Starting phenix.real_space_refine
on Thu Jul 24 03:14:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lrs_23498/07_2025/7lrs_23498.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lrs_23498/07_2025/7lrs_23498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2025/7lrs_23498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2025/7lrs_23498.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2025/7lrs_23498.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2025/7lrs_23498.cif"
  }
  resolution = 3.89
  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=   0.006
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      22      5.16       5
     C    3100      2.51       5
     N     812      2.21       5
     O     978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4912
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1551
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "D"
      Number of atoms: 1625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1625
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 1636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1636
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200}
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.69, per 1000 atoms: 1.16
  Number of scatterers: 4912
  At special positions: 0
  Unit cell: (79.515, 66.69, 140.22, 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      22     16.00
     O     978      8.00
     N     812      7.00
     C    3100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  97 " - pdb=" SG  CYS D 100B" distance=2.03
    Simple disulfide: pdb=" SG  CYS D 140 " - pdb=" SG  CYS D 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 134 " - pdb=" SG  CYS E 194 " distance=2.04

  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
    ALPHA1-3
      " BMA A   3 " - " MAN A   4 "
    ALPHA1-6
      " BMA A   3 " - " MAN A   5 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A   1 " - " ASN C 343 "
      " NAG B   1 " - " ASN D  96 "
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 607.3 milliseconds
  

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 16 sheets defined
      3.7% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 366 through 371
      removed outlier: 4.186A  pdb=" N   SER C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 87
      removed outlier: 3.795A  pdb=" N   THR D  87 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 202
      removed outlier: 3.664A  pdb=" N   LEU E 201 " --> pdb=" O   HIS E 198 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   SER E 202 " --> pdb=" O   GLN E 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 198 through 202'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 357 through 358
      removed outlier: 3.768A  pdb=" N   ILE C 402 " --> pdb=" O   TYR C 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'D' and resid 3 through 6
      removed outlier: 3.749A  pdb=" N   GLN D   3 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER D  25 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL D   5 " --> pdb=" O   LYS D  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.736A  pdb=" N   THR D 110 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS D  12 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 36
      removed outlier: 3.786A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 38 through 39
    Processing sheet with id=AA7, first strand: chain 'D' and resid 93 through 94
      removed outlier: 3.505A  pdb=" N   ILE D 102 " --> pdb=" O   ALA D  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 97 through 98
      removed outlier: 3.631A  pdb=" N   VAL D 100A" --> pdb=" O   SER D  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124
      removed outlier: 3.515A  pdb=" N   GLY D 139 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER D 180 " --> pdb=" O   CYS D 140 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TYR D 176 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 124
      removed outlier: 3.515A  pdb=" N   GLY D 139 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER D 180 " --> pdb=" O   CYS D 140 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TYR D 176 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 151 through 152
      removed outlier: 4.133A  pdb=" N   THR D 151 " --> pdb=" O   ASN D 199 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ASN D 199 " --> pdb=" O   THR D 151 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12
    Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 22
    Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 49
      removed outlier: 6.681A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL E  85 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 114 through 118
      removed outlier: 3.594A  pdb=" N   PHE E 116 " --> pdb=" O   LEU E 135 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL E 133 " --> pdb=" O   PHE E 118 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL E 132 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   TYR E 173 " --> pdb=" O   ASN E 138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 145 through 148
      removed outlier: 4.106A  pdb=" N   LYS E 145 " --> pdb=" O   THR E 197 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR E 197 " --> pdb=" O   LYS E 145 " (cutoff:3.500A)

    86 hydrogen bonds defined for protein.
