025/8ofz_16864.cif"
  }
  resolution = 3.2
  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
-------------------------------------------------------------------------------
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=  -0.015 sd=   0.441
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      32      5.16       5
     C    4952      2.51       5
     N    1124      2.21       5
     O    1260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s

  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: 7368
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1830
          Classifications: {'peptide': 244}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 230}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {'GOL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.08, per 1000 atoms: 0.15
  Number of scatterers: 7368
  At special positions: 0
  Unit cell: (82.39, 82.39, 67.41, 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      32     16.00
     O    1260      8.00
     N    1124      7.00
     C    4952      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 327.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      77.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 98
    Processing helix  chain 'A' and resid 102 through 122
    Processing helix  chain 'A' and resid 130 through 140
    Processing helix  chain 'A' and resid 146 through 178
      removed outlier: 4.255A  pdb=" N   GLY A 150 " --> pdb=" O   ARG A 146 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU A 173 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 195
      removed outlier: 4.062A  pdb=" N   PHE A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 227
    Processing helix  chain 'A' and resid 236 through 256
      removed outlier: 3.954A  pdb=" N   LEU A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ALA A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 276
      removed outlier: 3.518A  pdb=" N   ASP A 265 " --> pdb=" O   ASN A 261 " (cutoff:3.500A)
      Proline residue:  A 268  - end of helix
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 288 through 310
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'B' and resid 71 through 98
    Processing helix  chain 'B' and resid 102 through 122
    Processing helix  chain 'B' and resid 130 through 140
    Processing helix  chain 'B' and resid 146 through 178
      removed outlier: 4.255A  pdb=" N   GLY B 150 " --> pdb=" O   ARG B 146 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ASP B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU B 173 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 195
      removed outlier: 4.062A  pdb=" N   PHE B 194 " --> pdb=" O   ILE B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 227
    Processing helix  chain 'B' and resid 236 through 256
      removed outlier: 3.954A  pdb=" N   LEU B 254 " --> pdb=" O   ASN B 250 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ALA B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 276
      removed outlier: 3.518A  pdb=" N   ASP B 265 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
      Proline residue:  B 268  - end of helix
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 288 through 310
      Proline residue:  B 295  - end of helix
    Processing helix  chain 'C' and resid 71 through 98
    Processing helix  chain 'C' and resid 102 through 122
    Processing helix  chain 'C' and resid 130 through 140
    Processing helix  chain 'C' and resid 146 through 178
      removed outlier: 4.255A  pdb=" N   GLY C 150 " --> pdb=" O   ARG C 146 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ASP C 172 " --> pdb=" O   GLY C 168 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU C 173 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 195
      removed outlier: 4.062A  pdb=" N   PHE C 194 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 227
    Processing helix  chain 'C' and resid 236 through 256
      removed outlier: 3.954A  pdb=" N   LEU C 254 " --> pdb=" O   ASN C 250 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ALA C 255 " --> pdb=" O   ASN C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 276
      removed outlier: 3.518A  pdb=" N   ASP C 265 " --> pdb=" O   ASN C 261 " (cutoff:3.500A)
      Proline residue:  C 268  - end of helix
    Processing helix  chain 'C' and resid 278 through 283
    Processing helix  chain 'C' and resid 288 through 310
      Proline residue:  C 295  - end of helix
    Processing helix  chain 'D' and resid 71 through 98
    Processing helix  chain 'D' and resid 102 through 122
    Processing helix  chain 'D' and resid 130 through 140
    Processing helix  chain 'D' and resid 146 through 178
      removed outlier: 4.255A  pdb=" N   GLY D 150 " --> pdb=" O   ARG D 146 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ASP D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU D 173 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 195
      removed outlier: 4.062A  pdb=" N   PHE D 194 " --> pdb=" O   ILE D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 227
    Processing helix  chain 'D' and resid 236 through 256
      removed outlier: 3.954A  pdb=" N   LEU D 254 " --> pdb=" O   ASN D 250 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ALA D 255 " --> pdb=" O   ASN D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 276
      removed outlier: 3.518A  pdb=" N   ASP D 265 " --> pdb=" O   ASN D 261 " (cutoff:3.500A)
      Proline residue:  D 268  - end of helix
    Processing helix  chain 'D' and resid 278 through 283
    Processing helix  chain 'D' and resid 288 through 310
      Proline residue:  D 295  - end of helix

    544 hydrogen bonds defined for protein.
