Starting phenix.real_space_refine
on Thu Jun  5 02:12:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1p_41822/06_2025/8u1p_41822.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1p_41822/06_2025/8u1p_41822.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1p_41822/06_2025/8u1p_41822.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1p_41822/06_2025/8u1p_41822.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1p_41822/06_2025/8u1p_41822.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1p_41822/06_2025/8u1p_41822.cif"
  }
  resolution = 3.3
  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=   0.005 sd=   0.205
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      26      5.16       5
     C    3110      2.51       5
     N     807      2.21       5
     O     911      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4854
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1639
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 10, 'TRANS': 201}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 114
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 70
    Chain: "H"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 812
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 136
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 4, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "L"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 749
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 7, 'TRANS': 98}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 733
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 98}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 851
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 49
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    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
  Time building chain proxies: 3.79, per 1000 atoms: 0.78
  Number of scatterers: 4854
  At special positions: 0
  Unit cell: (63.86, 75.19, 148.32, 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      26     16.00
     O     911      8.00
     N     807      7.00
     C    3110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 100B" distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 131 "
      " NAG D   1 " - " ASN A 190 "
      " NAG E   1 " - " ASN A 204 "
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 636.3 milliseconds
  

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1230

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 17 sheets defined
      1.2% alpha, 35.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 121
      No H-bonds generated for 'chain 'A' and resid 119 through 121'
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 4.100A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49
      removed outlier: 6.876A  pdb=" N   CYS A  49 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ILE A 142 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU A  84 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG A 140 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLU A 139 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLU A 127 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 75
      removed outlier: 3.841A  pdb=" N   SER A  75 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A 152 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107
    Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 189
    Processing sheet with id=AA5, first strand: chain 'A' and resid 212 through 216
      removed outlier: 6.546A  pdb=" N   LEU A 213 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   LYS A 287 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL A 215 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 284 " --> pdb=" O   CYS A 273 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   CYS A 273 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277
    Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6
      removed outlier: 3.895A  pdb=" N   VAL H   5 " --> pdb=" O   ARG H  23 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ARG H  23 " --> pdb=" O   VAL H   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.691A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER H  58 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.691A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.566A  pdb=" N   THR L 105 " --> pdb=" O   VAL L  10 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA L  83 " --> pdb=" O   VAL L 104 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   TRP L  34 " --> pdb=" O   VAL L  46 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.566A  pdb=" N   THR L 105 " --> pdb=" O   VAL L  10 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA L  83 " --> pdb=" O   VAL L 104 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23
      removed outlier: 3.522A  pdb=" N   ALA L  18 " --> pdb=" O   ILE L  74 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE L  20 " --> pdb=" O   LEU L  72 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12
      removed outlier: 7.138A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54
      removed outlier: 6.662A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   LYS C  49 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU C  33 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN C  34 " --> pdb=" O   GLN C  89 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 67