    225 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: 1.35

  Time building geometry restraints manager: 1.65 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: 1550
        1.34 -     1.46: 1294
        1.46 -     1.58: 2160
        1.58 -     1.70: 0
        1.70 -     1.82: 26
  Bond restraints: 5030
  Sorted by residual:
  bond pdb=" C1  MAN A   4 "
       pdb=" C2  MAN A   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.580 -0.054 2.00e-02 2.50e+03 7.27e+00
  bond pdb=" C1  MAN A   5 "
       pdb=" C2  MAN A   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.567 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C1  MAN A   4 "
       pdb=" O5  MAN A   4 "
    ideal  model  delta    sigma   weight residual
    1.399  1.437 -0.038 2.00e-02 2.50e+03 3.61e+00
  bond pdb=" C5  MAN A   5 "
       pdb=" O5  MAN A   5 "
    ideal  model  delta    sigma   weight residual
    1.418  1.455 -0.037 2.00e-02 2.50e+03 3.46e+00
  bond pdb=" C1  BMA A   3 "
       pdb=" C2  BMA A   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.556 -0.037 2.00e-02 2.50e+03 3.40e+00
  ... (remaining 5025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 6592
        1.66 -     3.31: 200
        3.31 -     4.97: 43
        4.97 -     6.63: 10
        6.63 -     8.28: 2
  Bond angle restraints: 6847
  Sorted by residual:
  angle pdb=" CA  GLY C 502 "
        pdb=" C   GLY C 502 "
        pdb=" N   VAL C 503 "
      ideal   model   delta    sigma   weight residual
     114.23  116.84   -2.61 8.80e-01 1.29e+00 8.77e+00
  angle pdb=" C   PHE C 486 "
        pdb=" N   ASN C 487 "
        pdb=" CA  ASN C 487 "
      ideal   model   delta    sigma   weight residual
     122.08  126.25   -4.17 1.47e+00 4.63e-01 8.06e+00
  angle pdb=" C   THR E 109 "
        pdb=" N   VAL E 110 "
        pdb=" CA  VAL E 110 "
      ideal   model   delta    sigma   weight residual
     121.97  126.69   -4.72 1.80e+00 3.09e-01 6.87e+00
  angle pdb=" N   LYS D 201 "
        pdb=" CA  LYS D 201 "
        pdb=" C   LYS D 201 "
      ideal   model   delta    sigma   weight residual
     109.81  115.60   -5.79 2.21e+00 2.05e-01 6.87e+00
  angle pdb=" CA  ASP E 185 "
        pdb=" C   ASP E 185 "
        pdb=" N   TYR E 186 "
      ideal   model   delta    sigma   weight residual
     119.71  116.70    3.01 1.17e+00 7.31e-01 6.64e+00
  ... (remaining 6842 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.68: 2866
       22.68 -    45.36: 190
       45.36 -    68.03: 15
       68.03 -    90.71: 23
       90.71 -   113.39: 10
  Dihedral angle restraints: 3104
    sinusoidal: 1291
      harmonic: 1813
  Sorted by residual:
  dihedral pdb=" CB  CYS E  23 "
           pdb=" SG  CYS E  23 "
           pdb=" SG  CYS E  88 "
           pdb=" CB  CYS E  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.08  -70.08     1      1.00e+01 1.00e-02 6.33e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  92 "
           pdb=" CB  CYS D  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.13  -50.13     1      1.00e+01 1.00e-02 3.45e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.21   47.21     1      1.00e+01 1.00e-02 3.08e+01
  ... (remaining 3101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 638
       0.055 -    0.110: 121
       0.110 -    0.165: 22
       0.165 -    0.220: 2
       0.220 -    0.276: 3
  Chirality restraints: 786
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C5  BMA A   3 "
            pdb=" C4  BMA A   3 "
            pdb=" C6  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 783 not shown)

  Planarity restraints: 871
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 146 "   -0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO D 147 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 147 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 147 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E  79 "    0.024 5.00e-02 4.00e+02   3.63e-02 2.10e+00
        pdb=" N   PRO E  80 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO E  80 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E  80 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "   -0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO C 521 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 868 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 297
        2.72 -     3.27: 4858
        3.27 -     3.81: 7198
        3.81 -     4.36: 8340
        4.36 -     4.90: 14373
  Nonbonded interactions: 35066
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E  82 "
            pdb=" OH  TYR E  86 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   SER E 171 "
            pdb=" OG  SER E 171 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG  SER E 182 "
