Starting phenix.real_space_refine
on Mon Apr 28 12:38:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hc6_34653/04_2025/8hc6_34653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hc6_34653/04_2025/8hc6_34653.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hc6_34653/04_2025/8hc6_34653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hc6_34653/04_2025/8hc6_34653.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hc6_34653/04_2025/8hc6_34653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hc6_34653/04_2025/8hc6_34653.cif"
  }
  resolution = 4.69
  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=   0.058
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      27      5.16       5
     C    4704      2.51       5
     N    1226      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7377
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2134
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 15, 'TRANS': 251}
    Chain: "H"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1588
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1628
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203}
    Chain: "B"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1929
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 13, 'TRANS': 223}
          Chain breaks: 5
    Chain: "C"
      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: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          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
  Time building chain proxies: 4.72, per 1000 atoms: 0.64
  Number of scatterers: 7377
  At special positions: 0
  Unit cell: (112.2, 84.15, 158.4, 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      27     16.00
     O    1420      8.00
     N    1226      7.00
     C    4704      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, 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=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " 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
    NAG-ASN
      " NAG B1301 " - " ASN B  61 "
      " NAG B1302 " - " ASN B 122 "
      " NAG B1303 " - " ASN B 165 "
      " NAG B1304 " - " ASN B 234 "
      " NAG B1305 " - " ASN B 282 "
      " NAG C 601 " - " ASN C 331 "
      " NAG C 602 " - " ASN C 343 "
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 971.1 milliseconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1740

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 20 sheets defined
      4.3% alpha, 27.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.666A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 372
      removed outlier: 3.769A  pdb=" N   LEU C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'H' and resid 159 through 161
      No H-bonds generated for 'chain 'H' and resid 159 through 161'
    Processing helix  chain 'H' and resid 188 through 192
      removed outlier: 3.531A  pdb=" N   SER H 191 " --> pdb=" O   PRO H 188 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU H 192 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 188 through 192'
    Processing helix  chain 'L' and resid 184 through 188
      removed outlier: 4.126A  pdb=" N   GLU L 188 " --> pdb=" O   LYS L 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 184 through 188'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358
      removed outlier: 3.619A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL C 510 " --> pdb=" O   PHE C 400 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (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 'C' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'C' and resid 541 through 543
      removed outlier: 3.667A  pdb=" N   GLY C 548 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7
      removed outlier: 3.538A  pdb=" N   SER H   7 " --> pdb=" O   SER H  21 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR H  77 " --> pdb=" O   ASN H  72 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASN H  72 " --> pdb=" O   THR H  77 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59
      removed outlier: 4.979A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59
      removed outlier: 4.979A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 123 through 126
      removed outlier: 3.538A  pdb=" N   LYS H 146 " --> pdb=" O   SER H 123 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 123 through 126
      removed outlier: 3.538A  pdb=" N   LYS H 146 " --> pdb=" O   SER H 123 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 154 through 157
      removed outlier: 3.755A  pdb=" N   THR H 154 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN H 202 " --> pdb=" O   THR H 154 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   VAL H 201 " --> pdb=" O   VAL H 210 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   VAL H 210 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.790A  pdb=" N   CYS L  23 " --> pdb=" O   PHE L  71 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE L  71 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.548A  pdb=" N   VAL L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54
      removed outlier: 3.949A  pdb=" N   TYR L  49 " --> pdb=" O   THR L  53 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN L  38 " --> pdb=" O   SER L  85 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN L  90 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 117 through 119
      removed outlier: 3.761A  pdb=" N   PHE L 117 " --> pdb=" O   LEU L 136 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU L 136 " --> pdb=" O   PHE L 117 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL L 134 " --> pdb=" O   PHE L 119 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA L 131 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   CYS L 135 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER L 178 " --> pdb=" O   CYS L 135 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN L 161 " --> pdb=" O   THR L 179 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 149 through 151
      removed outlier: 4.273A  pdb=" N   TRP L 149 " --> pdb=" O   GLN L 156 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 192 through 193
      removed outlier: 3.622A  pdb=" N   PHE L 210 " --> pdb=" O   TYR L 193 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30
      removed outlier: 3.628A  pdb=" N   ALA B  27 " --> pdb=" O   TRP B  64 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 267 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE B  65 " --> pdb=" O   TYR B 265 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA B 264 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL B  90 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52
      removed outlier: 3.843A  pdb=" N   HIS B  49 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU B 277 " --> pdb=" O   HIS B  49 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR B  51 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   PHE B 275 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 141
      removed outlier: 4.519A  pdb=" N   GLY B 103 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ALA B 243 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ILE B 101 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   ARG B 102 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN B 121 " --> pdb=" O   ARG B 102 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TRP B 104 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU B 118 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS B 129 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   VAL B 120 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B 126 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL B 130 " --> pdb=" O   PHE B 168 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   PHE B 168 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)

    147 hydrogen bonds defined for protein.
