Starting phenix.real_space_refine
on Sat Jun  7 17:33:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u58_41914/06_2025/8u58_41914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u58_41914/06_2025/8u58_41914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u58_41914/06_2025/8u58_41914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u58_41914/06_2025/8u58_41914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u58_41914/06_2025/8u58_41914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u58_41914/06_2025/8u58_41914.cif"
  }
  resolution = 2.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5962      2.51       5
     N    1362      2.21       5
     O    1504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8884
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4428
          Classifications: {'peptide': 565}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 544}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C
  Time building chain proxies: 8.33, per 1000 atoms: 0.94
  Number of scatterers: 8884
  At special positions: 0
  Unit cell: (130.491, 99.5598, 69.5952, 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      56     16.00
     O    1504      8.00
     N    1362      7.00
     C    5962      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
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 309 "
      " NAG C 901 " - " ASN C 309 "
  Time building additional restraints: 2.21
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      89.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'C' and resid 38 through 40
      No H-bonds generated for 'chain 'C' and resid 38 through 40'
    Processing helix  chain 'C' and resid 41 through 62
    Processing helix  chain 'C' and resid 66 through 80
      removed outlier: 3.612A  pdb=" N   LYS C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLY C  72 " --> pdb=" O   THR C  68 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU C  73 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 93
    Processing helix  chain 'C' and resid 94 through 98
      removed outlier: 3.508A  pdb=" N   VAL C  98 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 125
    Processing helix  chain 'C' and resid 129 through 141
      Proline residue:  C 138  - end of helix
    Processing helix  chain 'C' and resid 149 through 159
      removed outlier: 3.507A  pdb=" N   ILE C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 165
    Processing helix  chain 'C' and resid 166 through 196
      removed outlier: 4.134A  pdb=" N   TYR C 170 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)
      Proline residue:  C 174  - end of helix
      Proline residue:  C 182  - end of helix
    Processing helix  chain 'C' and resid 202 through 216
    Processing helix  chain 'C' and resid 217 through 233
      removed outlier: 3.587A  pdb=" N   VAL C 223 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 264
      removed outlier: 4.223A  pdb=" N   ASN C 243 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   PHE C 244 " --> pdb=" O   TYR C 240 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   SER C 253 " --> pdb=" O   GLY C 249 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   GLY C 254 " --> pdb=" O   ASN C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 288
    Processing helix  chain 'C' and resid 288 through 302
    Processing helix  chain 'C' and resid 306 through 322
    Processing helix  chain 'C' and resid 326 through 337
      removed outlier: 4.170A  pdb=" N   ALA C 330 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 367
      removed outlier: 3.673A  pdb=" N   ALA C 355 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
      Proline residue:  C 356  - end of helix
    Processing helix  chain 'C' and resid 368 through 370
      No H-bonds generated for 'chain 'C' and resid 368 through 370'
    Processing helix  chain 'C' and resid 371 through 404
    Processing helix  chain 'C' and resid 405 through 409
    Processing helix  chain 'C' and resid 411 through 436
      removed outlier: 4.101A  pdb=" N   PHE C 434 " --> pdb=" O   MET C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 472
      removed outlier: 3.914A  pdb=" N   LEU C 445 " --> pdb=" O   VAL C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 503
      removed outlier: 4.197A  pdb=" N   ILE C 491 " --> pdb=" O   SER C 487 " (cutoff:3.500A)
      Proline residue:  C 492  - end of helix
    Processing helix  chain 'C' and resid 511 through 515
    Processing helix  chain 'C' and resid 516 through 542
    Processing helix  chain 'C' and resid 654 through 682
    Processing helix  chain 'C' and resid 688 through 712
      removed outlier: 5.656A  pdb=" N   GLY C 704 " --> pdb=" O   ASN C 700 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   PHE C 705 " --> pdb=" O   PHE C 701 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE C 706 " --> pdb=" O   GLY C 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 3.603A  pdb=" N   LYS A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 93
    Processing helix  chain 'A' and resid 94 through 98
      removed outlier: 3.522A  pdb=" N   VAL A  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 125
    Processing helix  chain 'A' and resid 129 through 141
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.505A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 166 through 196
      removed outlier: 4.134A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 202 through 216
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.582A  pdb=" N   VAL A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 264
      removed outlier: 4.219A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   SER A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   GLY A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 4.176A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.681A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 404
    Processing helix  chain 'A' and resid 405 through 409
    Processing helix  chain 'A' and resid 411 through 436
      removed outlier: 4.099A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 472
      removed outlier: 3.911A  pdb=" N   LEU A 445 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      removed outlier: 4.196A  pdb=" N   ILE A 491 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 516 through 542
    Processing helix  chain 'A' and resid 654 through 682
    Processing helix  chain 'A' and resid 688 through 712
      removed outlier: 5.652A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)

    732 hydrogen bonds defined for protein.