            pdb=" NZ  LYS E 188 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O4  MAN A   5 "
            pdb=" O6  MAN A   5 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OE2 GLU E 105 "
            pdb=" NE2 GLN E 166 "
     model   vdw
     2.302 3.120
  ... (remaining 35061 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             145.860
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.200
  Find NCS groups from input model:        0.070
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  167.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.003   0.054   5047  Z= 0.168
  Angle     :  0.728   8.282   6889  Z= 0.353
  Chirality :  0.048   0.276    786
  Planarity :  0.005   0.043    869
  Dihedral  : 16.973 113.391   1917
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.70 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.37 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.33), residues: 617
  helix: -4.54 (0.94), residues: 13
  sheet: -1.37 (0.38), residues: 207
  loop : -2.18 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 353 
 HIS   0.003   0.001   HIS D 200 
 PHE   0.013   0.001   PHE E 118 
 TYR   0.011   0.001   TYR D 145 
 ARG   0.004   0.001   ARG D  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    2)
  link_NAG-ASN         : angle       0.99703 (    6)
  link_ALPHA1-6        : bond        0.00969 (    1)
  link_ALPHA1-6        : angle       1.52289 (    3)
  link_BETA1-4         : bond        0.00370 (    4)
  link_BETA1-4         : angle       2.05235 (   12)
  link_ALPHA1-3        : bond        0.00729 (    1)
  link_ALPHA1-3        : angle       1.09259 (    3)
  hydrogen bonds       : bond        0.29489 (   75)
  hydrogen bonds       : angle      10.62608 (  225)
  SS BOND              : bond        0.00288 (    9)
  SS BOND              : angle       1.46575 (   18)
  covalent geometry    : bond        0.00350 ( 5030)
  covalent geometry    : angle       0.71932 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.505 
Fit side-chains
REVERT: D   82 LEU cc_start: 0.8695 (mt) cc_final: 0.8347 (mm)
REVERT: D   90 TYR cc_start: 0.8121 (m-10) cc_final: 0.7531 (m-80)
REVERT: D  155 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8181 (t0)
REVERT: D  201 LYS cc_start: 0.8906 (pptt) cc_final: 0.8632 (pptt)
REVERT: E   82 ASP cc_start: 0.8046 (t70) cc_final: 0.7829 (t0)
REVERT: E  123 GLU cc_start: 0.8605 (tp30) cc_final: 0.8375 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1727
  time to fit residues: 22.4466
Evaluate side-chains
  82 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  155 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0570
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.066971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.058021 restraints weight = 19368.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.059822 restraints weight = 10580.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.061044 restraints weight = 6639.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5047  Z= 0.148
  Angle     :  0.745  10.481   6889  Z= 0.358
  Chirality :  0.047   0.170    786
  Planarity :  0.005   0.043    869
  Dihedral  : 13.399  90.052    839
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 10.70 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.02 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.33), residues: 617
  helix: -4.01 (1.14), residues: 13
  sheet: -1.08 (0.38), residues: 200
  loop : -2.34 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.015   0.001   PHE E 118 
 TYR   0.011   0.001   TYR D 194 
 ARG   0.006   0.001   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    2)
  link_NAG-ASN         : angle       1.07101 (    6)
  link_ALPHA1-6        : bond        0.01647 (    1)
  link_ALPHA1-6        : angle       2.14526 (    3)
  link_BETA1-4         : bond        0.00482 (    4)
  link_BETA1-4         : angle       2.71957 (   12)
  link_ALPHA1-3        : bond        0.01474 (    1)
  link_ALPHA1-3        : angle       2.62811 (    3)
  hydrogen bonds       : bond        0.04088 (   75)
  hydrogen bonds       : angle       7.49316 (  225)
  SS BOND              : bond        0.00580 (    9)
  SS BOND              : angle       1.60894 (   18)
  covalent geometry    : bond        0.00331 ( 5030)
  covalent geometry    : angle       0.72939 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
REVERT: C  389 ASP cc_start: 0.8446 (p0) cc_final: 0.8135 (p0)
REVERT: D  155 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8340 (t0)
REVERT: D  176 TYR cc_start: 0.8010 (m-10) cc_final: 0.7707 (m-10)