    375 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: 1.92

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2336
        1.35 -     1.46: 1912
        1.46 -     1.58: 3276
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 7555
  Sorted by residual:
  bond pdb=" C1  NAG B1303 "
       pdb=" O5  NAG B1303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.60e+00
  bond pdb=" C1  NAG B1305 "
       pdb=" O5  NAG B1305 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C1  NAG B1304 "
       pdb=" O5  NAG B1304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.78e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.53e+00
  bond pdb=" C1  NAG C 602 "
       pdb=" O5  NAG C 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.50e+00
  ... (remaining 7550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 9927
        1.40 -     2.80: 282
        2.80 -     4.20: 47
        4.20 -     5.60: 10
        5.60 -     7.00: 6
  Bond angle restraints: 10272
  Sorted by residual:
  angle pdb=" C   ARG L 109 "
        pdb=" N   THR L 110 "
        pdb=" CA  THR L 110 "
      ideal   model   delta    sigma   weight residual
     121.54  128.05   -6.51 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" C   SER H 206 "
        pdb=" N   ASN H 207 "
        pdb=" CA  ASN H 207 "
      ideal   model   delta    sigma   weight residual
     121.54  127.10   -5.56 1.91e+00 2.74e-01 8.49e+00
  angle pdb=" N   VAL B 159 "
        pdb=" CA  VAL B 159 "
        pdb=" C   VAL B 159 "
      ideal   model   delta    sigma   weight residual
     113.53  110.68    2.85 9.80e-01 1.04e+00 8.47e+00
  angle pdb=" C   GLY H 100 "
        pdb=" N   ASP H 101 "
        pdb=" CA  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     121.54  126.94   -5.40 1.91e+00 2.74e-01 8.00e+00
  angle pdb=" N   CYS H 219 "
        pdb=" CA  CYS H 219 "
        pdb=" C   CYS H 219 "
      ideal   model   delta    sigma   weight residual
     114.04  110.59    3.45 1.24e+00 6.50e-01 7.75e+00
  ... (remaining 10267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 4057
       15.92 -    31.83: 407
       31.83 -    47.75: 81
       47.75 -    63.67: 16
       63.67 -    79.58: 15
  Dihedral angle restraints: 4576
    sinusoidal: 1868
      harmonic: 2708
  Sorted by residual:
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.38  -75.38     1      1.00e+01 1.00e-02 7.18e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.82  -48.82     1      1.00e+01 1.00e-02 3.28e+01
  dihedral pdb=" CB  CYS B  15 "
           pdb=" SG  CYS B  15 "
           pdb=" SG  CYS B 136 "
           pdb=" CB  CYS B 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.26  -45.26     1      1.00e+01 1.00e-02 2.84e+01
  ... (remaining 4573 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1009
       0.065 -    0.130: 150
       0.130 -    0.196: 5
       0.196 -    0.261: 2
       0.261 -    0.326: 1
  Chirality restraints: 1167
  Sorted by residual:
  chirality pdb=" C1  NAG B1303 "
            pdb=" ND2 ASN B 165 "
            pdb=" C2  NAG B1303 "
            pdb=" O5  NAG B1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C1  NAG B1304 "
            pdb=" ND2 ASN B 234 "
            pdb=" C2  NAG B1304 "
            pdb=" O5  NAG B1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  VAL L 147 "
            pdb=" CA  VAL L 147 "
            pdb=" CG1 VAL L 147 "
            pdb=" CG2 VAL L 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1164 not shown)

  Planarity restraints: 1317
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 524 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.88e+00
        pdb=" C   VAL C 524 "    0.029 2.00e-02 2.50e+03
        pdb=" O   VAL C 524 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   CYS C 525 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 235 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   ILE B 235 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ILE B 235 "    0.009 2.00e-02 2.50e+03