      removed outlier: 3.981A  pdb=" N   ASP C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.507A  pdb=" N   THR B  77 " --> pdb=" O   ASP B  72 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 57 through 59
      removed outlier: 6.838A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   TRP B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   MET B  34 " --> pdb=" O   TRP B  50 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    351 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 819
        1.32 -     1.45: 1422
        1.45 -     1.57: 2688
        1.57 -     1.70: 1
        1.70 -     1.82: 38
  Bond restraints: 4968
  Sorted by residual:
  bond pdb=" C   VAL A 224 "
       pdb=" N   LEU A 225 "
    ideal  model  delta    sigma   weight residual
    1.331  1.241  0.090 1.34e-02 5.57e+03 4.48e+01
  bond pdb=" C   LEU A 225 "
       pdb=" N   ALA A 226 "
    ideal  model  delta    sigma   weight residual
    1.331  1.246  0.084 1.48e-02 4.57e+03 3.26e+01
  bond pdb=" CA  ASN A 190 "
       pdb=" CB  ASN A 190 "
    ideal  model  delta    sigma   weight residual
    1.526  1.592 -0.066 1.76e-02 3.23e+03 1.42e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.473 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C   LEU A  98 "
       pdb=" N   PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 8.70e-03 1.32e+04 8.26e+00
  ... (remaining 4963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 6621
        2.64 -     5.28: 130
        5.28 -     7.92: 29
        7.92 -    10.55: 4
       10.55 -    13.19: 3
  Bond angle restraints: 6787
  Sorted by residual:
  angle pdb=" N   THR A 202 "
        pdb=" CA  THR A 202 "
        pdb=" C   THR A 202 "
      ideal   model   delta    sigma   weight residual
     108.34  120.69  -12.35 1.31e+00 5.83e-01 8.89e+01
  angle pdb=" C   ILE L  52 "
        pdb=" N   ARG L  53 "
        pdb=" CA  ARG L  53 "
      ideal   model   delta    sigma   weight residual
     120.94  134.13  -13.19 1.90e+00 2.77e-01 4.82e+01
  angle pdb=" C   ASN A 204 "
        pdb=" CA  ASN A 204 "
        pdb=" CB  ASN A 204 "
      ideal   model   delta    sigma   weight residual
     115.79  108.73    7.06 1.19e+00 7.06e-01 3.52e+01
  angle pdb=" C   TYR A 198 "
        pdb=" N   LEU A 199 "
        pdb=" CA  LEU A 199 "
      ideal   model   delta    sigma   weight residual
     123.30  114.96    8.34 1.44e+00 4.82e-01 3.36e+01
  angle pdb=" C   TYR L  49 "
        pdb=" N   ASP L  50 "
        pdb=" CA  ASP L  50 "
      ideal   model   delta    sigma   weight residual
     121.54  131.89  -10.35 1.91e+00 2.74e-01 2.94e+01
  ... (remaining 6782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 2752
       16.45 -    32.90: 154
       32.90 -    49.34: 31
       49.34 -    65.79: 7
       65.79 -    82.24: 5
  Dihedral angle restraints: 2949
    sinusoidal: 1018
      harmonic: 1931
  Sorted by residual:
  dihedral pdb=" CB  CYS B  97 "
           pdb=" SG  CYS B  97 "
           pdb=" SG  CYS B 100B"
           pdb=" CB  CYS B 100B"
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.94  -74.94     1      1.00e+01 1.00e-02 7.11e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.90  -58.90     1      1.00e+01 1.00e-02 4.64e+01
  dihedral pdb=" CA  LYS A 201 "
           pdb=" C   LYS A 201 "
           pdb=" N   THR A 202 "
           pdb=" CA  THR A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.23  -20.77     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 2946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.362: 780
       0.362 -    0.724: 1
       0.724 -    1.085: 0
       1.085 -    1.447: 0
       1.447 -    1.809: 1
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 204 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.59   -1.81 2.00e-01 2.50e+01 8.18e+01
  chirality pdb=" CB  ILE L  74 "
            pdb=" CA  ILE L  74 "
            pdb=" CG1 ILE L  74 "
            pdb=" CG2 ILE L  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.55e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A 131 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.92e+00
  ... (remaining 779 not shown)

  Planarity restraints: 868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 204 "    0.014 2.00e-02 2.50e+03   5.89e-02 4.34e+01
        pdb=" CG  ASN A 204 "   -0.074 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 204 "    0.068 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 204 "   -0.064 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "    0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  49 "   -0.044 2.00e-02 2.50e+03   2.87e-02 1.64e+01
        pdb=" CG  TYR L  49 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  49 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  49 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  49 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  49 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  49 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR L  49 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 204 "    0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" CG  ASN A 204 "   -0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 204 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 204 "    0.020 2.00e-02 2.50e+03
  ... (remaining 865 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1028
        2.79 -     3.32: 4197
        3.32 -     3.85: 7622
        3.85 -     4.37: 8658
        4.37 -     4.90: 15463
  Nonbonded interactions: 36968
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 182 "