REVERT: E  123 GLU cc_start: 0.8741 (tp30) cc_final: 0.8459 (tp30)
REVERT: E  167 ASP cc_start: 0.8317 (t70) cc_final: 0.8114 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 91
  average time/residue: 0.1964
  time to fit residues: 23.0675
Evaluate side-chains
  83 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  155 ASN
Chi-restraints excluded: chain D residue  198 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0170
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.065779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.056710 restraints weight = 19529.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.058580 restraints weight = 10519.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.059842 restraints weight = 6537.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5047  Z= 0.150
  Angle     :  0.713  10.963   6889  Z= 0.342
  Chirality :  0.046   0.151    786
  Planarity :  0.005   0.045    869
  Dihedral  : 11.772  81.994    839
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 10.05 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.91 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.68 (0.33), residues: 617
  helix: -2.18 (2.16), residues: 7
  sheet: -0.92 (0.39), residues: 189
  loop : -2.34 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.009   0.001   PHE D 146 
 TYR   0.016   0.001   TYR D 194 
 ARG   0.004   0.000   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00319 (    2)
  link_NAG-ASN         : angle       1.10149 (    6)
  link_ALPHA1-6        : bond        0.01931 (    1)
  link_ALPHA1-6        : angle       2.39294 (    3)
  link_BETA1-4         : bond        0.00493 (    4)
  link_BETA1-4         : angle       2.56151 (   12)
  link_ALPHA1-3        : bond        0.01501 (    1)
  link_ALPHA1-3        : angle       1.90175 (    3)
  hydrogen bonds       : bond        0.03448 (   75)
  hydrogen bonds       : angle       6.77967 (  225)
  SS BOND              : bond        0.00408 (    9)
  SS BOND              : angle       1.30464 (   18)
  covalent geometry    : bond        0.00330 ( 5030)
  covalent geometry    : angle       0.70073 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: D  155 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8285 (t0)
REVERT: D  176 TYR cc_start: 0.8046 (m-10) cc_final: 0.7666 (m-10)
REVERT: E   82 ASP cc_start: 0.8804 (t0) cc_final: 0.8569 (t0)
REVERT: E  123 GLU cc_start: 0.8714 (tp30) cc_final: 0.8492 (tp30)
REVERT: E  167 ASP cc_start: 0.8306 (t70) cc_final: 0.8041 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 88
  average time/residue: 0.2032
  time to fit residues: 23.9357
Evaluate side-chains
  82 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  155 ASN
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  194 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0370
   overall best weight:    0.2016

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

Flipped N/Q/H residues before XYZ refinement:
C 388 ASN
** C 409 GLN ** 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 = 0.3321 r_free = 0.3321 target = 0.067135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.058023 restraints weight = 19524.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.059916 restraints weight = 10506.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.061180 restraints weight = 6528.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5047  Z= 0.122
  Angle     :  0.689  10.688   6889  Z= 0.331
  Chirality :  0.046   0.148    786
  Planarity :  0.005   0.041    869
  Dihedral  : 10.258  72.022    839
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  9.56 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.40 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.61 (0.33), residues: 617
  helix: -3.66 (1.24), residues: 13
  sheet: -0.93 (0.38), residues: 200
  loop : -2.21 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.005   0.001   PHE D 146 
 TYR   0.012   0.001   TYR D 194 
 ARG   0.006   0.000   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00303 (    2)
  link_NAG-ASN         : angle       0.88896 (    6)
  link_ALPHA1-6        : bond        0.01784 (    1)
  link_ALPHA1-6        : angle       2.63565 (    3)
  link_BETA1-4         : bond        0.00458 (    4)
  link_BETA1-4         : angle       2.36522 (   12)
  link_ALPHA1-3        : bond        0.01349 (    1)
  link_ALPHA1-3        : angle       1.90964 (    3)
  hydrogen bonds       : bond        0.02842 (   75)
  hydrogen bonds       : angle       6.35721 (  225)
  SS BOND              : bond        0.00207 (    9)
  SS BOND              : angle       1.08915 (   18)
  covalent geometry    : bond        0.00273 ( 5030)