    1632 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: 0.85

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1260
        1.34 -     1.46: 2228
        1.46 -     1.58: 4048
        1.58 -     1.70: 0
        1.70 -     1.82: 52
  Bond restraints: 7588
  Sorted by residual:
  bond pdb=" C   PHE A 143 "
       pdb=" N   PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.332  1.367 -0.036 1.30e-02 5.92e+03 7.48e+00
  bond pdb=" C   PHE D 143 "
       pdb=" N   PRO D 144 "
    ideal  model  delta    sigma   weight residual
    1.332  1.367 -0.036 1.30e-02 5.92e+03 7.48e+00
  bond pdb=" C   PHE B 143 "
       pdb=" N   PRO B 144 "
    ideal  model  delta    sigma   weight residual
    1.332  1.367 -0.036 1.30e-02 5.92e+03 7.48e+00
  bond pdb=" C   PHE C 143 "
       pdb=" N   PRO C 144 "
    ideal  model  delta    sigma   weight residual
    1.332  1.367 -0.036 1.30e-02 5.92e+03 7.48e+00
  bond pdb=" C   VAL D 290 "
       pdb=" N   PRO D 291 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.032 1.19e-02 7.06e+03 7.15e+00
  ... (remaining 7583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 7308
        1.71 -     3.42: 2536
        3.42 -     5.13: 364
        5.13 -     6.84: 112
        6.84 -     8.55: 28
  Bond angle restraints: 10348
  Sorted by residual:
  angle pdb=" CA  ASN D 202 "
        pdb=" CB  ASN D 202 "
        pdb=" CG  ASN D 202 "
      ideal   model   delta    sigma   weight residual
     112.60  118.75   -6.15 1.00e+00 1.00e+00 3.78e+01
  angle pdb=" CA  ASN A 202 "
        pdb=" CB  ASN A 202 "
        pdb=" CG  ASN A 202 "
      ideal   model   delta    sigma   weight residual
     112.60  118.75   -6.15 1.00e+00 1.00e+00 3.78e+01
  angle pdb=" CA  ASN C 202 "
        pdb=" CB  ASN C 202 "
        pdb=" CG  ASN C 202 "
      ideal   model   delta    sigma   weight residual
     112.60  118.75   -6.15 1.00e+00 1.00e+00 3.78e+01
  angle pdb=" CA  ASN B 202 "
        pdb=" CB  ASN B 202 "
        pdb=" CG  ASN B 202 "
      ideal   model   delta    sigma   weight residual
     112.60  118.75   -6.15 1.00e+00 1.00e+00 3.78e+01
  angle pdb=" C   PRO D 291 "
        pdb=" CA  PRO D 291 "
        pdb=" CB  PRO D 291 "
      ideal   model   delta    sigma   weight residual
     111.85  104.63    7.22 1.42e+00 4.96e-01 2.59e+01
  ... (remaining 10343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.11: 3632
       14.11 -    28.21: 416
       28.21 -    42.31: 76
       42.31 -    56.42: 60
       56.42 -    70.52: 16
  Dihedral angle restraints: 4200
    sinusoidal: 1480
      harmonic: 2720
  Sorted by residual:
  dihedral pdb=" CA  SER A 125 "
           pdb=" C   SER A 125 "
           pdb=" N   GLY A 126 "
           pdb=" CA  GLY A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.15  -20.85     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  SER B 125 "
           pdb=" C   SER B 125 "
           pdb=" N   GLY B 126 "
           pdb=" CA  GLY B 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.15  -20.85     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  SER C 125 "
           pdb=" C   SER C 125 "
           pdb=" N   GLY C 126 "
           pdb=" CA  GLY C 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.15  -20.85     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 4197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 588
       0.044 -    0.089: 320
       0.089 -    0.133: 168
       0.133 -    0.177: 64
       0.177 -    0.221: 16
  Chirality restraints: 1156
  Sorted by residual:
  chirality pdb=" CA  HIS A 312 "
            pdb=" N   HIS A 312 "
            pdb=" C   HIS A 312 "
            pdb=" CB  HIS A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  HIS D 312 "
            pdb=" N   HIS D 312 "
            pdb=" C   HIS D 312 "
            pdb=" CB  HIS D 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  HIS C 312 "
            pdb=" N   HIS C 312 "
            pdb=" C   HIS C 312 "
            pdb=" CB  HIS C 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1153 not shown)

  Planarity restraints: 1300
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 246 "   -0.053 2.00e-02 2.50e+03   3.67e-02 2.36e+01
        pdb=" CG  PHE C 246 "    0.070 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 246 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 246 "    0.026 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 246 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 246 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 246 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 246 "   -0.053 2.00e-02 2.50e+03   3.67e-02 2.36e+01
        pdb=" CG  PHE D 246 "    0.070 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 246 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 246 "    0.026 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 246 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 246 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 246 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 246 "    0.053 2.00e-02 2.50e+03   3.67e-02 2.36e+01
        pdb=" CG  PHE B 246 "   -0.070 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 246 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 246 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 246 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 246 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 246 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1297 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1476
