Starting phenix.real_space_refine
on Thu Jul  2 07:22:20 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8hc6_34653/07_2026/8hc6_34653.cif"
  }
  resolution = 4.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 chiralities: 5
  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  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: 0.48
  Conformation dependent library (CDL) restraints added in 319.7 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: 0.24
  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: 1.07

  Time building geometry restraints manager: 0.69 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: 3928
       15.92 -    31.83: 401
       31.83 -    47.75: 73
       47.75 -    63.67: 12
       63.67 -    79.58: 15
  Dihedral angle restraints: 4429
    sinusoidal: 1721
      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 4426 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:             1.780
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.280
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
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  : 13.446  79.582   2659
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.74
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG L 212 
 TYR   0.008   0.001   TYR H  93 
 PHE   0.014   0.001   PHE L 140 
 TRP   0.004   0.001   TRP L  32 
 HIS   0.003   0.000   HIS H 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.14 ( 7555)
  covalent geometry    : angle       0.56566 /  0.28 (10272)
  SS BOND              : bond        0.00271 /  0.14 (   10)
  SS BOND              : angle       0.84249 /  0.55 (   20)
  hydrogen bonds       : bond        0.30925 / 20.30 (  131)
  hydrogen bonds       : angle      12.18200 /  8.35 (  375)
  link_NAG-ASN         : bond        0.00861 /  0.49 (    7)
  link_NAG-ASN         : angle       3.35360 /  2.36 (   21)

*********************** 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  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8590 (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: 0.5097 (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: 0.0719
  time to fit residues: 6.2857
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  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0270
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  35 HIS
L 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.084161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.068611 restraints weight = 48641.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.070027 restraints weight = 26086.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.070798 restraints weight = 18548.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.070921 restraints weight = 15424.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.071129 restraints weight = 14534.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7572  Z= 0.097
  Angle     :  0.502   9.862  10313  Z= 0.257
  Chirality :  0.043   0.355   1167
  Planarity :  0.003   0.030   1310
  Dihedral  :  3.142  14.323   1004
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.28), residues: 913
  helix: -3.15 (0.56), residues: 26
  sheet:  0.72 (0.34), residues: 248
  loop : -0.89 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 403 
 TYR   0.015   0.001   TYR L  49 
 PHE   0.009   0.001   PHE C 562 
 TRP   0.009   0.001   TRP L  35 
 HIS   0.003   0.001   HIS H 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.10 ( 7555)
  covalent geometry    : angle       0.48535 /  0.25 (10272)
  SS BOND              : bond        0.00648 /  0.33 (   10)
  SS BOND              : angle       0.72141 /  0.40 (   20)
  hydrogen bonds       : bond        0.04892 /  3.15 (  131)
  hydrogen bonds       : angle       7.56056 /  5.21 (  375)
  link_NAG-ASN         : bond        0.00682 /  0.40 (    7)
  link_NAG-ASN         : angle       2.82212 /  2.00 (   21)

*********************** 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
  61 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: H   35 HIS cc_start: 0.8695 (m-70) cc_final: 0.7654 (m-70)
REVERT: H   82 MET cc_start: 0.6403 (tmm) cc_final: 0.5560 (tmm)
REVERT: H  101 ASP cc_start: 0.7809 (t0) cc_final: 0.7443 (t0)
REVERT: H  104 ASP cc_start: 0.7520 (p0) cc_final: 0.6680 (t0)
REVERT: L  118 ILE cc_start: 0.7055 (pt) cc_final: 0.6785 (mp)
REVERT: B   42 VAL cc_start: 0.8857 (t) cc_final: 0.8400 (t)
REVERT: B   55 PHE cc_start: 0.6923 (m-80) cc_final: 0.6239 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0631
  time to fit residues: 5.6702
Evaluate side-chains
  38 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 79 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 409 GLN
C 422 ASN
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 167 GLN
B 196 ASN
B 239 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.075533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.056601 restraints weight = 46700.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.058101 restraints weight = 31083.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.059170 restraints weight = 22440.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.059954 restraints weight = 17419.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.060458 restraints weight = 14233.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   7572  Z= 0.230
  Angle     :  0.693  11.047  10313  Z= 0.360
  Chirality :  0.046   0.306   1167
  Planarity :  0.005   0.061   1310
  Dihedral  :  4.407  19.355   1004
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.27), residues: 913
  helix: -2.57 (0.77), residues: 30
  sheet:  0.15 (0.33), residues: 245
  loop : -1.20 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  44 
 TYR   0.021   0.002   TYR C 421 
 PHE   0.022   0.003   PHE B  58 
 TRP   0.019   0.002   TRP L  35 
 HIS   0.009   0.003   HIS H 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.23 ( 7555)
  covalent geometry    : angle       0.68364 /  0.36 (10272)
  SS BOND              : bond        0.00707 /  0.38 (   10)
  SS BOND              : angle       0.92063 /  0.57 (   20)
  hydrogen bonds       : bond        0.04801 /  3.28 (  131)
  hydrogen bonds       : angle       7.08965 /  4.74 (  375)
  link_NAG-ASN         : bond        0.00430 /  0.23 (    7)
  link_NAG-ASN         : angle       2.57970 /  1.77 (   21)