    2160 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: 2.60

  Time building geometry restraints manager: 2.61 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: 2350
        1.34 -     1.45: 1673
        1.45 -     1.57: 4981
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 9094
  Sorted by residual:
  bond pdb=" C1  NAG A 901 "
       pdb=" O5  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.45e+00
  bond pdb=" C1  NAG C 901 "
       pdb=" O5  NAG C 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.12e+00
  bond pdb=" CB  TYR C 320 "
       pdb=" CG  TYR C 320 "
    ideal  model  delta    sigma   weight residual
    1.512  1.465  0.047 2.20e-02 2.07e+03 4.59e+00
  bond pdb=" CB  TYR A 320 "
       pdb=" CG  TYR A 320 "
    ideal  model  delta    sigma   weight residual
    1.512  1.465  0.047 2.20e-02 2.07e+03 4.49e+00
  bond pdb=" C   PRO A 372 "
       pdb=" N   LYS A 373 "
    ideal  model  delta    sigma   weight residual
    1.337  1.305  0.032 1.61e-02 3.86e+03 4.03e+00
  ... (remaining 9089 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 11528
        1.89 -     3.78: 708
        3.78 -     5.68: 92
        5.68 -     7.57: 18
        7.57 -     9.46: 10
  Bond angle restraints: 12356
  Sorted by residual:
  angle pdb=" CA  TYR C 451 "
        pdb=" CB  TYR C 451 "
        pdb=" CG  TYR C 451 "
      ideal   model   delta    sigma   weight residual
     113.90  104.44    9.46 1.80e+00 3.09e-01 2.76e+01
  angle pdb=" CA  TYR A 451 "
        pdb=" CB  TYR A 451 "
        pdb=" CG  TYR A 451 "
      ideal   model   delta    sigma   weight residual
     113.90  104.47    9.43 1.80e+00 3.09e-01 2.75e+01
  angle pdb=" CA  TYR A 689 "
        pdb=" CB  TYR A 689 "
        pdb=" CG  TYR A 689 "
      ideal   model   delta    sigma   weight residual
     113.90  106.06    7.84 1.80e+00 3.09e-01 1.90e+01
  angle pdb=" CA  TYR C 689 "
        pdb=" CB  TYR C 689 "
        pdb=" CG  TYR C 689 "
      ideal   model   delta    sigma   weight residual
     113.90  106.08    7.82 1.80e+00 3.09e-01 1.89e+01
  angle pdb=" CA  TYR C 320 "
        pdb=" CB  TYR C 320 "
        pdb=" CG  TYR C 320 "
      ideal   model   delta    sigma   weight residual
     113.90  106.76    7.14 1.80e+00 3.09e-01 1.57e+01
  ... (remaining 12351 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 4953
       16.92 -    33.83: 323
       33.83 -    50.75: 36
       50.75 -    67.66: 10
       67.66 -    84.58: 4
  Dihedral angle restraints: 5326
    sinusoidal: 2050
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CA  ASN A  63 "
           pdb=" C   ASN A  63 "
           pdb=" N   VAL A  64 "
           pdb=" CA  VAL A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.15   22.85     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASN C  63 "
           pdb=" C   ASN C  63 "
           pdb=" N   VAL C  64 "
           pdb=" CA  VAL C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.24   22.76     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  MET A 179 "
           pdb=" C   MET A 179 "
           pdb=" N   LEU A 180 "
           pdb=" CA  LEU A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 964
       0.046 -    0.091: 419
       0.091 -    0.137: 92
       0.137 -    0.183: 21
       0.183 -    0.228: 6
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" C1  NAG C 901 "
            pdb=" ND2 ASN C 309 "
            pdb=" C2  NAG C 901 "
            pdb=" O5  NAG C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A 309 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  TYR C 451 "
            pdb=" N   TYR C 451 "
            pdb=" C   TYR C 451 "
            pdb=" CB  TYR C 451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1478
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 320 "    0.096 2.00e-02 2.50e+03   4.85e-02 4.71e+01
        pdb=" CG  TYR C 320 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 320 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 320 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 320 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 320 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 320 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR C 320 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 320 "   -0.096 2.00e-02 2.50e+03   4.85e-02 4.70e+01