            pdb=" O   GLY A 220 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG  SER H  98 "
            pdb=" O   ALA H 100 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" NH2 ARG L  53 "
            pdb=" O   GLU L  59 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OE2 GLU B  46 "
            pdb=" NH1 ARG B  62 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   SER C  50 "
            pdb=" OG  SER C  50 "
     model   vdw
     2.360 3.040
  ... (remaining 36963 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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:             3.140
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.320
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
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      :  0.005   0.090   4980  Z= 0.268
  Angle     :  1.098  20.826   6816  Z= 0.561
  Chirality :  0.088   1.809    782
  Planarity :  0.007   0.077    865
  Dihedral  : 11.479  82.240   1698
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.82 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.55 (0.36), residues: 213
  loop : -1.10 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 103 
 HIS   0.005   0.001   HIS B  35 
 PHE   0.033   0.003   PHE A 235 
 TYR   0.066   0.002   TYR L  49 
 ARG   0.014   0.002   ARG B  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04042 (    3)
  link_NAG-ASN         : angle      14.07829 (    9)
  link_BETA1-4         : bond        0.01629 (    2)
  link_BETA1-4         : angle       6.49458 (    6)
  hydrogen bonds       : bond        0.29259 (  129)
  hydrogen bonds       : angle      11.23736 (  351)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       1.10878 (   14)
  covalent geometry    : bond        0.00483 ( 4968)
  covalent geometry    : angle       0.95254 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8955 (mp) cc_final: 0.8687 (mt)
REVERT: L   41 GLN cc_start: 0.7919 (mp10) cc_final: 0.7648 (mp10)
REVERT: L   61 PHE cc_start: 0.7535 (m-80) cc_final: 0.7001 (m-80)
REVERT: C   35 TRP cc_start: 0.6972 (m100) cc_final: 0.6263 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1975
  time to fit residues: 29.2484
Evaluate side-chains
  92 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0010
   chunk 26 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 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 = 0.3732 r_free = 0.3732 target = 0.093077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.086970 restraints weight = 15249.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.64
r_work: 0.3537 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4980  Z= 0.218
  Angle     :  0.855  16.499   6816  Z= 0.421
  Chirality :  0.058   0.714    782
  Planarity :  0.006   0.055    865
  Dihedral  :  6.790  49.976    822
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  :  9.67 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.74 (0.32), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.71 (0.33), residues: 219
  loop : -1.13 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B  47 
 HIS   0.006   0.001   HIS B  35 
 PHE   0.026   0.002   PHE A 235 
 TYR   0.033   0.002   TYR L  49 
 ARG   0.005   0.001   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02067 (    3)
  link_NAG-ASN         : angle      10.15958 (    9)
  link_BETA1-4         : bond        0.00423 (    2)
  link_BETA1-4         : angle       4.63986 (    6)
  hydrogen bonds       : bond        0.04872 (  129)
  hydrogen bonds       : angle       7.96358 (  351)
  SS BOND              : bond        0.01007 (    7)
  SS BOND              : angle       1.52518 (   14)
  covalent geometry    : bond        0.00477 ( 4968)
  covalent geometry    : angle       0.75775 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 TYR cc_start: 0.8245 (p90) cc_final: 0.7898 (p90)
REVERT: L   60 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7167 (ptp90)
REVERT: C   35 TRP cc_start: 0.7693 (m100) cc_final: 0.6435 (m100)
REVERT: C   48 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7634 (pt)
REVERT: B   34 MET cc_start: 0.7221 (mmm) cc_final: 0.6448 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1739
  time to fit residues: 21.9673
Evaluate side-chains
  97 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 TYR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   60 ARG
Chi-restraints excluded: chain L residue   74 ILE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0030
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0020
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
A 281 ASN
L  36 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.092000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.085927 restraints weight = 15500.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.65
r_work: 0.3512 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4980  Z= 0.145
  Angle     :  0.739  14.087   6816  Z= 0.360
  Chirality :  0.053   0.590    782
  Planarity :  0.005   0.054    865
  Dihedral  :  6.729  51.822    822
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 14.62 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.65 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.80 (0.33), residues: 220
  loop : -1.09 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  47 
 HIS   0.004   0.001   HIS B  35 
 PHE   0.023   0.002   PHE A 235 
 TYR   0.021   0.002   TYR H  33 
 ARG   0.002   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01839 (    3)