*********************** 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
  50 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8550 (mmp) cc_final: 0.8118 (mmm)
REVERT: H   82 MET cc_start: 0.7530 (tmm) cc_final: 0.6705 (tmm)
REVERT: L  118 ILE cc_start: 0.7819 (pt) cc_final: 0.7376 (mt)
REVERT: B   40 ASP cc_start: 0.9297 (p0) cc_final: 0.9062 (p0)
REVERT: B   42 VAL cc_start: 0.9090 (t) cc_final: 0.8738 (t)
REVERT: B   49 HIS cc_start: 0.8068 (t70) cc_final: 0.7832 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0582
  time to fit residues: 4.4783
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  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 409 GLN
** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.075314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.059902 restraints weight = 46993.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.060124 restraints weight = 37569.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.060713 restraints weight = 34235.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.060941 restraints weight = 25046.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.061606 restraints weight = 22571.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7572  Z= 0.177
  Angle     :  0.598  12.141  10313  Z= 0.305
  Chirality :  0.045   0.322   1167
  Planarity :  0.004   0.048   1310
  Dihedral  :  4.288  19.258   1004
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.27), residues: 913
  helix: -2.55 (0.74), residues: 31
  sheet:  0.01 (0.33), residues: 250
  loop : -1.14 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  44 
 TYR   0.015   0.001   TYR B 279 
 PHE   0.012   0.002   PHE H 125 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.005   0.001   HIS H 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.18 ( 7555)
  covalent geometry    : angle       0.57826 /  0.30 (10272)
  SS BOND              : bond        0.00356 /  0.22 (   10)
  SS BOND              : angle       0.80227 /  0.50 (   20)
  hydrogen bonds       : bond        0.03913 /  2.66 (  131)
  hydrogen bonds       : angle       6.48540 /  4.37 (  375)
  link_NAG-ASN         : bond        0.00471 /  0.25 (    7)
  link_NAG-ASN         : angle       3.42278 /  2.30 (   21)

*********************** 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
  48 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8401 (mmp) cc_final: 0.7809 (mmm)
REVERT: H   82 MET cc_start: 0.7629 (tmm) cc_final: 0.6821 (tmm)
REVERT: L   62 PHE cc_start: 0.8193 (m-80) cc_final: 0.7960 (m-80)
REVERT: L   83 PHE cc_start: 0.8502 (m-80) cc_final: 0.8054 (m-80)
REVERT: L  118 ILE cc_start: 0.7553 (pt) cc_final: 0.7313 (mt)
REVERT: B   18 LEU cc_start: 0.3981 (mm) cc_final: 0.3552 (mm)
REVERT: B   40 ASP cc_start: 0.9314 (p0) cc_final: 0.9058 (p0)
REVERT: B   42 VAL cc_start: 0.9083 (t) cc_final: 0.8789 (t)
REVERT: B   49 HIS cc_start: 0.8390 (t70) cc_final: 0.8079 (t-170)
REVERT: B   53 ASP cc_start: 0.8750 (m-30) cc_final: 0.8497 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0607
  time to fit residues: 4.4013
Evaluate side-chains
  26 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0570
   overall best weight:    1.2104