        pdb=" CG  TYR A 320 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 320 "    0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 320 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 320 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 320 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 320 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 320 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 901 "   -0.066 2.00e-02 2.50e+03   5.47e-02 3.74e+01
        pdb=" C7  NAG A 901 "    0.004 2.00e-02 2.50e+03
        pdb=" C8  NAG A 901 "   -0.046 2.00e-02 2.50e+03
        pdb=" N2  NAG A 901 "    0.091 2.00e-02 2.50e+03
        pdb=" O7  NAG A 901 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1475 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 4804
        2.99 -     3.47: 10323
        3.47 -     3.95: 16113
        3.95 -     4.42: 19101
        4.42 -     4.90: 29395
  Nonbonded interactions: 79736
  Sorted by model distance:
  nonbonded pdb=" O   SER A 101 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.518 3.040
  nonbonded pdb=" O   SER C 101 "
            pdb=" OG  SER C 105 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" OE2 GLU A 299 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" O   ILE C 400 "
            pdb=" OG  SER C 404 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" O   ILE A 400 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.546 3.040
  ... (remaining 79731 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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:             1.490
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.940
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
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      :  0.007   0.052   9096  Z= 0.365
  Angle     :  1.061   9.462  12362  Z= 0.604
  Chirality :  0.053   0.228   1502
  Planarity :  0.009   0.095   1476
  Dihedral  : 11.796  84.578   3210
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.22), residues: 1110
  helix: -0.36 (0.15), residues: 902
  sheet:  None (None), residues: 0
  loop : -0.19 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.006   TRP A 100 
 HIS   0.007   0.003   HIS A 505 
 PHE   0.054   0.007   PHE A 694 
 TYR   0.096   0.009   TYR A 320 
 ARG   0.004   0.001   ARG A 687 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00968 (    2)
  link_NAG-ASN         : angle       5.06188 (    6)
  hydrogen bonds       : bond        0.11708 (  732)
  hydrogen bonds       : angle       6.64466 ( 2160)
  covalent geometry    : bond        0.00737 ( 9094)
  covalent geometry    : angle       1.05572 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  193 TRP cc_start: 0.6946 (t-100) cc_final: 0.6717 (t-100)
  outliers start: 0
  outliers final: 1
  residues processed: 202
  average time/residue: 1.0131
  time to fit residues: 221.1086
Evaluate side-chains
  78 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  710 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 143 GLN
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 167 GLN
** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 654 GLN
** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 167 GLN
A 654 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.133105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.098217 restraints weight = 16604.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.25
r_work: 0.3373 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9096  Z= 0.194
  Angle     :  0.693   8.469  12362  Z= 0.356
  Chirality :  0.046   0.173   1502
  Planarity :  0.005   0.034   1476
  Dihedral  :  4.933  34.849   1224
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 10.16 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.25), residues: 1110
  helix:  1.51 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.40 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 396 
 HIS   0.004   0.001   HIS A 310 
 PHE   0.022   0.002   PHE C 221 
 TYR   0.028   0.002   TYR C 455 
 ARG   0.006   0.001   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00483 (    2)
  link_NAG-ASN         : angle       1.93597 (    6)
  hydrogen bonds       : bond        0.05334 (  732)
  hydrogen bonds       : angle       4.91716 ( 2160)
  covalent geometry    : bond        0.00441 ( 9094)
  covalent geometry    : angle       0.69197 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: C  112 SER cc_start: 0.8986 (m) cc_final: 0.8723 (t)