        pdb=" N   THR B 236 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 329 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.81e+00
        pdb=" N   PRO C 330 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 330 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 330 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1314 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2188
        2.82 -     3.34: 5884
        3.34 -     3.86: 11654
        3.86 -     4.38: 12475
        4.38 -     4.90: 21939
  Nonbonded interactions: 54140
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  37 "
            pdb=" O   LEU B  54 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   PRO H 126 "
            pdb=" OG  SER L 122 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OH  TYR C 501 "
            pdb=" O   GLY L  30 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" O   LYS B 278 "
            pdb=" OG1 THR B 286 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   LEU C 455 "
            pdb=" OH  TYR H  33 "
     model   vdw
     2.353 3.040
  ... (remaining 54135 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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.360
  Find NCS groups from input model:        0.110
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
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   0.043   7572  Z= 0.141
  Angle     :  0.586  11.147  10313  Z= 0.289
  Chirality :  0.045   0.326   1167
  Planarity :  0.004   0.034   1310
  Dihedral  : 13.451  79.582   2806
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.49 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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: -0.78 (0.27), residues: 913
  helix: -3.66 (0.60), residues: 24
  sheet:  0.99 (0.34), residues: 235
  loop : -1.05 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP L  32 
 HIS   0.003   0.000   HIS H 203 
 PHE   0.014   0.001   PHE L 140 
 TYR   0.008   0.001   TYR H  93 
 ARG   0.003   0.000   ARG L 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00861 (    7)
  link_NAG-ASN         : angle       3.35360 (   21)
  hydrogen bonds       : bond        0.30925 (  131)
  hydrogen bonds       : angle      12.18200 (  375)
  SS BOND              : bond        0.00271 (   10)
  SS BOND              : angle       0.84249 (   20)
  covalent geometry    : bond        0.00281 ( 7555)
  covalent geometry    : angle       0.56566 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8591 (tpt) cc_final: 0.8215 (tpp)
REVERT: H   35 HIS cc_start: 0.8593 (m90) cc_final: 0.8238 (m170)
REVERT: H   82 MET cc_start: 0.6132 (tmm) cc_final: 0.5096 (tmm)
REVERT: H  101 ASP cc_start: 0.7600 (t0) cc_final: 0.7335 (t0)
REVERT: L   62 PHE cc_start: 0.8011 (m-80) cc_final: 0.7776 (m-80)
REVERT: B   42 VAL cc_start: 0.8923 (t) cc_final: 0.8481 (t)
REVERT: B   55 PHE cc_start: 0.7434 (m-80) cc_final: 0.6410 (m-10)
REVERT: B   80 ASP cc_start: 0.7432 (m-30) cc_final: 0.7149 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1878
  time to fit residues: 16.5297
Evaluate side-chains
  37 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0370
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.080077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.063606 restraints weight = 47143.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.064311 restraints weight = 25423.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.064953 restraints weight = 20604.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7572  Z= 0.155
  Angle     :  0.575   9.985  10313  Z= 0.296
  Chirality :  0.044   0.355   1167
  Planarity :  0.004   0.029   1310
  Dihedral  :  5.041  49.437   1151
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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: -0.77 (0.27), residues: 913
  helix: -2.93 (0.69), residues: 20
  sheet:  0.55 (0.34), residues: 256
  loop : -0.93 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L  35 