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.075493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.059046 restraints weight = 46656.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.059533 restraints weight = 25508.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.060096 restraints weight = 21274.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.060333 restraints weight = 17975.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.060455 restraints weight = 16733.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7572  Z= 0.126
  Angle     :  0.554  10.442  10313  Z= 0.278
  Chirality :  0.044   0.321   1167
  Planarity :  0.004   0.047   1310
  Dihedral  :  4.074  19.725   1004
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.27), residues: 913
  helix: -2.56 (0.74), residues: 30
  sheet:  0.12 (0.33), residues: 255
  loop : -1.11 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  44 
 TYR   0.008   0.001   TYR C 421 
 PHE   0.010   0.001   PHE B  86 
 TRP   0.007   0.001   TRP L  35 
 HIS   0.005   0.001   HIS H 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 7555)
  covalent geometry    : angle       0.53275 /  0.27 (10272)
  SS BOND              : bond        0.00298 /  0.19 (   10)
  SS BOND              : angle       0.69864 /  0.43 (   20)
  hydrogen bonds       : bond        0.03548 /  2.42 (  131)
  hydrogen bonds       : angle       6.27540 /  4.22 (  375)
  link_NAG-ASN         : bond        0.00570 /  0.34 (    7)
  link_NAG-ASN         : angle       3.36659 /  2.25 (   21)

*********************** 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
  44 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8631 (mmp) cc_final: 0.7894 (mmm)
REVERT: H   82 MET cc_start: 0.7519 (tmm) cc_final: 0.6921 (tmm)
REVERT: L   62 PHE cc_start: 0.8335 (m-80) cc_final: 0.8071 (m-80)
REVERT: L  118 ILE cc_start: 0.7683 (pt) cc_final: 0.7341 (mt)
REVERT: B   18 LEU cc_start: 0.4127 (mm) cc_final: 0.3640 (mm)
REVERT: B   42 VAL cc_start: 0.9096 (t) cc_final: 0.8840 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0564
  time to fit residues: 3.9583
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  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 200 ASN
** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.074659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.057712 restraints weight = 48280.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.058169 restraints weight = 27262.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.058521 restraints weight = 21405.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.058761 restraints weight = 18927.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.058900 restraints weight = 17299.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7572  Z= 0.175
  Angle     :  0.593  10.890  10313  Z= 0.302
  Chirality :  0.044   0.319   1167
  Planarity :  0.004   0.040   1310
  Dihedral  :  4.424  19.384   1004
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.27), residues: 913
  helix: -2.77 (0.73), residues: 30
  sheet: -0.08 (0.32), residues: 262
  loop : -1.16 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  34 
 TYR   0.013   0.001   TYR B 279 
 PHE   0.011   0.002   PHE B  86 
 TRP   0.009   0.001   TRP H 157 
 HIS   0.006   0.001   HIS H 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 7555)
  covalent geometry    : angle       0.57607 /  0.30 (10272)
  SS BOND              : bond        0.00403 /  0.26 (   10)
  SS BOND              : angle       0.82736 /  0.53 (   20)
  hydrogen bonds       : bond        0.03782 /  2.56 (  131)
  hydrogen bonds       : angle       6.41732 /  4.33 (  375)
  link_NAG-ASN         : bond        0.00552 /  0.35 (    7)
  link_NAG-ASN         : angle       3.08433 /  2.10 (   21)

*********************** 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
  41 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8709 (mmp) cc_final: 0.7958 (mmm)
REVERT: H   82 MET cc_start: 0.7747 (tmm) cc_final: 0.7244 (tmm)
REVERT: L    4 MET cc_start: 0.8061 (mmp) cc_final: 0.7407 (ptm)
REVERT: L   83 PHE cc_start: 0.8334 (m-80) cc_final: 0.7938 (m-80)
REVERT: L  118 ILE cc_start: 0.7844 (pt) cc_final: 0.7524 (mt)
REVERT: B  191 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8207 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0501
  time to fit residues: 3.3887
Evaluate side-chains
  19 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 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 = 0.3565 r_free = 0.3565 target = 0.068378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.052447 restraints weight = 49991.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.051939 restraints weight = 33597.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.052510 restraints weight = 28236.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.052766 restraints weight = 22709.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.052887 restraints weight = 21302.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.6205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082   7572  Z= 0.379
  Angle     :  0.919  15.396  10313  Z= 0.472
  Chirality :  0.051   0.309   1167
  Planarity :  0.006   0.065   1310
  Dihedral  :  6.164  30.814   1004
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 27.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.26), residues: 913
  helix: -3.33 (0.59), residues: 36
  sheet: -0.47 (0.31), residues: 240
  loop : -1.61 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L 143 
 TYR   0.034   0.003   TYR L 187 
 PHE   0.029   0.003   PHE B  43 
 TRP   0.028   0.003   TRP H 157 
 HIS   0.019   0.004   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00813 /  0.38 ( 7555)
  covalent geometry    : angle       0.90690 /  0.47 (10272)
  SS BOND              : bond        0.00638 /  0.40 (   10)
  SS BOND              : angle       1.30037 /  0.82 (   20)
  hydrogen bonds       : bond        0.05201 /  3.46 (  131)
  hydrogen bonds       : angle       7.49892 /  5.00 (  375)
  link_NAG-ASN         : bond        0.00565 /  0.29 (    7)
  link_NAG-ASN         : angle       3.25167 /  2.10 (   21)