REVERT: C  130 ARG cc_start: 0.7701 (ptt180) cc_final: 0.7499 (ptp90)
REVERT: C  242 GLU cc_start: 0.8279 (tp30) cc_final: 0.8040 (tp30)
REVERT: C  382 VAL cc_start: 0.8020 (t) cc_final: 0.7789 (t)
REVERT: A   37 MET cc_start: 0.7540 (ttm) cc_final: 0.7216 (ttm)
REVERT: A  112 SER cc_start: 0.9018 (m) cc_final: 0.8774 (t)
REVERT: A  193 TRP cc_start: 0.8154 (t-100) cc_final: 0.7714 (t-100)
REVERT: A  242 GLU cc_start: 0.8309 (tp30) cc_final: 0.8060 (tp30)
REVERT: A  382 VAL cc_start: 0.8049 (t) cc_final: 0.7836 (t)
REVERT: A  540 MET cc_start: 0.6279 (mmm) cc_final: 0.5980 (tmt)
  outliers start: 26
  outliers final: 3
  residues processed: 132
  average time/residue: 1.0286
  time to fit residues: 148.5336
Evaluate side-chains
  84 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  239 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 145 ASN
** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 HIS
A 658 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.131541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.095256 restraints weight = 16917.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.33
r_work: 0.3346 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.6079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9096  Z= 0.177
  Angle     :  0.642  11.697  12362  Z= 0.321
  Chirality :  0.042   0.158   1502
  Planarity :  0.004   0.036   1476
  Dihedral  :  4.611  30.792   1222
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  9.96 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.25), residues: 1110
  helix:  1.89 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.76 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 193 
 HIS   0.003   0.001   HIS C 716 
 PHE   0.025   0.002   PHE C 221 
 TYR   0.035   0.002   TYR C 455 
 ARG   0.006   0.001   ARG A 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00350 (    2)
  link_NAG-ASN         : angle       1.67291 (    6)
  hydrogen bonds       : bond        0.05285 (  732)
  hydrogen bonds       : angle       4.70901 ( 2160)
  covalent geometry    : bond        0.00404 ( 9094)
  covalent geometry    : angle       0.64137 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 2.332 
Fit side-chains
REVERT: C  145 ASN cc_start: 0.9164 (OUTLIER) cc_final: 0.8934 (t0)
REVERT: C  234 ASP cc_start: 0.7960 (m-30) cc_final: 0.7256 (t0)
REVERT: C  338 MET cc_start: 0.8502 (mtt) cc_final: 0.8188 (mtm)
REVERT: C  352 PHE cc_start: 0.6795 (m-10) cc_final: 0.6259 (t80)
REVERT: C  401 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7469 (tp)
REVERT: C  452 SER cc_start: 0.9040 (t) cc_final: 0.8615 (p)
REVERT: C  519 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6958 (mp0)
REVERT: C  540 MET cc_start: 0.6369 (mmm) cc_final: 0.6036 (tmt)
REVERT: A   37 MET cc_start: 0.7815 (ttm) cc_final: 0.7439 (ttp)
REVERT: A  193 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7930 (m-90)
REVERT: A  234 ASP cc_start: 0.7969 (m-30) cc_final: 0.7279 (t0)
REVERT: A  338 MET cc_start: 0.8426 (mtt) cc_final: 0.8096 (mtm)
REVERT: A  352 PHE cc_start: 0.6805 (m-10) cc_final: 0.6251 (t80)
REVERT: A  401 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7477 (tp)
REVERT: A  429 MET cc_start: 0.7549 (tpt) cc_final: 0.7218 (tpp)
REVERT: A  519 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6890 (mp0)
REVERT: A  540 MET cc_start: 0.6376 (mmm) cc_final: 0.6169 (tmt)
  outliers start: 29
  outliers final: 9
  residues processed: 119
  average time/residue: 1.0245
  time to fit residues: 133.9329
Evaluate side-chains
  83 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  145 ASN
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ILE
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  401 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 49 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 106 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 412 HIS
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.131491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.095426 restraints weight = 17032.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.32
r_work: 0.3344 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.6672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9096  Z= 0.158
  Angle     :  0.606  13.443  12362  Z= 0.300
  Chirality :  0.042   0.348   1502
  Planarity :  0.004   0.034   1476
  Dihedral  :  4.419  30.004   1222
