Starting phenix.real_space_refine
on Tue Feb  3 17:14:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s3o_54543/02_2026/9s3o_54543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s3o_54543/02_2026/9s3o_54543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s3o_54543/02_2026/9s3o_54543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s3o_54543/02_2026/9s3o_54543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s3o_54543/02_2026/9s3o_54543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s3o_54543/02_2026/9s3o_54543.cif"
  }
  resolution = 3.9
  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=   0.005 sd=   0.062
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      20      5.16       5
     C    3461      2.51       5
     N     908      2.21       5
     O     995      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5384
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2681
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 9, 'TRANS': 328}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 57
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7}
          Unresolved non-hydrogen planarities: 53
    Chain: "D"
      Number of atoms: 2689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2689
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 9, 'TRANS': 352}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 204
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 11, 'GLN:plan1': 5, 'ASN:plan1': 4, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 121
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.20, per 1000 atoms: 0.22
  Number of scatterers: 5384
  At special positions: 0
  Unit cell: (64.94, 122.24, 71.625, 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      20     16.00
     O     995      8.00
     N     908      7.00
     C    3461      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D 306 " 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 D 901 " - " ASN D 232 "
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 322.4 milliseconds
  

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1302

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      43.6% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 32
    Processing helix  chain 'B' and resid 54 through 69
    Processing helix  chain 'B' and resid 81 through 92
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 139 through 142
      removed outlier: 3.726A  pdb=" N   GLY B 142 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 139 through 142'
    Processing helix  chain 'B' and resid 143 through 157
    Processing helix  chain 'B' and resid 169 through 183
    Processing helix  chain 'B' and resid 193 through 208
      removed outlier: 3.728A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   SER B 206 " --> pdb=" O   GLU B 202 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL B 207 " --> pdb=" O   GLN B 203 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLY B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 226
      removed outlier: 3.732A  pdb=" N   ILE B 226 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 235
    Processing helix  chain 'B' and resid 248 through 261
    Processing helix  chain 'B' and resid 274 through 296
      removed outlier: 3.780A  pdb=" N   ARG B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.596A  pdb=" N   GLN B 330 " --> pdb=" O   ARG B 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 326 through 330'
    Processing helix  chain 'D' and resid 14 through 27
    Processing helix  chain 'D' and resid 45 through 58
    Processing helix  chain 'D' and resid 72 through 84
    Processing helix  chain 'D' and resid 111 through 119
      removed outlier: 4.299A  pdb=" N   GLU D 117 " --> pdb=" O   LEU D 113 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR D 118 " --> pdb=" O   SER D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 148
    Processing helix  chain 'D' and resid 163 through 178
    Processing helix  chain 'D' and resid 188 through 203
      removed outlier: 3.501A  pdb=" N   ASP D 194 " --> pdb=" O   ASP D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 254
      removed outlier: 3.591A  pdb=" N   ARG D 252 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER D 254 " --> pdb=" O   ILE D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 293
    Processing helix  chain 'D' and resid 316 through 326
      removed outlier: 3.801A  pdb=" N   ILE D 320 " --> pdb=" O   GLN D 316 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ALA D 323 " --> pdb=" O   GLU D 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7
      removed outlier: 6.969A  pdb=" N   VAL B   6 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 9 through 11
      removed outlier: 6.421A  pdb=" N   GLY B   9 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU B  96 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 164
      removed outlier: 7.589A  pdb=" N   PHE B 133 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   ILE B 163 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   PHE B 135 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   LYS B 187 " --> pdb=" O   CYS B 132 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   PHE B 188 " --> pdb=" O   HIS B 215 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   PHE B 241 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   VAL B 238 " --> pdb=" O   LEU B 358 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY B 367 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   GLU B 357 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   LYS B 365 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LYS B 359 " --> pdb=" O   PRO B 363 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 335
    Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 10
      removed outlier: 6.703A  pdb=" N   GLY D   7 " --> pdb=" O   ASP D  39 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   LEU D  41 " --> pdb=" O   GLY D   7 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   PHE D   9 " --> pdb=" O   LEU D  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 64 through 65
      removed outlier: 6.706A  pdb=" N   ILE D  64 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 153 through 156
      removed outlier: 6.665A  pdb=" N   TYR D 126 " --> pdb=" O   ILE D 154 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   VAL D 156 " --> pdb=" O   TYR D 126 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   TYR D 128 " --> pdb=" O   VAL D 156 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU D 127 " --> pdb=" O   ILE D 184 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL D 183 " --> pdb=" O   HIS D 210 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE D 212 " --> pdb=" O   VAL D 183 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   PHE D 236 " --> pdb=" O   ILE D 213 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL D 233 " --> pdb=" O   LEU D 354 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY D 363 " --> pdb=" O   ILE D 351 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   GLU D 353 " --> pdb=" O   LYS D 361 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   LYS D 361 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 328 through 331

    248 hydrogen bonds defined for protein.