*********************** 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
  33 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8804 (mmp) cc_final: 0.8198 (mmm)
REVERT: H   82 MET cc_start: 0.7550 (tmm) cc_final: 0.6614 (tmm)
REVERT: L  118 ILE cc_start: 0.8133 (pt) cc_final: 0.7824 (mt)
REVERT: B   40 ASP cc_start: 0.9367 (p0) cc_final: 0.8754 (p0)
REVERT: B   42 VAL cc_start: 0.9225 (t) cc_final: 0.8823 (p)
REVERT: B  280 ASN cc_start: 0.9329 (t0) cc_final: 0.9025 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0653
  time to fit residues: 3.3024
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  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 86 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    2.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 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 = 0.3603 r_free = 0.3603 target = 0.070158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.052421 restraints weight = 48286.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.053097 restraints weight = 25998.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.053553 restraints weight = 20505.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.053908 restraints weight = 17074.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.054005 restraints weight = 15501.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.6141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7572  Z= 0.206
  Angle     :  0.673  13.459  10313  Z= 0.345
  Chirality :  0.046   0.327   1167
  Planarity :  0.005   0.050   1310
  Dihedral  :  5.455  27.645   1004
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.27), residues: 913
  helix: -3.20 (0.64), residues: 36
  sheet: -0.65 (0.30), residues: 274
  loop : -1.41 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  44 
 TYR   0.020   0.002   TYR L 187 
 PHE   0.016   0.002   PHE B  58 
 TRP   0.013   0.002   TRP H 157 
 HIS   0.014   0.002   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.21 ( 7555)
  covalent geometry    : angle       0.66040 /  0.34 (10272)
  SS BOND              : bond        0.00497 /  0.33 (   10)
  SS BOND              : angle       1.00658 /  0.70 (   20)
  hydrogen bonds       : bond        0.03917 /  2.60 (  131)
  hydrogen bonds       : angle       6.98153 /  4.68 (  375)
  link_NAG-ASN         : bond        0.00500 /  0.31 (    7)
  link_NAG-ASN         : angle       2.89999 /  1.98 (   21)

*********************** 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
  36 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8889 (mmp) cc_final: 0.8255 (mmm)
REVERT: H   82 MET cc_start: 0.7880 (tmm) cc_final: 0.7302 (tmm)
REVERT: L    4 MET cc_start: 0.8231 (mmp) cc_final: 0.7652 (ptp)
REVERT: L  118 ILE cc_start: 0.7729 (pt) cc_final: 0.7490 (mt)
REVERT: B   40 ASP cc_start: 0.9377 (p0) cc_final: 0.8764 (p0)
REVERT: B   42 VAL cc_start: 0.9256 (t) cc_final: 0.8832 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0752
  time to fit residues: 4.1048
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  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 68 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 22 optimal weight:    0.3980
   chunk 41 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.071112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.054006 restraints weight = 47295.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.054165 restraints weight = 25594.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.054528 restraints weight = 23328.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.054805 restraints weight = 19158.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.055130 restraints weight = 17152.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.6130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7572  Z= 0.149
  Angle     :  0.609  11.572  10313  Z= 0.311
  Chirality :  0.045   0.325   1167
  Planarity :  0.004   0.045   1310
  Dihedral  :  4.998  28.038   1004
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.27), residues: 913
  helix: -3.43 (0.62), residues: 38
  sheet: -0.49 (0.31), residues: 258
  loop : -1.23 (0.25), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  44 
 TYR   0.015   0.001   TYR L 187 
 PHE   0.013   0.001   PHE B  86 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.011   0.002   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 ( 7555)
  covalent geometry    : angle       0.59529 /  0.31 (10272)
  SS BOND              : bond        0.00480 /  0.30 (   10)
  SS BOND              : angle       0.86736 /  0.60 (   20)
  hydrogen bonds       : bond        0.03585 /  2.38 (  131)
  hydrogen bonds       : angle       6.57087 /  4.41 (  375)
  link_NAG-ASN         : bond        0.00492 /  0.29 (    7)
  link_NAG-ASN         : angle       2.79674 /  1.93 (   21)