  link_NAG-ASN         : angle       8.92721 (    9)
  link_BETA1-4         : bond        0.00563 (    2)
  link_BETA1-4         : angle       4.28802 (    6)
  hydrogen bonds       : bond        0.03818 (  129)
  hydrogen bonds       : angle       6.87859 (  351)
  SS BOND              : bond        0.00345 (    7)
  SS BOND              : angle       1.11969 (   14)
  covalent geometry    : bond        0.00317 ( 4968)
  covalent geometry    : angle       0.65157 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 TRP cc_start: 0.7811 (m100) cc_final: 0.6547 (m100)
  outliers start: 16
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2517
  time to fit residues: 33.1148
Evaluate side-chains
  100 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  198 TYR
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain B residue   92 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.086670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.080761 restraints weight = 15826.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.54
r_work: 0.3393 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   4980  Z= 0.228
  Angle     :  0.797  14.024   6816  Z= 0.397
  Chirality :  0.055   0.577    782
  Planarity :  0.006   0.054    865
  Dihedral  :  7.328  57.270    822
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 16.75 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.85 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.73 (0.33), residues: 221
  loop : -1.28 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B  47 
 HIS   0.005   0.002   HIS B  35 
 PHE   0.019   0.003   PHE B  63 
 TYR   0.025   0.002   TYR H  33 
 ARG   0.003   0.001   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01745 (    3)
  link_NAG-ASN         : angle       8.31369 (    9)
  link_BETA1-4         : bond        0.00293 (    2)
  link_BETA1-4         : angle       4.47441 (    6)
  hydrogen bonds       : bond        0.03639 (  129)
  hydrogen bonds       : angle       6.88239 (  351)
  SS BOND              : bond        0.00713 (    7)
  SS BOND              : angle       1.31150 (   14)
  covalent geometry    : bond        0.00514 ( 4968)
  covalent geometry    : angle       0.72480 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: L   60 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7617 (ptp90)
REVERT: C   35 TRP cc_start: 0.8084 (m100) cc_final: 0.6497 (m100)
REVERT: C   78 LEU cc_start: 0.8048 (tp) cc_final: 0.7773 (tp)
REVERT: B   46 GLU cc_start: 0.8507 (tt0) cc_final: 0.8298 (tt0)
  outliers start: 21
  outliers final: 14
  residues processed: 104
  average time/residue: 0.2903
  time to fit residues: 39.2945
Evaluate side-chains
  101 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  198 TYR
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain B residue   69 MET
Chi-restraints excluded: chain B residue   86 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0770
   chunk 16 optimal weight:    0.0570
   chunk 57 optimal weight:    0.0980
   chunk 15 optimal weight:    0.3980
   chunk 51 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.1656

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.089647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.083500 restraints weight = 15683.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.67
r_work: 0.3450 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4980  Z= 0.122
  Angle     :  0.707  12.981   6816  Z= 0.345
  Chirality :  0.052   0.524    782
  Planarity :  0.005   0.049    865
  Dihedral  :  7.079  56.567    822
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 19.58 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.81 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.73 (0.34), residues: 221
  loop : -1.24 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.013   0.002   PHE A 188 
 TYR   0.017   0.001   TYR H 100B
 ARG   0.003   0.000   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01647 (    3)
  link_NAG-ASN         : angle       7.83182 (    9)
  link_BETA1-4         : bond        0.00534 (    2)
  link_BETA1-4         : angle       3.87747 (    6)
  hydrogen bonds       : bond        0.03340 (  129)
  hydrogen bonds       : angle       6.34722 (  351)
  SS BOND              : bond        0.00291 (    7)
  SS BOND              : angle       1.41643 (   14)
  covalent geometry    : bond        0.00267 ( 4968)
  covalent geometry    : angle       0.63480 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: L   60 ARG cc_start: 0.7543 (ptp90) cc_final: 0.7289 (ptp90)
REVERT: L   81 ASP cc_start: 0.7903 (t0) cc_final: 0.7682 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 104
  average time/residue: 0.4071
  time to fit residues: 53.0092
Evaluate side-chains
  101 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0770
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.087236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.081147 restraints weight = 15933.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.60
r_work: 0.3400 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4980  Z= 0.176
  Angle     :  0.740  13.024   6816  Z= 0.362
  Chirality :  0.053   0.539    782
  Planarity :  0.005   0.051    865
  Dihedral  :  7.150  57.894    822
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 21.70 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.89 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.65 (0.33), residues: 223