  covalent geometry    : angle       0.67809 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.575 
Fit side-chains
REVERT: D  155 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8251 (t0)
REVERT: D  176 TYR cc_start: 0.8054 (m-10) cc_final: 0.7725 (m-10)
REVERT: E   82 ASP cc_start: 0.8770 (t0) cc_final: 0.8522 (t0)
REVERT: E  123 GLU cc_start: 0.8626 (tp30) cc_final: 0.8374 (tp30)
REVERT: E  167 ASP cc_start: 0.8302 (t70) cc_final: 0.8083 (m-30)
REVERT: E  186 TYR cc_start: 0.7560 (t80) cc_final: 0.7323 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 89
  average time/residue: 0.1919
  time to fit residues: 21.9187
Evaluate side-chains
  83 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  155 ASN
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  194 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 519 HIS
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  90 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.063995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.054845 restraints weight = 19696.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.056751 restraints weight = 10497.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.058056 restraints weight = 6472.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5047  Z= 0.188
  Angle     :  0.741  11.854   6889  Z= 0.361
  Chirality :  0.046   0.165    786
  Planarity :  0.006   0.051    869
  Dihedral  :  9.933  70.545    839
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 11.18 %
    Favored  : 88.01 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.44 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.74 (0.32), residues: 617
  helix: -3.44 (1.32), residues: 13
  sheet: -0.88 (0.40), residues: 187
  loop : -2.37 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.017   0.001   PHE D 146 
 TYR   0.021   0.001   TYR C 380 
 ARG   0.015   0.001   ARG E  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00384 (    2)
  link_NAG-ASN         : angle       1.37967 (    6)
  link_ALPHA1-6        : bond        0.02230 (    1)
  link_ALPHA1-6        : angle       2.61680 (    3)
  link_BETA1-4         : bond        0.00530 (    4)
  link_BETA1-4         : angle       2.39115 (   12)
  link_ALPHA1-3        : bond        0.01551 (    1)
  link_ALPHA1-3        : angle       2.14633 (    3)
  hydrogen bonds       : bond        0.02977 (   75)
  hydrogen bonds       : angle       6.24311 (  225)
  SS BOND              : bond        0.00348 (    9)
  SS BOND              : angle       1.71472 (   18)
  covalent geometry    : bond        0.00415 ( 5030)
  covalent geometry    : angle       0.72712 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: C  498 GLN cc_start: 0.8903 (mm110) cc_final: 0.8590 (mm110)
REVERT: D   10 GLU cc_start: 0.8406 (mp0) cc_final: 0.8143 (mp0)
REVERT: D  155 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8272 (t0)
REVERT: D  176 TYR cc_start: 0.8162 (m-10) cc_final: 0.7662 (m-10)
REVERT: E   82 ASP cc_start: 0.8918 (t0) cc_final: 0.8537 (t0)
REVERT: E  123 GLU cc_start: 0.8719 (tp30) cc_final: 0.8466 (tp30)
REVERT: E  167 ASP cc_start: 0.8431 (t70) cc_final: 0.8134 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 87
  average time/residue: 0.2306
  time to fit residues: 25.7698
Evaluate side-chains
  90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  155 ASN
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  189 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.064156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.055220 restraints weight = 19656.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.057075 restraints weight = 10655.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.058329 restraints weight = 6624.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5047  Z= 0.175
  Angle     :  0.745  11.957   6889  Z= 0.360
  Chirality :  0.046   0.178    786
  Planarity :  0.006   0.081    869
  Dihedral  :  9.618  68.102    839
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 10.37 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.81 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.74 (0.32), residues: 617
  helix: -3.46 (1.31), residues: 13
  sheet: -0.89 (0.40), residues: 187
  loop : -2.37 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.009   0.002   HIS C 519 
 PHE   0.010   0.001   PHE C 392 
 TYR   0.030   0.002   TYR C 380 
 ARG   0.018   0.001   ARG D  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00359 (    2)
  link_NAG-ASN         : angle       1.34333 (    6)
  link_ALPHA1-6        : bond        0.02336 (    1)
  link_ALPHA1-6        : angle       2.43971 (    3)
  link_BETA1-4         : bond        0.00430 (    4)