        2.83 -     3.35: 7988
        3.35 -     3.87: 14156
        3.87 -     4.38: 16436
        4.38 -     4.90: 27130
  Nonbonded interactions: 67186
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  94 "
            pdb=" O   ASN C 251 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG1 THR A  94 "
            pdb=" O   ASN B 251 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG1 THR C  94 "
            pdb=" O   ASN D 251 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   ASN A 251 "
            pdb=" OG1 THR D  94 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG  SER A 131 "
            pdb=" OG  SER A 263 "
     model   vdw
     2.560 3.040
  ... (remaining 67181 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.090
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5707
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      :  0.010   0.046   7588  Z= 0.650
  Angle     :  1.740   8.545  10348  Z= 1.227
  Chirality :  0.070   0.221   1156
  Planarity :  0.014   0.150   1300
  Dihedral  : 14.614  70.519   2504
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  :  5.52 %
    Favored  : 88.95 %
  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: -1.35 (0.23), residues: 968
  helix: -0.34 (0.17), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.90 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.005   ARG B 146 
 TYR   0.040   0.009   TYR C 206 
 PHE   0.070   0.009   PHE C 246 
 TRP   0.016   0.004   TRP C 192 
 HIS   0.010   0.003   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00971 ( 7588)
  covalent geometry    : angle       1.74031 (10348)
  hydrogen bonds       : bond        0.17003 (  544)
  hydrogen bonds       : angle       7.64525 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7608 (tp30) cc_final: 0.6884 (tp30)
REVERT: A  146 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6008 (mmp80)
REVERT: A  175 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4934 (mttp)
REVERT: A  177 HIS cc_start: 0.6632 (t70) cc_final: 0.6418 (t-90)
REVERT: B   77 GLU cc_start: 0.7608 (tp30) cc_final: 0.6885 (tp30)
REVERT: B  146 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6007 (mmp80)
REVERT: B  175 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4934 (mttp)
REVERT: B  177 HIS cc_start: 0.6631 (t70) cc_final: 0.6417 (t-90)
REVERT: C   77 GLU cc_start: 0.7607 (tp30) cc_final: 0.6884 (tp30)
REVERT: C  146 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6008 (mmp80)
REVERT: C  175 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4935 (mttp)
REVERT: C  177 HIS cc_start: 0.6632 (t70) cc_final: 0.6418 (t-90)
REVERT: D   77 GLU cc_start: 0.7608 (tp30) cc_final: 0.6884 (tp30)
REVERT: D  146 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6008 (mmp80)
REVERT: D  175 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4934 (mttp)
REVERT: D  177 HIS cc_start: 0.6632 (t70) cc_final: 0.6417 (t-90)
  outliers start: 40
  outliers final: 8
  residues processed: 184
  average time/residue: 0.0686
  time to fit residues: 17.0840
Evaluate side-chains
  148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  175 LYS
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  312 HIS
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  175 LYS
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  312 HIS
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  175 LYS
Chi-restraints excluded: chain C residue  229 ASN
Chi-restraints excluded: chain C residue  312 HIS
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  175 LYS
Chi-restraints excluded: chain D residue  229 ASN
Chi-restraints excluded: chain D residue  312 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 137 ASN
B  81 ASN
B 137 ASN
C  81 ASN
C 137 ASN
D  81 ASN
D 137 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.128229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.111205 restraints weight = 8302.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.51
r_work: 0.2968 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2834 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7588  Z= 0.149
  Angle     :  0.614   5.797  10348  Z= 0.325
  Chirality :  0.041   0.122   1156
  Planarity :  0.005   0.035   1300
  Dihedral  :  7.888  58.453   1104
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.94 %
    Favored  : 88.95 %
  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:  0.91 (0.26), residues: 968
  helix:  1.65 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.80 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  72 
 TYR   0.015   0.002   TYR C 206 
 PHE   0.018   0.002   PHE C 140 
 TRP   0.006   0.001   TRP B 289 
 HIS   0.001   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7588)
  covalent geometry    : angle       0.61391 (10348)
  hydrogen bonds       : bond        0.04362 (  544)
  hydrogen bonds       : angle       5.14297 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6998 (mmp-170)
REVERT: A  175 LYS cc_start: 0.7632 (tttt) cc_final: 0.7070 (mttp)
REVERT: A  177 HIS cc_start: 0.8016 (t70) cc_final: 0.7761 (t-90)