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.87 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.25), residues: 1110
  helix:  2.07 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.69 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 396 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.023   0.002   PHE A 221 
 TYR   0.017   0.001   TYR A 455 
 ARG   0.003   0.000   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00430 (    2)
  link_NAG-ASN         : angle       1.39521 (    6)
  hydrogen bonds       : bond        0.04799 (  732)
  hydrogen bonds       : angle       4.56921 ( 2160)
  covalent geometry    : bond        0.00360 ( 9094)
  covalent geometry    : angle       0.60552 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 1.028 
Fit side-chains
REVERT: C   37 MET cc_start: 0.7891 (ttm) cc_final: 0.7521 (ttm)
REVERT: C  338 MET cc_start: 0.8490 (mtt) cc_final: 0.8152 (mtm)
REVERT: C  352 PHE cc_start: 0.6694 (m-10) cc_final: 0.6003 (t80)
REVERT: C  401 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7519 (mp)
REVERT: C  452 SER cc_start: 0.9003 (t) cc_final: 0.8613 (p)
REVERT: C  540 MET cc_start: 0.6547 (mmm) cc_final: 0.6146 (tmt)
REVERT: A   37 MET cc_start: 0.8002 (ttm) cc_final: 0.7542 (ttm)
REVERT: A  193 TRP cc_start: 0.8275 (t-100) cc_final: 0.7894 (m-90)
REVERT: A  338 MET cc_start: 0.8512 (mtt) cc_final: 0.8155 (mtm)
REVERT: A  352 PHE cc_start: 0.6681 (m-10) cc_final: 0.5987 (t80)
REVERT: A  401 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7534 (tp)
  outliers start: 21
  outliers final: 6
  residues processed: 94
  average time/residue: 0.9598
  time to fit residues: 99.0998
Evaluate side-chains
  82 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  401 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0770
   chunk 1 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 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 = 0.4087 r_free = 0.4087 target = 0.131836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.096210 restraints weight = 17058.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.31
r_work: 0.3361 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.7035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9096  Z= 0.138
  Angle     :  0.572   9.298  12362  Z= 0.283
  Chirality :  0.042   0.363   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.309  29.344   1222
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  :  9.55 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.25), residues: 1110
  helix:  2.20 (0.17), residues: 894
  sheet:  None (None), residues: 0
  loop :  0.68 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.022   0.001   PHE A 221 
 TYR   0.022   0.001   TYR C 455 
 ARG   0.003   0.000   ARG C 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    2)
  link_NAG-ASN         : angle       1.41787 (    6)
  hydrogen bonds       : bond        0.04541 (  732)
  hydrogen bonds       : angle       4.47866 ( 2160)
  covalent geometry    : bond        0.00303 ( 9094)
  covalent geometry    : angle       0.57102 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 84
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 MET cc_start: 0.8493 (mtt) cc_final: 0.8166 (mtm)
REVERT: C  352 PHE cc_start: 0.6614 (m-10) cc_final: 0.5937 (t80)
REVERT: C  401 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7437 (tp)
REVERT: C  402 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6597 (tt)
REVERT: C  452 SER cc_start: 0.9011 (t) cc_final: 0.8547 (p)
REVERT: C  455 TYR cc_start: 0.7396 (m-80) cc_final: 0.6672 (m-80)
REVERT: C  521 MET cc_start: 0.5539 (mmt) cc_final: 0.5170 (mmm)
REVERT: C  696 CYS cc_start: 0.7757 (m) cc_final: 0.7550 (t)
REVERT: A   37 MET cc_start: 0.8022 (ttm) cc_final: 0.7573 (ttm)
REVERT: A  193 TRP cc_start: 0.8206 (t-100) cc_final: 0.7875 (m-90)
REVERT: A  338 MET cc_start: 0.8505 (mtt) cc_final: 0.8171 (mtm)
REVERT: A  352 PHE cc_start: 0.6630 (m-10) cc_final: 0.5932 (t80)
REVERT: A  402 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6618 (tt)
REVERT: A  452 SER cc_start: 0.8996 (t) cc_final: 0.8609 (p)
  outliers start: 36
  outliers final: 9
  residues processed: 109
  average time/residue: 0.8197
  time to fit residues: 98.6664
Evaluate side-chains
  95 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  401 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  402 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 33 optimal weight:    0.1980