  link_BETA1-4         : angle       2.31661 (   12)
  link_ALPHA1-3        : bond        0.01529 (    1)
  link_ALPHA1-3        : angle       1.99780 (    3)
  hydrogen bonds       : bond        0.02844 (   75)
  hydrogen bonds       : angle       6.28781 (  225)
  SS BOND              : bond        0.00283 (    9)
  SS BOND              : angle       1.61490 (   18)
  covalent geometry    : bond        0.00383 ( 5030)
  covalent geometry    : angle       0.73237 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: C  498 GLN cc_start: 0.8864 (mm110) cc_final: 0.8600 (mm-40)
REVERT: D   10 GLU cc_start: 0.8432 (mp0) cc_final: 0.8149 (mp0)
REVERT: D  155 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8272 (t0)
REVERT: E   82 ASP cc_start: 0.8890 (t0) cc_final: 0.8438 (t0)
REVERT: E  118 PHE cc_start: 0.7629 (m-10) cc_final: 0.7402 (m-10)
REVERT: E  123 GLU cc_start: 0.8675 (tp30) cc_final: 0.8438 (tp30)
REVERT: E  167 ASP cc_start: 0.8416 (t70) cc_final: 0.8106 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 87
  average time/residue: 0.2254
  time to fit residues: 25.5177
Evaluate side-chains
  87 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  155 ASN
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  189 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
C 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.064549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.055534 restraints weight = 19367.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.057416 restraints weight = 10457.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.058642 restraints weight = 6475.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5047  Z= 0.149
  Angle     :  0.729  11.936   6889  Z= 0.352
  Chirality :  0.046   0.181    786
  Planarity :  0.005   0.047    869
  Dihedral  :  9.118  64.248    839
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 11.02 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.25 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.72 (0.32), residues: 617
  helix: -3.48 (1.29), residues: 13
  sheet: -0.88 (0.39), residues: 187
  loop : -2.35 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.008   0.002   HIS C 519 
 PHE   0.007   0.001   PHE C 392 
 TYR   0.028   0.001   TYR C 380 
 ARG   0.004   0.000   ARG E  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00302 (    2)
  link_NAG-ASN         : angle       1.19059 (    6)
  link_ALPHA1-6        : bond        0.02147 (    1)
  link_ALPHA1-6        : angle       2.21974 (    3)
  link_BETA1-4         : bond        0.00399 (    4)
  link_BETA1-4         : angle       2.16293 (   12)
  link_ALPHA1-3        : bond        0.01375 (    1)
  link_ALPHA1-3        : angle       1.85271 (    3)
  hydrogen bonds       : bond        0.02710 (   75)
  hydrogen bonds       : angle       5.86611 (  225)
  SS BOND              : bond        0.00292 (    9)
  SS BOND              : angle       1.39145 (   18)
  covalent geometry    : bond        0.00334 ( 5030)
  covalent geometry    : angle       0.71818 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: C  388 ASN cc_start: 0.7866 (m-40) cc_final: 0.7584 (m-40)
REVERT: C  498 GLN cc_start: 0.8877 (mm110) cc_final: 0.8569 (mm-40)
REVERT: D   72 ASP cc_start: 0.8698 (t0) cc_final: 0.8496 (t0)
REVERT: D  155 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8223 (t0)
REVERT: D  176 TYR cc_start: 0.8111 (m-10) cc_final: 0.7821 (m-10)
REVERT: E   82 ASP cc_start: 0.8882 (t0) cc_final: 0.8445 (t0)
REVERT: E  123 GLU cc_start: 0.8613 (tp30) cc_final: 0.8389 (tp30)
REVERT: E  167 ASP cc_start: 0.8409 (t70) cc_final: 0.8107 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 86
  average time/residue: 0.3064
  time to fit residues: 34.0369
Evaluate side-chains
  90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  155 ASN
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  189 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0270
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0030
   overall best weight:    0.5648

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

Flipped N/Q/H residues before XYZ refinement:
C 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.064606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.055563 restraints weight = 19594.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.057427 restraints weight = 10608.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.058689 restraints weight = 6602.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5047  Z= 0.148
  Angle     :  0.727  11.898   6889  Z= 0.353
  Chirality :  0.046   0.200    786
  Planarity :  0.005   0.047    869
  Dihedral  :  8.712  61.273    839