REVERT: B  146 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6998 (mmp-170)
REVERT: B  175 LYS cc_start: 0.7637 (tttt) cc_final: 0.7077 (mttp)
REVERT: B  177 HIS cc_start: 0.8024 (t70) cc_final: 0.7765 (t-90)
REVERT: C  146 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6996 (mmp-170)
REVERT: C  175 LYS cc_start: 0.7629 (tttt) cc_final: 0.7071 (mttp)
REVERT: C  177 HIS cc_start: 0.8018 (t70) cc_final: 0.7759 (t-90)
REVERT: D  146 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6995 (mmp-170)
REVERT: D  175 LYS cc_start: 0.7643 (tttt) cc_final: 0.7078 (mttp)
REVERT: D  177 HIS cc_start: 0.8024 (t70) cc_final: 0.7774 (t-90)
  outliers start: 8
  outliers final: 4
  residues processed: 172
  average time/residue: 0.0638
  time to fit residues: 15.3128
Evaluate side-chains
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  312 HIS
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  312 HIS
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  312 HIS
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  312 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.129549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.112744 restraints weight = 8227.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.49
r_work: 0.2984 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7588  Z= 0.133
  Angle     :  0.581   5.924  10348  Z= 0.303
  Chirality :  0.039   0.120   1156
  Planarity :  0.005   0.039   1300
  Dihedral  :  7.013  51.551   1080
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.94 %
    Favored  : 88.40 %
  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:  1.11 (0.26), residues: 968
  helix:  1.88 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.92 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG D  72 
 TYR   0.012   0.001   TYR B 206 
 PHE   0.015   0.002   PHE D 140 
 TRP   0.008   0.001   TRP A 289 
 HIS   0.001   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7588)
  covalent geometry    : angle       0.58088 (10348)
  hydrogen bonds       : bond        0.03796 (  544)
  hydrogen bonds       : angle       4.82579 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6899 (mmp-170)
REVERT: A  175 LYS cc_start: 0.7649 (tttt) cc_final: 0.7267 (mttp)
REVERT: B  146 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6898 (mmp-170)
REVERT: B  175 LYS cc_start: 0.7631 (tttt) cc_final: 0.7241 (mttp)
REVERT: C  146 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6900 (mmp-170)
REVERT: C  175 LYS cc_start: 0.7632 (tttt) cc_final: 0.7255 (mttp)
REVERT: D  146 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6896 (mmp-170)
REVERT: D  175 LYS cc_start: 0.7641 (tttt) cc_final: 0.7260 (mttp)
  outliers start: 12
  outliers final: 4
  residues processed: 180
  average time/residue: 0.0613
  time to fit residues: 15.1191
Evaluate side-chains
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  312 HIS
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  312 HIS
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  312 HIS
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  312 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.130123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.113281 restraints weight = 8357.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.53
r_work: 0.2985 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7588  Z= 0.125
  Angle     :  0.576   6.580  10348  Z= 0.291
  Chirality :  0.039   0.120   1156
  Planarity :  0.005   0.040   1300
  Dihedral  :  6.543  45.843   1080
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.26 %
    Favored  : 85.08 %
  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:  1.24 (0.26), residues: 968
  helix:  2.00 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.92 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  72 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.014   0.001   PHE D 140 
 TRP   0.006   0.001   TRP A 289 
 HIS   0.004   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7588)
  covalent geometry    : angle       0.57570 (10348)
  hydrogen bonds       : bond        0.03465 (  544)
  hydrogen bonds       : angle       4.69404 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7040 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7763 (mttt)
REVERT: A  175 LYS cc_start: 0.7451 (tttt) cc_final: 0.7187 (mttp)
REVERT: A  312 HIS cc_start: 0.6310 (OUTLIER) cc_final: 0.5860 (m-70)
REVERT: B  146 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7042 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7757 (mttt)
REVERT: B  175 LYS cc_start: 0.7451 (tttt) cc_final: 0.7190 (mttp)
REVERT: B  312 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.5867 (m-70)
REVERT: C  146 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7035 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7749 (mttt)
REVERT: C  175 LYS cc_start: 0.7461 (tttt) cc_final: 0.7206 (mttp)
REVERT: C  312 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5870 (m-70)
REVERT: D  146 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7035 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7751 (mttt)
REVERT: D  175 LYS cc_start: 0.7465 (tttt) cc_final: 0.7208 (mttp)
REVERT: D  312 HIS cc_start: 0.6307 (OUTLIER) cc_final: 0.5858 (m-70)
  outliers start: 12