   chunk 46 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0570
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 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 = 0.4072 r_free = 0.4072 target = 0.130966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.095264 restraints weight = 17105.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.30
r_work: 0.3340 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.7417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9096  Z= 0.150
  Angle     :  0.583  10.035  12362  Z= 0.289
  Chirality :  0.043   0.344   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.271  27.803   1222
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.77 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.25), residues: 1110
  helix:  2.20 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.65 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 396 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.022   0.001   PHE C 221 
 TYR   0.017   0.001   TYR C 451 
 ARG   0.002   0.000   ARG C 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00370 (    2)
  link_NAG-ASN         : angle       1.31373 (    6)
  hydrogen bonds       : bond        0.04535 (  732)
  hydrogen bonds       : angle       4.51168 ( 2160)
  covalent geometry    : bond        0.00341 ( 9094)
  covalent geometry    : angle       0.58202 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 MET cc_start: 0.8539 (mtt) cc_final: 0.8230 (mtm)
REVERT: C  352 PHE cc_start: 0.6669 (m-10) cc_final: 0.5973 (t80)
REVERT: C  402 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6564 (tt)
REVERT: C  452 SER cc_start: 0.9045 (t) cc_final: 0.8646 (p)
REVERT: C  519 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7039 (mp0)
REVERT: C  521 MET cc_start: 0.5566 (mmt) cc_final: 0.5157 (mmm)
REVERT: C  696 CYS cc_start: 0.7774 (m) cc_final: 0.7518 (t)
REVERT: A   37 MET cc_start: 0.8095 (ttm) cc_final: 0.7628 (ttm)
REVERT: A  193 TRP cc_start: 0.8203 (t-100) cc_final: 0.7884 (m-90)
REVERT: A  338 MET cc_start: 0.8521 (mtt) cc_final: 0.8319 (mtp)
REVERT: A  352 PHE cc_start: 0.6627 (m-10) cc_final: 0.5934 (t80)
REVERT: A  402 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6607 (tt)
REVERT: A  452 SER cc_start: 0.9004 (t) cc_final: 0.8517 (p)
REVERT: A  455 TYR cc_start: 0.7427 (m-80) cc_final: 0.6640 (m-80)
REVERT: A  519 GLU cc_start: 0.7674 (mm-30) cc_final: 0.6829 (mp0)
  outliers start: 24
  outliers final: 11
  residues processed: 103
  average time/residue: 1.0875
  time to fit residues: 121.8187
Evaluate side-chains
  91 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  673 LEU
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  673 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 96 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 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 = 0.4060 r_free = 0.4060 target = 0.130111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.094255 restraints weight = 17090.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.30
r_work: 0.3323 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.7705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9096  Z= 0.163
  Angle     :  0.590  10.023  12362  Z= 0.294
  Chirality :  0.043   0.349   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.236  26.252   1222
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 10.77 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.25), residues: 1110
  helix:  2.16 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.67 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 460 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.023   0.001   PHE C 221 
 TYR   0.019   0.001   TYR C 455 
 ARG   0.001   0.000   ARG C 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (    2)
  link_NAG-ASN         : angle       1.28795 (    6)
  hydrogen bonds       : bond        0.04611 (  732)
  hydrogen bonds       : angle       4.53774 ( 2160)
  covalent geometry    : bond        0.00375 ( 9094)
  covalent geometry    : angle       0.58902 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 MET cc_start: 0.8521 (mtt) cc_final: 0.8200 (mtm)
REVERT: C  352 PHE cc_start: 0.6725 (m-10) cc_final: 0.5977 (t80)
REVERT: C  402 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6416 (tt)