    723 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: 0.85

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1737
        1.34 -     1.46: 856
        1.46 -     1.57: 2879
        1.57 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 5503
  Sorted by residual:
  bond pdb=" CB  GLN D 281 "
       pdb=" CG  GLN D 281 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CB  GLU D  16 "
       pdb=" CG  GLU D  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.28e-01
  bond pdb=" CB  GLU B 229 "
       pdb=" CG  GLU B 229 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.21e-01
  bond pdb=" CA  LYS B 374 "
       pdb=" C   LYS B 374 "
    ideal  model  delta    sigma   weight residual
    1.528  1.536 -0.008 8.80e-03 1.29e+04 9.08e-01
  bond pdb=" CB  GLU D 285 "
       pdb=" CG  GLU D 285 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.30e-01
  ... (remaining 5498 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 7308
        1.88 -     3.75: 163
        3.75 -     5.63: 15
        5.63 -     7.51: 2
        7.51 -     9.38: 1
  Bond angle restraints: 7489
  Sorted by residual:
  angle pdb=" N   ILE D 345 "
        pdb=" CA  ILE D 345 "
        pdb=" C   ILE D 345 "
      ideal   model   delta    sigma   weight residual
     113.71  110.69    3.02 9.50e-01 1.11e+00 1.01e+01
  angle pdb=" C   GLU B 185 "
        pdb=" N   LYS B 186 "
        pdb=" CA  LYS B 186 "
      ideal   model   delta    sigma   weight residual
     121.54  127.22   -5.68 1.91e+00 2.74e-01 8.84e+00
  angle pdb=" C   LEU D 290 "
        pdb=" N   ARG D 291 "
        pdb=" CA  ARG D 291 "
      ideal   model   delta    sigma   weight residual
     120.31  116.12    4.19 1.52e+00 4.33e-01 7.61e+00
  angle pdb=" CG  ARG D  21 "
        pdb=" CD  ARG D  21 "
        pdb=" NE  ARG D  21 "
      ideal   model   delta    sigma   weight residual
     112.00  117.90   -5.90 2.20e+00 2.07e-01 7.19e+00
  angle pdb=" CA  LEU D   8 "
        pdb=" CB  LEU D   8 "
        pdb=" CG  LEU D   8 "
      ideal   model   delta    sigma   weight residual
     116.30  125.68   -9.38 3.50e+00 8.16e-02 7.19e+00
  ... (remaining 7484 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 2995
       17.28 -    34.57: 174
       34.57 -    51.85: 16
       51.85 -    69.13: 12
       69.13 -    86.42: 5
  Dihedral angle restraints: 3202
    sinusoidal: 1175
      harmonic: 2027
  Sorted by residual:
  dihedral pdb=" CA  TRP D 314 "
           pdb=" C   TRP D 314 "
           pdb=" N   GLY D 315 "
           pdb=" CA  GLY D 315 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.03  -17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TYR D 118 "
           pdb=" C   TYR D 118 "
           pdb=" N   TYR D 119 "
           pdb=" CA  TYR D 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.95   17.05     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU B 129 "
           pdb=" CG  GLU B 129 "
           pdb=" CD  GLU B 129 "
           pdb=" OE1 GLU B 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.42   86.42     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 3199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 504
       0.028 -    0.057: 215
       0.057 -    0.085: 88
       0.085 -    0.114: 45
       0.114 -    0.142: 10
  Chirality restraints: 862
  Sorted by residual:
  chirality pdb=" CA  VAL D 233 "
            pdb=" N   VAL D 233 "
            pdb=" C   VAL D 233 "
            pdb=" CB  VAL D 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE D 351 "
            pdb=" N   ILE D 351 "
            pdb=" C   ILE D 351 "
            pdb=" CB  ILE D 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  VAL B 211 "
            pdb=" N   VAL B 211 "
            pdb=" C   VAL B 211 "
            pdb=" CB  VAL B 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.15e-01
  ... (remaining 859 not shown)

  Planarity restraints: 958
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D  92 "   -0.040 5.00e-02 4.00e+02   6.12e-02 6.00e+00
        pdb=" N   PRO D  93 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO D  93 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D  93 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  89 "    0.035 5.00e-02 4.00e+02   5.28e-02 4.46e+00
        pdb=" N   PRO D  90 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO D  90 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D  90 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 314 "    0.014 2.00e-02 2.50e+03   1.21e-02 3.63e+00
        pdb=" CG  TRP D 314 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 314 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 314 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 314 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 314 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 314 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 314 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 314 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 314 "    0.004 2.00e-02 2.50e+03