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0673
  time to fit residues: 17.4990
Evaluate side-chains
  160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  312 HIS
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  312 HIS
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  312 HIS
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  312 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    0.0170
   chunk 47 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.7018

-------------------------------------------------------------------------------
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 = 0.3318 r_free = 0.3318 target = 0.131680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.114417 restraints weight = 8277.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.54
r_work: 0.3005 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7588  Z= 0.117
  Angle     :  0.564   6.325  10348  Z= 0.284
  Chirality :  0.038   0.119   1156
  Planarity :  0.004   0.041   1300
  Dihedral  :  6.317  45.603   1080
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.36 %
    Favored  : 82.87 %
  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:  1.40 (0.27), residues: 968
  helix:  2.08 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.75 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  72 
 TYR   0.012   0.001   TYR D 206 
 PHE   0.012   0.001   PHE C 140 
 TRP   0.006   0.001   TRP A 289 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7588)
  covalent geometry    : angle       0.56354 (10348)
  hydrogen bonds       : bond        0.03311 (  544)
  hydrogen bonds       : angle       4.63115 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.8183 (tp30) cc_final: 0.7594 (tp30)
REVERT: A  146 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7107 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7844 (tttp)
REVERT: A  172 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (m-30)
REVERT: B   77 GLU cc_start: 0.8186 (tp30) cc_final: 0.7595 (tp30)
REVERT: B  146 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7108 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7842 (tttp)
REVERT: B  172 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8109 (m-30)
REVERT: C   77 GLU cc_start: 0.8184 (tp30) cc_final: 0.7591 (tp30)
REVERT: C  146 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7100 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7843 (tttp)
REVERT: C  172 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8095 (m-30)
REVERT: D   77 GLU cc_start: 0.8195 (tp30) cc_final: 0.7604 (tp30)
REVERT: D  146 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7105 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7856 (tttp)
REVERT: D  172 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8092 (m-30)
  outliers start: 20
  outliers final: 8
  residues processed: 180
  average time/residue: 0.0651
  time to fit residues: 16.1449
Evaluate side-chains
  172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  172 ASP
Chi-restraints excluded: chain C residue  229 ASN
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  172 ASP
Chi-restraints excluded: chain D residue  229 ASN
Chi-restraints excluded: chain D residue  303 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0040
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 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 = 0.3291 r_free = 0.3291 target = 0.129674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.112649 restraints weight = 8316.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.50
r_work: 0.2975 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7588  Z= 0.133
  Angle     :  0.582   7.317  10348  Z= 0.291
  Chirality :  0.039   0.122   1156
  Planarity :  0.005   0.042   1300
  Dihedral  :  5.634  44.247   1072
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.92 %
    Favored  : 82.32 %
  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:  1.42 (0.27), residues: 968
  helix:  2.05 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.64 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  72 
 TYR   0.011   0.001   TYR A 206 
 PHE   0.014   0.002   PHE D 140 
 TRP   0.004   0.001   TRP A 289 
 HIS   0.000   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7588)
  covalent geometry    : angle       0.58235 (10348)
  hydrogen bonds       : bond        0.03388 (  544)
  hydrogen bonds       : angle       4.67537 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  116 MET cc_start: 0.8815 (mmm) cc_final: 0.8578 (mmt)
REVERT: A  146 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7135 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7955 (tttp)
REVERT: B  116 MET cc_start: 0.8810 (mmm) cc_final: 0.8579 (mmt)
REVERT: B  146 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7133 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7958 (tttp)
REVERT: C  116 MET cc_start: 0.8811 (mmm) cc_final: 0.8578 (mmt)
REVERT: C  146 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7126 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7959 (tttp)
REVERT: D  116 MET cc_start: 0.8808 (mmm) cc_final: 0.8564 (mmt)
REVERT: D  146 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7126 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7960 (tttp)
  outliers start: 20