REVERT: C  452 SER cc_start: 0.9112 (t) cc_final: 0.8693 (p)
REVERT: C  455 TYR cc_start: 0.7448 (m-80) cc_final: 0.6693 (m-80)
REVERT: C  521 MET cc_start: 0.5437 (mmt) cc_final: 0.5072 (mmm)
REVERT: A  193 TRP cc_start: 0.8182 (t-100) cc_final: 0.7886 (m-90)
REVERT: A  352 PHE cc_start: 0.6696 (m-10) cc_final: 0.5958 (t80)
REVERT: A  402 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6554 (tt)
REVERT: A  452 SER cc_start: 0.9088 (t) cc_final: 0.8728 (p)
REVERT: A  667 ILE cc_start: 0.8355 (mt) cc_final: 0.8154 (mm)
  outliers start: 26
  outliers final: 7
  residues processed: 100
  average time/residue: 0.8892
  time to fit residues: 97.8746
Evaluate side-chains
  88 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 94 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 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 = 0.4063 r_free = 0.4063 target = 0.130241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.094460 restraints weight = 17355.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.30
r_work: 0.3330 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.7919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9096  Z= 0.153
  Angle     :  0.607  12.355  12362  Z= 0.298
  Chirality :  0.043   0.351   1502
  Planarity :  0.004   0.033   1476
  Dihedral  :  4.218  25.006   1222
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.99 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.25), residues: 1110
  helix:  2.15 (0.17), residues: 898
  sheet:  None (None), residues: 0
  loop :  0.71 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 396 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.021   0.001   PHE A 221 
 TYR   0.014   0.001   TYR C 451 
 ARG   0.001   0.000   ARG C 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (    2)
  link_NAG-ASN         : angle       1.30900 (    6)
  hydrogen bonds       : bond        0.04539 (  732)
  hydrogen bonds       : angle       4.56644 ( 2160)
  covalent geometry    : bond        0.00348 ( 9094)
  covalent geometry    : angle       0.60689 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: C  352 PHE cc_start: 0.6746 (m-10) cc_final: 0.6006 (t80)
REVERT: C  452 SER cc_start: 0.9105 (t) cc_final: 0.8665 (p)
REVERT: C  455 TYR cc_start: 0.7416 (m-80) cc_final: 0.6686 (m-80)
REVERT: C  521 MET cc_start: 0.5339 (mmt) cc_final: 0.5000 (mmm)
REVERT: A  193 TRP cc_start: 0.8185 (t-100) cc_final: 0.7876 (m-90)
REVERT: A  352 PHE cc_start: 0.6696 (m-10) cc_final: 0.5979 (t80)
REVERT: A  452 SER cc_start: 0.9115 (t) cc_final: 0.8722 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 91
  average time/residue: 0.9651
  time to fit residues: 96.2077
Evaluate side-chains
  87 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ASN
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain A residue   97 ASN
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 89 optimal weight:    0.0670
   chunk 80 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0770
   chunk 58 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 409 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.131486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.096207 restraints weight = 17193.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.31
r_work: 0.3373 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.8093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9096  Z= 0.134
  Angle     :  0.593  11.228  12362  Z= 0.291
  Chirality :  0.042   0.353   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.163  24.664   1222
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.01 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.25), residues: 1110
  helix:  2.17 (0.17), residues: 902
  sheet:  None (None), residues: 0
  loop :  0.63 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.018   0.001   PHE A 221 
 TYR   0.016   0.001   TYR A 407 
 ARG   0.002   0.000   ARG C 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    2)
  link_NAG-ASN         : angle       1.36813 (    6)
  hydrogen bonds       : bond        0.04347 (  732)
  hydrogen bonds       : angle       4.48656 ( 2160)
  covalent geometry    : bond        0.00293 ( 9094)
  covalent geometry    : angle       0.59245 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: C  352 PHE cc_start: 0.6713 (m-10) cc_final: 0.5995 (t80)
REVERT: C  409 GLN cc_start: 0.8491 (tp40) cc_final: 0.8096 (tt0)