  loop : -1.28 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B  47 
 HIS   0.003   0.001   HIS A 184 
 PHE   0.016   0.002   PHE A 235 
 TYR   0.018   0.002   TYR A 198 
 ARG   0.005   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01584 (    3)
  link_NAG-ASN         : angle       7.50072 (    9)
  link_BETA1-4         : bond        0.00481 (    2)
  link_BETA1-4         : angle       3.95256 (    6)
  hydrogen bonds       : bond        0.03221 (  129)
  hydrogen bonds       : angle       6.37821 (  351)
  SS BOND              : bond        0.00506 (    7)
  SS BOND              : angle       1.29386 (   14)
  covalent geometry    : bond        0.00402 ( 4968)
  covalent geometry    : angle       0.67627 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.7178 (t80)
REVERT: L   60 ARG cc_start: 0.7503 (ptp90) cc_final: 0.7282 (ptp90)
REVERT: C   35 TRP cc_start: 0.7990 (m100) cc_final: 0.6334 (m100)
  outliers start: 18
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1959
  time to fit residues: 23.6857
Evaluate side-chains
  101 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0470
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.087233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.081168 restraints weight = 15675.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.57
r_work: 0.3409 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4980  Z= 0.155
  Angle     :  0.724  12.661   6816  Z= 0.354
  Chirality :  0.052   0.522    782
  Planarity :  0.005   0.049    865
  Dihedral  :  7.134  58.477    822
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 20.52 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.93 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.61 (0.34), residues: 221
  loop : -1.30 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  50 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.015   0.002   PHE A 235 
 TYR   0.016   0.002   TYR H  97 
 ARG   0.010   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01526 (    3)
  link_NAG-ASN         : angle       7.29459 (    9)
  link_BETA1-4         : bond        0.00427 (    2)
  link_BETA1-4         : angle       3.78644 (    6)
  hydrogen bonds       : bond        0.03081 (  129)
  hydrogen bonds       : angle       6.32191 (  351)
  SS BOND              : bond        0.00451 (    7)
  SS BOND              : angle       1.28764 (   14)
  covalent geometry    : bond        0.00353 ( 4968)
  covalent geometry    : angle       0.66340 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.6630 (m-10) cc_final: 0.6391 (m-10)
REVERT: H   71 MET cc_start: 0.6492 (ptt) cc_final: 0.6093 (ptp)
REVERT: L   49 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7252 (t80)
REVERT: C   35 TRP cc_start: 0.7947 (m100) cc_final: 0.6243 (m100)
  outliers start: 19
  outliers final: 15
  residues processed: 98
  average time/residue: 0.2042
  time to fit residues: 25.9533
Evaluate side-chains
  101 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain B residue   86 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 60 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN
C  38 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.076404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.070667 restraints weight = 16299.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.50
r_work: 0.3337 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4980  Z= 0.215
  Angle     :  0.778  12.833   6816  Z= 0.387
  Chirality :  0.054   0.538    782
  Planarity :  0.005   0.049    865
  Dihedral  :  7.376  59.545    822
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 22.41 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.08 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.51 (0.34), residues: 220
  loop : -1.40 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B  47 
 HIS   0.004   0.001   HIS B  79 
 PHE   0.018   0.002   PHE A 235 
 TYR   0.020   0.002   TYR L  49 
 ARG   0.009   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01459 (    3)
  link_NAG-ASN         : angle       7.24969 (    9)
  link_BETA1-4         : bond        0.00501 (    2)
  link_BETA1-4         : angle       3.94342 (    6)
  hydrogen bonds       : bond        0.03224 (  129)
  hydrogen bonds       : angle       6.58485 (  351)
  SS BOND              : bond        0.00589 (    7)
  SS BOND              : angle       1.34184 (   14)
  covalent geometry    : bond        0.00490 ( 4968)
  covalent geometry    : angle       0.72131 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8446 (t)
REVERT: A  235 PHE cc_start: 0.7226 (m-10) cc_final: 0.7001 (m-10)
REVERT: H   71 MET cc_start: 0.6873 (ptt) cc_final: 0.6397 (ptp)
REVERT: L   49 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.7564 (t80)
REVERT: C   78 LEU cc_start: 0.8127 (tp) cc_final: 0.7859 (tp)
REVERT: B   46 GLU cc_start: 0.8569 (tt0) cc_final: 0.8367 (tt0)
  outliers start: 18
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1850
  time to fit residues: 23.7945
Evaluate side-chains
  100 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    8.9990
   chunk 5 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 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 = 0.3510 r_free = 0.3510 target = 0.076737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.071071 restraints weight = 16332.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.48
r_work: 0.3346 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.4911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4980  Z= 0.180