  ... (remaining 955 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 3276
        3.03 -     3.50: 5312
        3.50 -     3.97: 8204
        3.97 -     4.43: 9133
        4.43 -     4.90: 14791
  Nonbonded interactions: 40716
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 229 "
            pdb=" OE1 GLU B 229 "
     model   vdw
     2.563 3.120
  nonbonded pdb=" N   GLU D  16 "
            pdb=" OE1 GLU D  16 "
     model   vdw
     2.578 3.120
  nonbonded pdb=" O   VAL D 199 "
            pdb=" O   GLY D 203 "
     model   vdw
     2.581 3.040
  nonbonded pdb=" O   ASP D 186 "
            pdb=" OD1 ASP D 186 "
     model   vdw
     2.613 3.040
  nonbonded pdb=" OE1 GLN D 237 "
            pdb=" N   ILE D 238 "
     model   vdw
     2.622 3.120
  ... (remaining 40711 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:             4.500
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.720
  Find NCS groups from input model:        0.020
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
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   0.036   5505  Z= 0.144
  Angle     :  0.645   9.384   7494  Z= 0.369
  Chirality :  0.041   0.142    862
  Planarity :  0.005   0.061    957
  Dihedral  : 12.021  86.416   1897
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.33 (0.32), residues: 688
  helix:  1.27 (0.31), residues: 288
  sheet: -1.66 (0.45), residues: 121
  loop : -1.07 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 326 
 TYR   0.011   0.001   TYR D  17 
 PHE   0.020   0.001   PHE B 291 
 TRP   0.032   0.002   TRP D 314 
 HIS   0.008   0.001   HIS B 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5503)
  covalent geometry    : angle       0.64109 ( 7489)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.59593 (    2)
  hydrogen bonds       : bond        0.16603 (  248)
  hydrogen bonds       : angle       5.67944 (  723)
  link_NAG-ASN         : bond        0.00164 (    1)
  link_NAG-ASN         : angle       3.45378 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  255 MET cc_start: 0.7469 (tpt) cc_final: 0.6793 (tpp)
REVERT: D  267 THR cc_start: 0.8180 (m) cc_final: 0.7940 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0783
  time to fit residues: 13.2853
Evaluate side-chains
  75 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.091352 restraints weight = 11267.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093885 restraints weight = 7100.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.095724 restraints weight = 5041.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.096972 restraints weight = 3860.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.097959 restraints weight = 3159.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5505  Z= 0.126
  Angle     :  0.525   6.631   7494  Z= 0.281
  Chirality :  0.043   0.139    862
  Planarity :  0.004   0.047    957
  Dihedral  :  3.938  16.536    775
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.04 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.01 (0.32), residues: 688
  helix:  1.70 (0.31), residues: 292
  sheet: -1.42 (0.47), residues: 116
  loop : -1.21 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 326 
 TYR   0.012   0.001   TYR D 168 
 PHE   0.017   0.001   PHE D  92 
 TRP   0.040   0.002   TRP D 314 
 HIS   0.005   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5503)
  covalent geometry    : angle       0.52087 ( 7489)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.22646 (    2)
  hydrogen bonds       : bond        0.04131 (  248)
  hydrogen bonds       : angle       4.40251 (  723)
  link_NAG-ASN         : bond        0.00487 (    1)
  link_NAG-ASN         : angle       3.49976 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 GLN cc_start: 0.8015 (mp10) cc_final: 0.7811 (mp10)
REVERT: B  164 CYS cc_start: 0.8347 (t) cc_final: 0.7959 (t)
REVERT: D  352 MET cc_start: 0.8731 (mtm) cc_final: 0.8528 (mtm)
  outliers start: 6
  outliers final: 5
  residues processed: 86
  average time/residue: 0.0636
  time to fit residues: 7.1988
Evaluate side-chains
  70 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  250 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.105556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.089798 restraints weight = 11065.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.092311 restraints weight = 6877.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.094146 restraints weight = 4849.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.095216 restraints weight = 3705.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.096324 restraints weight = 3062.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5505  Z= 0.151