REVERT: C  452 SER cc_start: 0.9131 (t) cc_final: 0.8717 (p)
REVERT: C  455 TYR cc_start: 0.7253 (m-80) cc_final: 0.6699 (m-80)
REVERT: C  521 MET cc_start: 0.5188 (mmt) cc_final: 0.4909 (mmm)
REVERT: A  193 TRP cc_start: 0.8119 (t-100) cc_final: 0.7866 (m-90)
REVERT: A  234 ASP cc_start: 0.8303 (m-30) cc_final: 0.7788 (t0)
REVERT: A  352 PHE cc_start: 0.6671 (m-10) cc_final: 0.5978 (t80)
REVERT: A  452 SER cc_start: 0.9123 (t) cc_final: 0.8742 (p)
  outliers start: 13
  outliers final: 5
  residues processed: 96
  average time/residue: 0.9460
  time to fit residues: 99.4834
Evaluate side-chains
  85 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  402 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 HIS
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.130473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.095077 restraints weight = 17168.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.30
r_work: 0.3336 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.8256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9096  Z= 0.148
  Angle     :  0.618  11.312  12362  Z= 0.301
  Chirality :  0.043   0.363   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.153  23.307   1222
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.11 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.25), residues: 1110
  helix:  2.14 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.69 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 460 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.020   0.001   PHE C 221 
 TYR   0.018   0.001   TYR A 451 
 ARG   0.001   0.000   ARG C 130 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00308 (    2)
  link_NAG-ASN         : angle       1.32298 (    6)
  hydrogen bonds       : bond        0.04481 (  732)
  hydrogen bonds       : angle       4.50900 ( 2160)
  covalent geometry    : bond        0.00336 ( 9094)
  covalent geometry    : angle       0.61786 (12356)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: C  352 PHE cc_start: 0.6738 (m-10) cc_final: 0.6008 (t80)
REVERT: C  409 GLN cc_start: 0.8601 (tp40) cc_final: 0.8374 (tt0)
REVERT: C  452 SER cc_start: 0.9149 (t) cc_final: 0.8730 (p)
REVERT: C  455 TYR cc_start: 0.7305 (m-80) cc_final: 0.6746 (m-80)
REVERT: C  521 MET cc_start: 0.5125 (mmt) cc_final: 0.4882 (mmm)
REVERT: A  193 TRP cc_start: 0.8148 (t-100) cc_final: 0.7905 (m-90)
REVERT: A  211 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8771 (mm)
REVERT: A  352 PHE cc_start: 0.6733 (m-10) cc_final: 0.6004 (t80)
REVERT: A  452 SER cc_start: 0.9134 (t) cc_final: 0.8756 (p)
REVERT: A  519 GLU cc_start: 0.7753 (mm-30) cc_final: 0.6851 (mp0)
  outliers start: 13
  outliers final: 6
  residues processed: 89
  average time/residue: 1.0173
  time to fit residues: 98.3597
Evaluate side-chains
  95 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  419 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  419 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 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 = 0.4035 r_free = 0.4035 target = 0.128249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.092211 restraints weight = 17119.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.29
r_work: 0.3282 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.8370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   9096  Z= 0.208
  Angle     :  0.660  11.459  12362  Z= 0.323
  Chirality :  0.044   0.380   1502
  Planarity :  0.004   0.032   1476
  Dihedral  :  4.231  20.487   1222
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.21 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.25), residues: 1110
  helix:  2.03 (0.17), residues: 896
  sheet:  None (None), residues: 0
  loop :  0.72 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 100 
 HIS   0.004   0.001   HIS A 716 
 PHE   0.025   0.002   PHE A 221 
 TYR   0.015   0.002   TYR A 451 
 ARG   0.001   0.000   ARG C  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00271 (    2)
  link_NAG-ASN         : angle       1.21937 (    6)
  hydrogen bonds       : bond        0.04812 (  732)
  hydrogen bonds       : angle       4.65102 ( 2160)
  covalent geometry    : bond        0.00492 ( 9094)
  covalent geometry    : angle       0.65924 (12356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7593.51 seconds
wall clock time: 131 minutes 51.91 seconds (7911.91 seconds total)