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.21 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.74 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.75 (0.32), residues: 617
  helix: -3.54 (1.25), residues: 13
  sheet: -0.94 (0.39), residues: 187
  loop : -2.34 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.011   0.002   HIS C 519 
 PHE   0.017   0.001   PHE E  62 
 TYR   0.033   0.001   TYR C 380 
 ARG   0.008   0.001   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00292 (    2)
  link_NAG-ASN         : angle       1.12897 (    6)
  link_ALPHA1-6        : bond        0.02431 (    1)
  link_ALPHA1-6        : angle       2.04754 (    3)
  link_BETA1-4         : bond        0.00419 (    4)
  link_BETA1-4         : angle       2.04825 (   12)
  link_ALPHA1-3        : bond        0.01476 (    1)
  link_ALPHA1-3        : angle       1.96902 (    3)
  hydrogen bonds       : bond        0.02714 (   75)
  hydrogen bonds       : angle       5.80575 (  225)
  SS BOND              : bond        0.00270 (    9)
  SS BOND              : angle       1.51772 (   18)
  covalent geometry    : bond        0.00330 ( 5030)
  covalent geometry    : angle       0.71710 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.805 
Fit side-chains
REVERT: C  388 ASN cc_start: 0.7821 (m-40) cc_final: 0.7575 (m-40)
REVERT: C  498 GLN cc_start: 0.8859 (mm110) cc_final: 0.8563 (mm-40)
REVERT: D  176 TYR cc_start: 0.8079 (m-10) cc_final: 0.7796 (m-10)
REVERT: E   62 PHE cc_start: 0.8280 (m-10) cc_final: 0.8040 (m-10)
REVERT: E   82 ASP cc_start: 0.8916 (t0) cc_final: 0.8466 (t0)
REVERT: E  123 GLU cc_start: 0.8599 (tp30) cc_final: 0.8381 (tp30)
REVERT: E  167 ASP cc_start: 0.8384 (t70) cc_final: 0.8055 (m-30)
  outliers start: 11
  outliers final: 10
  residues processed: 87
  average time/residue: 0.2726
  time to fit residues: 30.6150
Evaluate side-chains
  89 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  189 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0470
   chunk 37 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   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 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.065114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.056082 restraints weight = 19328.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.057972 restraints weight = 10329.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.059224 restraints weight = 6374.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5047  Z= 0.145
  Angle     :  0.737  11.822   6889  Z= 0.359
  Chirality :  0.046   0.212    786
  Planarity :  0.005   0.047    869
  Dihedral  :  8.271  58.474    837
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.37 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.85 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.73 (0.32), residues: 617
  helix: -3.55 (1.24), residues: 13
  sheet: -0.95 (0.39), residues: 187
  loop : -2.32 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.009   0.002   HIS C 519 
 PHE   0.035   0.001   PHE D 146 
 TYR   0.025   0.001   TYR C 380 
 ARG   0.002   0.000   ARG D  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00277 (    2)
  link_NAG-ASN         : angle       1.06762 (    6)
  link_ALPHA1-6        : bond        0.02386 (    1)
  link_ALPHA1-6        : angle       1.84064 (    3)
  link_BETA1-4         : bond        0.00423 (    4)
  link_BETA1-4         : angle       1.93407 (   12)
  link_ALPHA1-3        : bond        0.01358 (    1)
  link_ALPHA1-3        : angle       1.91839 (    3)
  hydrogen bonds       : bond        0.02588 (   75)
  hydrogen bonds       : angle       5.65877 (  225)
  SS BOND              : bond        0.00344 (    9)
  SS BOND              : angle       1.39924 (   18)
  covalent geometry    : bond        0.00325 ( 5030)
  covalent geometry    : angle       0.72855 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 2.632 
Fit side-chains
REVERT: C  388 ASN cc_start: 0.7826 (m-40) cc_final: 0.7563 (m-40)
REVERT: C  465 GLU cc_start: 0.8782 (tp30) cc_final: 0.8460 (tp30)
REVERT: C  498 GLN cc_start: 0.8879 (mm110) cc_final: 0.8576 (mm-40)
REVERT: D  176 TYR cc_start: 0.8099 (m-10) cc_final: 0.7897 (m-10)
REVERT: D  181 VAL cc_start: 0.9371 (t) cc_final: 0.9171 (p)
REVERT: E   82 ASP cc_start: 0.8939 (t0) cc_final: 0.8486 (t0)
REVERT: E  123 GLU cc_start: 0.8575 (tp30) cc_final: 0.8351 (tp30)
REVERT: E  167 ASP cc_start: 0.8415 (t70) cc_final: 0.8083 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 87
  average time/residue: 0.3335
  time to fit residues: 38.0170
Evaluate side-chains