  outliers final: 8
  residues processed: 180
  average time/residue: 0.0689
  time to fit residues: 16.6905
Evaluate side-chains
  172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  261 ASN
Chi-restraints excluded: chain D residue  303 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0670
   chunk 11 optimal weight:    0.0050
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 24 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.7134

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 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 = 0.3324 r_free = 0.3324 target = 0.132546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.115464 restraints weight = 8281.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.50
r_work: 0.3016 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7588  Z= 0.116
  Angle     :  0.575   7.458  10348  Z= 0.283
  Chirality :  0.038   0.121   1156
  Planarity :  0.005   0.041   1300
  Dihedral  :  5.495  42.089   1072
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.47 %
    Favored  : 82.32 %
  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:  1.58 (0.27), residues: 968
  helix:  2.15 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.51 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  72 
 TYR   0.018   0.002   TYR A 306 
 PHE   0.012   0.001   PHE D 140 
 TRP   0.005   0.001   TRP A 289 
 HIS   0.001   0.000   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7588)
  covalent geometry    : angle       0.57501 (10348)
  hydrogen bonds       : bond        0.03192 (  544)
  hydrogen bonds       : angle       4.60660 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7135 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8283 (mtmm) cc_final: 0.8012 (tttp)
REVERT: B  146 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7128 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8271 (mtmm) cc_final: 0.8006 (tttp)
REVERT: C  146 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7129 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8276 (mtmm) cc_final: 0.8007 (tttp)
REVERT: D  146 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7136 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8281 (mtmm) cc_final: 0.8008 (tttp)
  outliers start: 16
  outliers final: 12
  residues processed: 168
  average time/residue: 0.0665
  time to fit residues: 15.1853
Evaluate side-chains
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  229 ASN
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  229 ASN
Chi-restraints excluded: chain D residue  261 ASN
Chi-restraints excluded: chain D residue  303 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 94 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 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 = 0.3312 r_free = 0.3312 target = 0.131822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.114481 restraints weight = 8351.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.54
r_work: 0.3002 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7588  Z= 0.121
  Angle     :  0.577   7.763  10348  Z= 0.285
  Chirality :  0.038   0.119   1156
  Planarity :  0.005   0.041   1300
  Dihedral  :  5.481  42.291   1072
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.57 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.27), residues: 968
  helix:  2.17 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.44 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  72 
 TYR   0.019   0.001   TYR A 306 
 PHE   0.012   0.001   PHE D 140 
 TRP   0.004   0.001   TRP A 289 
 HIS   0.000   0.000   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7588)
  covalent geometry    : angle       0.57731 (10348)
  hydrogen bonds       : bond        0.03256 (  544)
  hydrogen bonds       : angle       4.62934 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7141 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8074 (tttp)
REVERT: B  146 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7138 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8072 (tttp)
REVERT: C  146 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7135 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8060 (tttp)
REVERT: D  146 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7139 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8064 (tttp)
  outliers start: 16
  outliers final: 12
  residues processed: 172
  average time/residue: 0.0644
  time to fit residues: 15.3354
Evaluate side-chains
  172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  229 ASN
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  229 ASN
Chi-restraints excluded: chain D residue  261 ASN
Chi-restraints excluded: chain D residue  303 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 68 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 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 = 0.3331 r_free = 0.3331 target = 0.133468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.116100 restraints weight = 8152.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.54
r_work: 0.3022 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7588  Z= 0.116
  Angle     :  0.583   7.791  10348  Z= 0.285
  Chirality :  0.038   0.116   1156
  Planarity :  0.005   0.041   1300
  Dihedral  :  5.422  42.191   1072