 HIS   0.005   0.001   HIS H 203 
 PHE   0.013   0.001   PHE B 220 
 TYR   0.015   0.001   TYR L  49 
 ARG   0.005   0.001   ARG B 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00529 (    7)
  link_NAG-ASN         : angle       2.78327 (   21)
  hydrogen bonds       : bond        0.04388 (  131)
  hydrogen bonds       : angle       7.22783 (  375)
  SS BOND              : bond        0.00680 (   10)
  SS BOND              : angle       0.94407 (   20)
  covalent geometry    : bond        0.00329 ( 7555)
  covalent geometry    : angle       0.56032 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
REVERT: C  434 ILE cc_start: 0.8401 (mm) cc_final: 0.8185 (mm)
REVERT: H   35 HIS cc_start: 0.9027 (m90) cc_final: 0.8109 (m90)
REVERT: H   82 MET cc_start: 0.6691 (tmm) cc_final: 0.5897 (tmm)
REVERT: L  118 ILE cc_start: 0.7318 (pt) cc_final: 0.7038 (mp)
REVERT: B   42 VAL cc_start: 0.8938 (t) cc_final: 0.8511 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1544
  time to fit residues: 12.6930
Evaluate side-chains
  31 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0020
   chunk 59 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 74 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.3390

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

Flipped N/Q/H residues before XYZ refinement:
H 200 ASN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 GLN
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.077847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.060091 restraints weight = 47067.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.061753 restraints weight = 29242.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.062791 restraints weight = 17783.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7572  Z= 0.138
  Angle     :  0.539   9.422  10313  Z= 0.275
  Chirality :  0.044   0.317   1167
  Planarity :  0.004   0.064   1310
  Dihedral  :  4.579  50.163   1151
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    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: -0.97 (0.27), residues: 913
  helix: -2.59 (0.73), residues: 31
  sheet:  0.48 (0.33), residues: 254
  loop : -1.08 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  35 
 HIS   0.004   0.001   HIS H 203 
 PHE   0.014   0.002   PHE B 133 
 TYR   0.011   0.001   TYR H  33 
 ARG   0.004   0.001   ARG B  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00597 (    7)
  link_NAG-ASN         : angle       3.22802 (   21)
  hydrogen bonds       : bond        0.04482 (  131)
  hydrogen bonds       : angle       6.79063 (  375)
  SS BOND              : bond        0.00276 (   10)
  SS BOND              : angle       0.75679 (   20)
  covalent geometry    : bond        0.00306 ( 7555)
  covalent geometry    : angle       0.51886 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8579 (mmp) cc_final: 0.7969 (mmm)
REVERT: H   35 HIS cc_start: 0.9148 (m90) cc_final: 0.8562 (m90)
REVERT: H   82 MET cc_start: 0.6920 (tmm) cc_final: 0.6188 (tmm)
REVERT: L  118 ILE cc_start: 0.7386 (pt) cc_final: 0.7045 (mp)
REVERT: B   40 ASP cc_start: 0.9258 (p0) cc_final: 0.9054 (p0)
REVERT: B   42 VAL cc_start: 0.9063 (t) cc_final: 0.8661 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1438
  time to fit residues: 12.1625
Evaluate side-chains
  25 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 66 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.2786

-------------------------------------------------------------------------------
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**
H  35 HIS
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 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 = 0.3716 r_free = 0.3716 target = 0.074089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.058551 restraints weight = 46913.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.058501 restraints weight = 40558.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.059012 restraints weight = 38385.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7572  Z= 0.223