  88 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 4.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  189 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 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 = 0.3259 r_free = 0.3259 target = 0.064224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.055192 restraints weight = 19450.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.057006 restraints weight = 10580.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.058235 restraints weight = 6599.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5047  Z= 0.173
  Angle     :  0.756  12.256   6889  Z= 0.372
  Chirality :  0.046   0.225    786
  Planarity :  0.005   0.049    869
  Dihedral  :  8.207  58.721    837
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 10.86 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.29 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.75 (0.32), residues: 617
  helix: -3.50 (1.27), residues: 13
  sheet: -1.02 (0.39), residues: 187
  loop : -2.30 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.004   0.001   HIS D 200 
 PHE   0.012   0.001   PHE E  62 
 TYR   0.011   0.001   TYR C 380 
 ARG   0.011   0.001   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00375 (    2)
  link_NAG-ASN         : angle       1.27926 (    6)
  link_ALPHA1-6        : bond        0.02388 (    1)
  link_ALPHA1-6        : angle       1.84562 (    3)
  link_BETA1-4         : bond        0.00413 (    4)
  link_BETA1-4         : angle       1.97135 (   12)
  link_ALPHA1-3        : bond        0.01503 (    1)
  link_ALPHA1-3        : angle       2.12753 (    3)
  hydrogen bonds       : bond        0.02736 (   75)
  hydrogen bonds       : angle       5.68511 (  225)
  SS BOND              : bond        0.00382 (    9)
  SS BOND              : angle       1.51269 (   18)
  covalent geometry    : bond        0.00384 ( 5030)
  covalent geometry    : angle       0.74680 ( 6847)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 1.311 
Fit side-chains
REVERT: C  388 ASN cc_start: 0.7827 (m-40) cc_final: 0.7571 (m-40)
REVERT: C  465 GLU cc_start: 0.8768 (tp30) cc_final: 0.8486 (tp30)
REVERT: C  498 GLN cc_start: 0.8860 (mm110) cc_final: 0.8558 (mm-40)
REVERT: D  176 TYR cc_start: 0.8145 (m-10) cc_final: 0.7844 (m-10)
REVERT: E   82 ASP cc_start: 0.8941 (t0) cc_final: 0.8541 (t0)
REVERT: E  123 GLU cc_start: 0.8567 (tp30) cc_final: 0.8360 (tp30)
REVERT: E  167 ASP cc_start: 0.8433 (t70) cc_final: 0.8089 (m-30)
  outliers start: 8
  outliers final: 8
  residues processed: 85
  average time/residue: 0.3693
  time to fit residues: 41.2291
Evaluate side-chains
  88 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   56 ASN
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  189 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 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 = 0.3252 r_free = 0.3252 target = 0.063995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.055085 restraints weight = 19666.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.056883 restraints weight = 10718.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.058109 restraints weight = 6710.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   5047  Z= 0.178
  Angle     :  0.757  12.456   6889  Z= 0.373
  Chirality :  0.046   0.228    786
  Planarity :  0.005   0.050    869
  Dihedral  :  8.161  58.750    837
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 10.21 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.67 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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 (0.32), residues: 617
  helix: -3.52 (1.26), residues: 13
  sheet: -1.13 (0.39), residues: 187
  loop : -2.30 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.003   0.001   HIS D 200 
 PHE   0.026   0.002   PHE E  62 
 TYR   0.008   0.001   TYR D 194 
 ARG   0.003   0.001   ARG E 142 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00388 (    2)
  link_NAG-ASN         : angle       1.32868 (    6)
  link_ALPHA1-6        : bond        0.02438 (    1)
  link_ALPHA1-6        : angle       1.76130 (    3)
  link_BETA1-4         : bond        0.00431 (    4)
  link_BETA1-4         : angle       1.99500 (   12)
  link_ALPHA1-3        : bond        0.01529 (    1)
  link_ALPHA1-3        : angle       2.09318 (    3)
  hydrogen bonds       : bond        0.02779 (   75)
  hydrogen bonds       : angle       5.59685 (  225)
  SS BOND              : bond        0.00297 (    9)
  SS BOND              : angle       1.41600 (   18)
  covalent geometry    : bond        0.00406 ( 5030)
  covalent geometry    : angle       0.74849 ( 6847)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3900.70 seconds
wall clock time: 75 minutes 57.34 seconds (4557.34 seconds total)