  Angle     :  0.517   5.717   7494  Z= 0.277
  Chirality :  0.043   0.245    862
  Planarity :  0.004   0.047    957
  Dihedral  :  4.005  16.699    775
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.04 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.16 (0.32), residues: 688
  helix:  1.99 (0.31), residues: 292
  sheet: -1.44 (0.46), residues: 116
  loop : -1.25 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  24 
 TYR   0.012   0.001   TYR D 168 
 PHE   0.017   0.001   PHE D 172 
 TRP   0.034   0.002   TRP D 314 
 HIS   0.003   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5503)
  covalent geometry    : angle       0.51222 ( 7489)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.24353 (    2)
  hydrogen bonds       : bond        0.04022 (  248)
  hydrogen bonds       : angle       4.16864 (  723)
  link_NAG-ASN         : bond        0.00564 (    1)
  link_NAG-ASN         : angle       3.45584 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: B  164 CYS cc_start: 0.8501 (t) cc_final: 0.8134 (t)
REVERT: B  255 MET cc_start: 0.6815 (tpp) cc_final: 0.5412 (tpp)
REVERT: D   91 SER cc_start: 0.9003 (m) cc_final: 0.8535 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0585
  time to fit residues: 5.7713
Evaluate side-chains
  70 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  265 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.107067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.092231 restraints weight = 10877.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094571 restraints weight = 6929.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.096259 restraints weight = 4980.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.097407 restraints weight = 3825.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098386 restraints weight = 3141.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5505  Z= 0.108
  Angle     :  0.486   5.556   7494  Z= 0.259
  Chirality :  0.041   0.163    862
  Planarity :  0.003   0.045    957
  Dihedral  :  3.838  15.501    775
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 10.04 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.28 (0.32), residues: 688
  helix:  2.09 (0.31), residues: 292
  sheet: -1.23 (0.47), residues: 117
  loop : -1.25 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.009   0.001   TYR D 168 
 PHE   0.010   0.001   PHE B 188 
 TRP   0.022   0.002   TRP D 314 
 HIS   0.003   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5503)
  covalent geometry    : angle       0.48258 ( 7489)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.16237 (    2)
  hydrogen bonds       : bond        0.03400 (  248)
  hydrogen bonds       : angle       3.97047 (  723)
  link_NAG-ASN         : bond        0.00406 (    1)
  link_NAG-ASN         : angle       3.05986 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: B  164 CYS cc_start: 0.8420 (t) cc_final: 0.8055 (t)
REVERT: D   91 SER cc_start: 0.9020 (m) cc_final: 0.8554 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 77
  average time/residue: 0.0442
  time to fit residues: 4.8280
Evaluate side-chains
  74 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7740

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.091794 restraints weight = 11112.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.094141 restraints weight = 7115.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.095874 restraints weight = 5135.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.097114 restraints weight = 3953.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097674 restraints weight = 3226.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5505  Z= 0.099
  Angle     :  0.467   4.998   7494  Z= 0.250
  Chirality :  0.041   0.136    862
  Planarity :  0.003   0.041    957
  Dihedral  :  3.714  14.829    775
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.50 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.46 (0.33), residues: 688
  helix:  2.22 (0.31), residues: 292
  sheet: -1.08 (0.48), residues: 117
  loop : -1.17 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.008   0.001   TYR B  77 
 PHE   0.010   0.001   PHE D 172 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.003   0.001   HIS D 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 5503)
  covalent geometry    : angle       0.46375 ( 7489)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.15285 (    2)
  hydrogen bonds       : bond        0.03133 (  248)
  hydrogen bonds       : angle       3.78397 (  723)
  link_NAG-ASN         : bond        0.00354 (    1)