  Angle     :  0.671  11.541  10313  Z= 0.344
  Chirality :  0.046   0.322   1167
  Planarity :  0.005   0.047   1310
  Dihedral  :  5.252  41.073   1151
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.94 %
    Favored  : 95.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.27), residues: 913
  helix: -2.68 (0.75), residues: 30
  sheet: -0.11 (0.33), residues: 248
  loop : -1.22 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 436 
 HIS   0.008   0.002   HIS H 203 
 PHE   0.019   0.003   PHE L  83 
 TYR   0.026   0.002   TYR B 279 
 ARG   0.007   0.001   ARG B  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00509 (    7)
  link_NAG-ASN         : angle       3.02713 (   21)
  hydrogen bonds       : bond        0.04156 (  131)
  hydrogen bonds       : angle       6.61461 (  375)
  SS BOND              : bond        0.00640 (   10)
  SS BOND              : angle       0.95307 (   20)
  covalent geometry    : bond        0.00484 ( 7555)
  covalent geometry    : angle       0.65655 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: C  406 GLU cc_start: 0.8382 (pm20) cc_final: 0.8158 (pm20)
REVERT: H   34 MET cc_start: 0.8589 (mmp) cc_final: 0.7939 (mmm)
REVERT: H   82 MET cc_start: 0.7594 (tmm) cc_final: 0.6980 (tmm)
REVERT: L    4 MET cc_start: 0.8282 (mmp) cc_final: 0.7317 (ptm)
REVERT: L   83 PHE cc_start: 0.8530 (m-80) cc_final: 0.8090 (m-80)
REVERT: L  118 ILE cc_start: 0.7629 (pt) cc_final: 0.7365 (mt)
REVERT: B   40 ASP cc_start: 0.9343 (p0) cc_final: 0.9094 (p0)
REVERT: B   49 HIS cc_start: 0.8505 (t70) cc_final: 0.8059 (t-170)
REVERT: B  198 ASP cc_start: 0.9262 (t0) cc_final: 0.9043 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1432
  time to fit residues: 11.2703
Evaluate side-chains
  27 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.076078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.059327 restraints weight = 46632.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.059804 restraints weight = 25212.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.060175 restraints weight = 20081.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7572  Z= 0.117
  Angle     :  0.544  10.097  10313  Z= 0.273
  Chirality :  0.044   0.326   1167
  Planarity :  0.004   0.047   1310
  Dihedral  :  4.820  37.666   1151
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.27), residues: 913
  helix: -2.58 (0.72), residues: 31
  sheet:  0.11 (0.33), residues: 261
  loop : -1.09 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H 203 
 PHE   0.010   0.001   PHE B  86 
 TYR   0.009   0.001   TYR H  94 
 ARG   0.003   0.000   ARG B  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00713 (    7)
  link_NAG-ASN         : angle       3.14407 (   21)
  hydrogen bonds       : bond        0.03486 (  131)
  hydrogen bonds       : angle       6.26047 (  375)
  SS BOND              : bond        0.00310 (   10)
  SS BOND              : angle       0.69222 (   20)
  covalent geometry    : bond        0.00259 ( 7555)
  covalent geometry    : angle       0.52502 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8687 (mmp) cc_final: 0.7922 (mmm)
REVERT: H   82 MET cc_start: 0.7515 (tmm) cc_final: 0.7003 (tmm)
REVERT: L    4 MET cc_start: 0.8162 (mmp) cc_final: 0.7510 (ptm)
REVERT: L   62 PHE cc_start: 0.8368 (m-80) cc_final: 0.8034 (m-80)
REVERT: L  118 ILE cc_start: 0.7533 (pt) cc_final: 0.7256 (mt)
REVERT: B   42 VAL cc_start: 0.9016 (t) cc_final: 0.8767 (t)
REVERT: B   49 HIS cc_start: 0.8417 (t70) cc_final: 0.8097 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1533
  time to fit residues: 10.8927
Evaluate side-chains
  27 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0000
   chunk 81 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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**