  Angle     :  0.752  12.414   6816  Z= 0.372
  Chirality :  0.053   0.514    782
  Planarity :  0.005   0.057    865
  Dihedral  :  7.277  59.505    822
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 22.64 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.12 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.44 (0.34), residues: 220
  loop : -1.40 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B  47 
 HIS   0.003   0.001   HIS A 184 
 PHE   0.016   0.002   PHE A 235 
 TYR   0.020   0.002   TYR H  97 
 ARG   0.009   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01431 (    3)
  link_NAG-ASN         : angle       7.03309 (    9)
  link_BETA1-4         : bond        0.00465 (    2)
  link_BETA1-4         : angle       3.70642 (    6)
  hydrogen bonds       : bond        0.03127 (  129)
  hydrogen bonds       : angle       6.43195 (  351)
  SS BOND              : bond        0.00435 (    7)
  SS BOND              : angle       1.36438 (   14)
  covalent geometry    : bond        0.00409 ( 4968)
  covalent geometry    : angle       0.69693 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.7205 (m-10) cc_final: 0.6794 (m-10)
REVERT: H   71 MET cc_start: 0.6881 (ptt) cc_final: 0.6396 (ptp)
REVERT: L   49 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7584 (t80)
REVERT: L   81 ASP cc_start: 0.8014 (t0) cc_final: 0.7342 (t0)
REVERT: C   78 LEU cc_start: 0.8101 (tp) cc_final: 0.7870 (tp)
REVERT: C   93 ARG cc_start: 0.6198 (mtm180) cc_final: 0.5812 (mtm-85)
REVERT: B   33 TYR cc_start: 0.8513 (m-80) cc_final: 0.8303 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1949
  time to fit residues: 24.5258
Evaluate side-chains
  102 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 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 = 0.3488 r_free = 0.3488 target = 0.075795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.070148 restraints weight = 16474.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.48
r_work: 0.3326 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4980  Z= 0.199
  Angle     :  0.770  12.387   6816  Z= 0.383
  Chirality :  0.054   0.520    782
  Planarity :  0.005   0.055    865
  Dihedral  :  7.279  59.341    822
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.93 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.17 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.45 (0.35), residues: 220
  loop : -1.46 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B  47 
 HIS   0.004   0.001   HIS B  35 
 PHE   0.019   0.002   PHE A 235 
 TYR   0.017   0.002   TYR L  49 
 ARG   0.010   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01357 (    3)
  link_NAG-ASN         : angle       6.93321 (    9)
  link_BETA1-4         : bond        0.00469 (    2)
  link_BETA1-4         : angle       3.86057 (    6)
  hydrogen bonds       : bond        0.03204 (  129)
  hydrogen bonds       : angle       6.56212 (  351)
  SS BOND              : bond        0.00495 (    7)
  SS BOND              : angle       1.38831 (   14)
  covalent geometry    : bond        0.00451 ( 4968)
  covalent geometry    : angle       0.71682 ( 6787)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.7416 (m-10) cc_final: 0.7127 (m-10)
REVERT: H   71 MET cc_start: 0.7048 (ptt) cc_final: 0.6583 (ptp)
REVERT: L   49 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.7663 (t80)
REVERT: C   78 LEU cc_start: 0.8169 (tp) cc_final: 0.7938 (tp)
REVERT: C   93 ARG cc_start: 0.6371 (mtm180) cc_final: 0.5960 (mtm-85)
  outliers start: 16
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2012
  time to fit residues: 26.1369
Evaluate side-chains
  106 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 58 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0070
   chunk 26 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 57 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
** C  34 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 = 0.3559 r_free = 0.3559 target = 0.084469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.078439 restraints weight = 16252.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.55
r_work: 0.3361 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4980  Z= 0.143
  Angle     :  0.736  11.874   6816  Z= 0.362
  Chirality :  0.052   0.496    782
  Planarity :  0.005   0.053    865
  Dihedral  :  7.034  57.315    822
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.58 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.04 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.57 (0.35), residues: 217
  loop : -1.38 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B  50 
 HIS   0.004   0.001   HIS B  35 
 PHE   0.016   0.002   PHE A 235 
 TYR   0.021   0.002   TYR B  96 
 ARG   0.010   0.001   ARG C  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01328 (    3)
  link_NAG-ASN         : angle       6.71739 (    9)
  link_BETA1-4         : bond        0.00556 (    2)
  link_BETA1-4         : angle       3.68780 (    6)
  hydrogen bonds       : bond        0.03085 (  129)
  hydrogen bonds       : angle       6.29555 (  351)
  SS BOND              : bond        0.00392 (    7)
  SS BOND              : angle       1.13864 (   14)
  covalent geometry    : bond        0.00325 ( 4968)
  covalent geometry    : angle       0.68515 ( 6787)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3022.74 seconds
wall clock time: 54 minutes 48.74 seconds (3288.74 seconds total)