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.02 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.27), residues: 968
  helix:  2.24 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.40 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  72 
 TYR   0.019   0.001   TYR A 306 
 PHE   0.012   0.001   PHE B 140 
 TRP   0.005   0.001   TRP B 289 
 HIS   0.000   0.000   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7588)
  covalent geometry    : angle       0.58280 (10348)
  hydrogen bonds       : bond        0.03193 (  544)
  hydrogen bonds       : angle       4.58903 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7112 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8037 (tttp)
REVERT: B  146 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7106 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8032 (tttp)
REVERT: C  146 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7102 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8294 (mtmm) cc_final: 0.8023 (tttp)
REVERT: D  146 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7107 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8297 (mtmm) cc_final: 0.8027 (tttp)
  outliers start: 16
  outliers final: 12
  residues processed: 164
  average time/residue: 0.0716
  time to fit residues: 15.9291
Evaluate side-chains
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  229 ASN
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  229 ASN
Chi-restraints excluded: chain D residue  261 ASN
Chi-restraints excluded: chain D residue  303 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 91 optimal weight:    0.2980
   chunk 1 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 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 = 0.3319 r_free = 0.3319 target = 0.132154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.114865 restraints weight = 8459.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.49
r_work: 0.3032 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7588  Z= 0.123
  Angle     :  0.593   7.939  10348  Z= 0.289
  Chirality :  0.038   0.118   1156
  Planarity :  0.005   0.041   1300
  Dihedral  :  5.445  43.077   1072
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.47 %
    Favored  : 82.32 %
  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:  1.71 (0.27), residues: 968
  helix:  2.21 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.36 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  72 
 TYR   0.020   0.001   TYR B 306 
 PHE   0.013   0.001   PHE C 140 
 TRP   0.004   0.001   TRP A 289 
 HIS   0.000   0.000   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7588)
  covalent geometry    : angle       0.59311 (10348)
  hydrogen bonds       : bond        0.03283 (  544)
  hydrogen bonds       : angle       4.62965 ( 1632)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7110 (mmp-170)
REVERT: A  147 LYS cc_start: 0.8278 (mtmm) cc_final: 0.8008 (tttp)
REVERT: B  146 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7113 (mmp-170)
REVERT: B  147 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8005 (tttp)
REVERT: C  146 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7106 (mmp-170)
REVERT: C  147 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7995 (tttp)
REVERT: D  146 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7110 (mmp-170)
REVERT: D  147 LYS cc_start: 0.8275 (mtmm) cc_final: 0.8002 (tttp)
  outliers start: 16
  outliers final: 12
  residues processed: 164
  average time/residue: 0.0721
  time to fit residues: 15.9300
Evaluate side-chains
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  229 ASN
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain C residue  146 ARG
Chi-restraints excluded: chain C residue  229 ASN
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  229 ASN
Chi-restraints excluded: chain D residue  261 ASN
Chi-restraints excluded: chain D residue  303 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 91 optimal weight:   10.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 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 = 0.3295 r_free = 0.3295 target = 0.130298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.112717 restraints weight = 8520.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.51
r_work: 0.2999 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7588  Z= 0.127
  Angle     :  0.598   8.337  10348  Z= 0.292
  Chirality :  0.039   0.119   1156
  Planarity :  0.005   0.042   1300
  Dihedral  :  5.491  44.483   1072
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.02 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.27), residues: 968
  helix:  2.19 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.34 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  72 
 TYR   0.021   0.001   TYR B 306 
 PHE   0.013   0.002   PHE B 140 
 TRP   0.003   0.001   TRP C 289 
 HIS   0.001   0.000   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7588)
  covalent geometry    : angle       0.59808 (10348)
  hydrogen bonds       : bond        0.03336 (  544)
  hydrogen bonds       : angle       4.68539 ( 1632)

===============================================================================
Job complete
usr+sys time: 1278.50 seconds
wall clock time: 22 minutes 43.65 seconds (1363.65 seconds total)