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.074351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.057078 restraints weight = 46752.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.057838 restraints weight = 30455.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.058680 restraints weight = 20226.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7572  Z= 0.149
  Angle     :  0.569   9.901  10313  Z= 0.290
  Chirality :  0.044   0.320   1167
  Planarity :  0.004   0.043   1310
  Dihedral  :  4.666  35.616   1151
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.27), residues: 913
  helix: -2.72 (0.74), residues: 30
  sheet: -0.16 (0.33), residues: 254
  loop : -1.10 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 157 
 HIS   0.005   0.001   HIS H 203 
 PHE   0.011   0.001   PHE B  65 
 TYR   0.011   0.001   TYR L 187 
 ARG   0.005   0.001   ARG B  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00557 (    7)
  link_NAG-ASN         : angle       2.84896 (   21)
  hydrogen bonds       : bond        0.03505 (  131)
  hydrogen bonds       : angle       6.21758 (  375)
  SS BOND              : bond        0.00302 (   10)
  SS BOND              : angle       0.80517 (   20)
  covalent geometry    : bond        0.00329 ( 7555)
  covalent geometry    : angle       0.55437 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8695 (mmp) cc_final: 0.7918 (mmm)
REVERT: H   82 MET cc_start: 0.7669 (tmm) cc_final: 0.7235 (tmm)
REVERT: L    4 MET cc_start: 0.8097 (mmp) cc_final: 0.7639 (ptp)
REVERT: L   83 PHE cc_start: 0.8309 (m-80) cc_final: 0.8011 (m-80)
REVERT: L  118 ILE cc_start: 0.7839 (pt) cc_final: 0.7563 (mt)
REVERT: B  191 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7836 (mt-10)
REVERT: B  198 ASP cc_start: 0.9240 (t0) cc_final: 0.9031 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1415
  time to fit residues: 10.7449
Evaluate side-chains
  25 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 17 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0060
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** B  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.076158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.058761 restraints weight = 48117.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.059461 restraints weight = 32038.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.060324 restraints weight = 21126.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7572  Z= 0.099
  Angle     :  0.525   8.990  10313  Z= 0.267
  Chirality :  0.044   0.327   1167
  Planarity :  0.004   0.042   1310
  Dihedral  :  4.373  32.951   1151
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.27), residues: 913
  helix: -2.88 (0.72), residues: 30
  sheet: -0.10 (0.33), residues: 252
  loop : -1.08 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.015   0.001   HIS B  49 
 PHE   0.015   0.001   PHE B  43 
 TYR   0.010   0.001   TYR C 369 
 ARG   0.002   0.000   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00651 (    7)
  link_NAG-ASN         : angle       2.72804 (   21)
  hydrogen bonds       : bond        0.03107 (  131)
  hydrogen bonds       : angle       5.99799 (  375)
  SS BOND              : bond        0.00358 (   10)
  SS BOND              : angle       0.88078 (   20)
  covalent geometry    : bond        0.00223 ( 7555)
  covalent geometry    : angle       0.51009 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8876 (mmp) cc_final: 0.8149 (mmm)
REVERT: H   82 MET cc_start: 0.7680 (tmm) cc_final: 0.7117 (tmm)
REVERT: L    4 MET cc_start: 0.7979 (mmp) cc_final: 0.7617 (ptp)
REVERT: L   62 PHE cc_start: 0.8210 (m-80) cc_final: 0.7960 (m-80)
REVERT: L  118 ILE cc_start: 0.7590 (pt) cc_final: 0.7288 (mt)
REVERT: B   40 ASP cc_start: 0.9445 (p0) cc_final: 0.8951 (p0)
REVERT: B   42 VAL cc_start: 0.9355 (t) cc_final: 0.8867 (p)
REVERT: B   49 HIS cc_start: 0.8242 (t70) cc_final: 0.7703 (t70)
REVERT: B  191 GLU cc_start: 0.8815 (mt-10) cc_final: 0.7741 (mt-10)
REVERT: B  198 ASP cc_start: 0.9260 (t0) cc_final: 0.8977 (t0)
REVERT: B  223 LEU cc_start: 0.9151 (mm) cc_final: 0.8861 (mm)