*********************** 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
  40 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8789 (mmp) cc_final: 0.8132 (mmm)
REVERT: H   82 MET cc_start: 0.7492 (tmm) cc_final: 0.6805 (tmm)
REVERT: L    4 MET cc_start: 0.8152 (mmp) cc_final: 0.7755 (ptp)
REVERT: L   62 PHE cc_start: 0.8122 (m-80) cc_final: 0.7913 (m-80)
REVERT: B   40 ASP cc_start: 0.9422 (p0) cc_final: 0.8869 (p0)
REVERT: B   42 VAL cc_start: 0.9372 (t) cc_final: 0.8975 (p)
REVERT: B  198 ASP cc_start: 0.9190 (t0) cc_final: 0.8961 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0748
  time to fit residues: 4.5585
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  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   overall best weight:    3.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 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 = 0.3564 r_free = 0.3564 target = 0.068535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.050473 restraints weight = 49382.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.051578 restraints weight = 29561.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.052114 restraints weight = 19486.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.052343 restraints weight = 19163.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.052473 restraints weight = 16030.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.6752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   7572  Z= 0.274
  Angle     :  0.761  13.605  10313  Z= 0.389
  Chirality :  0.048   0.325   1167
  Planarity :  0.005   0.052   1310
  Dihedral  :  5.601  31.179   1004
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  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 : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.27), residues: 913
  helix: -3.28 (0.62), residues: 36
  sheet: -0.66 (0.31), residues: 254
  loop : -1.52 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  44 
 TYR   0.025   0.002   TYR L 187 
 PHE   0.031   0.003   PHE H 125 
 TRP   0.022   0.003   TRP H 157 
 HIS   0.017   0.003   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00598 /  0.27 ( 7555)
  covalent geometry    : angle       0.75025 /  0.39 (10272)
  SS BOND              : bond        0.00531 /  0.34 (   10)
  SS BOND              : angle       0.96831 /  0.64 (   20)
  hydrogen bonds       : bond        0.04511 /  3.00 (  131)
  hydrogen bonds       : angle       6.95535 /  4.70 (  375)
  link_NAG-ASN         : bond        0.00491 /  0.26 (    7)
  link_NAG-ASN         : angle       2.90911 /  1.95 (   21)

********************** 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
  34 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8869 (mmp) cc_final: 0.8191 (mmm)
REVERT: H   82 MET cc_start: 0.7917 (tmm) cc_final: 0.7366 (tmm)
REVERT: L    4 MET cc_start: 0.8236 (mmp) cc_final: 0.7695 (ptp)
REVERT: L   62 PHE cc_start: 0.8403 (m-80) cc_final: 0.8148 (m-80)
REVERT: L  171 ASP cc_start: 0.8345 (t0) cc_final: 0.8104 (t0)
REVERT: B   40 ASP cc_start: 0.9451 (p0) cc_final: 0.8920 (p0)
REVERT: B   42 VAL cc_start: 0.9198 (t) cc_final: 0.8803 (p)
REVERT: B  198 ASP cc_start: 0.9166 (t0) cc_final: 0.8941 (t0)
REVERT: B  223 LEU cc_start: 0.9558 (mm) cc_final: 0.9073 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0589
  time to fit residues: 3.1494
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  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 67 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0010
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 HIS
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.071575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.054165 restraints weight = 47406.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.054713 restraints weight = 25276.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.054855 restraints weight = 21204.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.056172 restraints weight = 18162.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.056042 restraints weight = 14887.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.6388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7572  Z= 0.112
  Angle     :  0.588  10.774  10313  Z= 0.299
  Chirality :  0.046   0.328   1167
  Planarity :  0.004   0.041   1310
  Dihedral  :  4.818  28.707   1004
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.27), residues: 913
  helix: -3.20 (0.64), residues: 37
  sheet: -0.43 (0.31), residues: 264
  loop : -1.28 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  44 
 TYR   0.014   0.001   TYR B 204 
 PHE   0.011   0.001   PHE B  86 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.008   0.001   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 7555)
  covalent geometry    : angle       0.57492 /  0.30 (10272)
  SS BOND              : bond        0.00468 /  0.30 (   10)
  SS BOND              : angle       0.89512 /  0.63 (   20)
  hydrogen bonds       : bond        0.03399 /  2.21 (  131)
  hydrogen bonds       : angle       6.36380 /  4.30 (  375)
  link_NAG-ASN         : bond        0.00569 /  0.32 (    7)
  link_NAG-ASN         : angle       2.68761 /  1.88 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1069.64 seconds
wall clock time: 19 minutes 16.83 seconds (1156.83 seconds total)