REVERT: B  280 ASN cc_start: 0.9127 (t0) cc_final: 0.8923 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1373
  time to fit residues: 11.7851
Evaluate side-chains
  29 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 52 optimal weight:    0.3980
   chunk 62 optimal weight:    6.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
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**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.071362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.053598 restraints weight = 47803.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.054383 restraints weight = 25978.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.054789 restraints weight = 20512.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7572  Z= 0.232
  Angle     :  0.676  11.222  10313  Z= 0.346
  Chirality :  0.045   0.307   1167
  Planarity :  0.005   0.048   1310
  Dihedral  :  5.128  37.720   1151
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.27), residues: 913
  helix: -2.99 (0.71), residues: 36
  sheet: -0.31 (0.31), residues: 270
  loop : -1.17 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 157 
 HIS   0.018   0.003   HIS B  49 
 PHE   0.022   0.002   PHE B  43 
 TYR   0.018   0.002   TYR L 187 
 ARG   0.011   0.001   ARG B  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00471 (    7)
  link_NAG-ASN         : angle       2.67987 (   21)
  hydrogen bonds       : bond        0.03934 (  131)
  hydrogen bonds       : angle       6.60066 (  375)
  SS BOND              : bond        0.00520 (   10)
  SS BOND              : angle       0.90301 (   20)
  covalent geometry    : bond        0.00504 ( 7555)
  covalent geometry    : angle       0.66520 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8888 (mmp) cc_final: 0.8238 (mmm)
REVERT: H   82 MET cc_start: 0.7510 (tmm) cc_final: 0.6986 (tmm)
REVERT: L    4 MET cc_start: 0.8104 (mmp) cc_final: 0.7679 (ptm)
REVERT: L  118 ILE cc_start: 0.8028 (pt) cc_final: 0.7721 (mt)
REVERT: B   40 ASP cc_start: 0.9395 (p0) cc_final: 0.9156 (p0)
REVERT: B   42 VAL cc_start: 0.9394 (t) cc_final: 0.9098 (t)
REVERT: B  198 ASP cc_start: 0.9243 (t0) cc_final: 0.9033 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1487
  time to fit residues: 10.0169
Evaluate side-chains
  22 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.072569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054660 restraints weight = 48988.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.055742 restraints weight = 33542.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.056507 restraints weight = 21264.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.5409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7572  Z= 0.152
  Angle     :  0.580  10.660  10313  Z= 0.297
  Chirality :  0.045   0.317   1167
  Planarity :  0.005   0.057   1310
  Dihedral  :  4.928  36.812   1151
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.28), residues: 913
  helix: -3.06 (0.68), residues: 36
  sheet: -0.21 (0.32), residues: 262
  loop : -1.13 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 258 
 HIS   0.015   0.002   HIS B  49 
 PHE   0.013   0.001   PHE B  43 
 TYR   0.012   0.001   TYR L 187 
 ARG   0.008   0.001   ARG B  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00482 (    7)
  link_NAG-ASN         : angle       2.58434 (   21)
  hydrogen bonds       : bond        0.03493 (  131)
  hydrogen bonds       : angle       6.37414 (  375)
  SS BOND              : bond        0.00411 (   10)
  SS BOND              : angle       0.82729 (   20)
  covalent geometry    : bond        0.00339 ( 7555)
  covalent geometry    : angle       0.56764 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8898 (mmp) cc_final: 0.8244 (mmm)
REVERT: H   82 MET cc_start: 0.7501 (tmm) cc_final: 0.6986 (tmm)
REVERT: L    4 MET cc_start: 0.8042 (mmp) cc_final: 0.7681 (ptm)
REVERT: L  118 ILE cc_start: 0.7696 (pt) cc_final: 0.7458 (mt)
REVERT: B   40 ASP cc_start: 0.9375 (p0) cc_final: 0.9134 (p0)
REVERT: B   42 VAL cc_start: 0.9376 (t) cc_final: 0.9063 (t)
REVERT: B  198 ASP cc_start: 0.9142 (t0) cc_final: 0.8927 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1418
  time to fit residues: 9.9758
Evaluate side-chains
  21 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 48 optimal weight:    0.2980
   chunk 82 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 185 ASN
B 207 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.073873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.056684 restraints weight = 48920.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.057596 restraints weight = 27550.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.058262 restraints weight = 19600.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.5317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7572  Z= 0.103
  Angle     :  0.547   9.033  10313  Z= 0.278
  Chirality :  0.045   0.315   1167
  Planarity :  0.004   0.043   1310
  Dihedral  :  4.611  34.155   1151
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.27), residues: 913
  helix: -2.96 (0.66), residues: 31
  sheet: -0.26 (0.33), residues: 252
  loop : -1.05 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 258 
 HIS   0.011   0.002   HIS B 207 
 PHE   0.013   0.001   PHE B 133 
 TYR   0.009   0.001   TYR H  94 
 ARG   0.006   0.000   ARG B 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00555 (    7)
  link_NAG-ASN         : angle       2.51329 (   21)
  hydrogen bonds       : bond        0.03061 (  131)
  hydrogen bonds       : angle       6.08562 (  375)
  SS BOND              : bond        0.00397 (   10)
  SS BOND              : angle       0.86853 (   20)
  covalent geometry    : bond        0.00237 ( 7555)
  covalent geometry    : angle       0.53514 (10272)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8812 (mmp) cc_final: 0.8098 (mmm)
REVERT: H   82 MET cc_start: 0.7411 (tmm) cc_final: 0.6899 (tmm)
REVERT: L    4 MET cc_start: 0.7955 (mmp) cc_final: 0.7600 (ptp)
REVERT: B   40 ASP cc_start: 0.9319 (p0) cc_final: 0.9096 (p0)
REVERT: B   42 VAL cc_start: 0.9371 (t) cc_final: 0.9024 (t)
REVERT: B   53 ASP cc_start: 0.8576 (m-30) cc_final: 0.8335 (m-30)
REVERT: B  198 ASP cc_start: 0.9136 (t0) cc_final: 0.8880 (t0)
REVERT: B  280 ASN cc_start: 0.9263 (t0) cc_final: 0.9046 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1428
  time to fit residues: 9.9534
Evaluate side-chains
  23 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 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 = 0.3666 r_free = 0.3666 target = 0.072700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.055174 restraints weight = 47624.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056021 restraints weight = 25320.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.056521 restraints weight = 19363.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.5529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7572  Z= 0.133
  Angle     :  0.562   9.519  10313  Z= 0.287
  Chirality :  0.045   0.318   1167
  Planarity :  0.004   0.040   1310
  Dihedral  :  4.684  36.518   1151
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.27), residues: 913
  helix: -2.92 (0.71), residues: 30
  sheet: -0.25 (0.32), residues: 254
  loop : -1.05 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 258 
 HIS   0.015   0.002   HIS B  49 
 PHE   0.010   0.001   PHE B  43 
 TYR   0.011   0.001   TYR L 187 
 ARG   0.006   0.001   ARG B  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00486 (    7)
  link_NAG-ASN         : angle       2.50114 (   21)
  hydrogen bonds       : bond        0.03223 (  131)
  hydrogen bonds       : angle       6.11119 (  375)
  SS BOND              : bond        0.00383 (   10)
  SS BOND              : angle       0.86747 (   20)
  covalent geometry    : bond        0.00299 ( 7555)
  covalent geometry    : angle       0.55061 (10272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2266.07 seconds
wall clock time: 40 minutes 15.92 seconds (2415.92 seconds total)