  link_NAG-ASN         : angle       2.84933 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 GLN cc_start: 0.7992 (mp10) cc_final: 0.7768 (mp10)
REVERT: B  164 CYS cc_start: 0.8382 (t) cc_final: 0.8029 (t)
REVERT: B  261 LEU cc_start: 0.8208 (mp) cc_final: 0.7845 (tp)
REVERT: D   91 SER cc_start: 0.9067 (m) cc_final: 0.8571 (p)
REVERT: D  352 MET cc_start: 0.8759 (mtm) cc_final: 0.8333 (mtt)
  outliers start: 14
  outliers final: 11
  residues processed: 76
  average time/residue: 0.0522
  time to fit residues: 5.4894
Evaluate side-chains
  77 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 28 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0470
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.5880

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

Flipped N/Q/H residues before XYZ refinement:
D  56 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.108006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.092869 restraints weight = 10982.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.095235 restraints weight = 7044.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096962 restraints weight = 5057.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.098198 restraints weight = 3903.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.099022 restraints weight = 3193.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5505  Z= 0.090
  Angle     :  0.460   5.370   7494  Z= 0.244
  Chirality :  0.041   0.139    862
  Planarity :  0.003   0.040    957
  Dihedral  :  3.543  14.866    775
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.14 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.65 (0.33), residues: 688
  helix:  2.36 (0.31), residues: 292
  sheet: -0.87 (0.48), residues: 122
  loop : -1.10 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 288 
 TYR   0.008   0.001   TYR B  77 
 PHE   0.009   0.001   PHE B 188 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.003   0.001   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 5503)
  covalent geometry    : angle       0.45760 ( 7489)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.15664 (    2)
  hydrogen bonds       : bond        0.02886 (  248)
  hydrogen bonds       : angle       3.65420 (  723)
  link_NAG-ASN         : bond        0.00284 (    1)
  link_NAG-ASN         : angle       2.62198 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 GLN cc_start: 0.7975 (mp10) cc_final: 0.7760 (mp10)
REVERT: B  164 CYS cc_start: 0.8305 (t) cc_final: 0.7968 (t)
REVERT: B  261 LEU cc_start: 0.8192 (mp) cc_final: 0.7859 (tp)
REVERT: D  352 MET cc_start: 0.8753 (mtm) cc_final: 0.8444 (mtt)
  outliers start: 15
  outliers final: 14
  residues processed: 79
  average time/residue: 0.0539
  time to fit residues: 5.9417
Evaluate side-chains
  78 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  202 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 35 optimal weight:   10.0000
   chunk 63 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.107618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.092412 restraints weight = 11054.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094778 restraints weight = 7096.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.096451 restraints weight = 5112.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.097696 restraints weight = 3973.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.098521 restraints weight = 3254.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5505  Z= 0.096
  Angle     :  0.479   7.815   7494  Z= 0.250
  Chirality :  0.040   0.132    862
  Planarity :  0.003   0.039    957
  Dihedral  :  3.512  14.729    775
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.96 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.33), residues: 688
  helix:  2.42 (0.31), residues: 292
  sheet: -0.82 (0.48), residues: 124
  loop : -1.08 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  33 
 TYR   0.008   0.001   TYR B  77 
 PHE   0.009   0.001   PHE D 172 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.004   0.001   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 5503)
  covalent geometry    : angle       0.47665 ( 7489)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.17621 (    2)
  hydrogen bonds       : bond        0.02886 (  248)
  hydrogen bonds       : angle       3.58255 (  723)
  link_NAG-ASN         : bond        0.00305 (    1)
  link_NAG-ASN         : angle       2.56947 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B    7 GLN cc_start: 0.7985 (mp10) cc_final: 0.7774 (mp10)
REVERT: B  164 CYS cc_start: 0.8330 (t) cc_final: 0.8001 (t)
REVERT: B  261 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7862 (tp)
REVERT: D   91 SER cc_start: 0.9080 (m) cc_final: 0.8570 (p)
REVERT: D  352 MET cc_start: 0.8750 (mtm) cc_final: 0.8333 (mtt)
  outliers start: 14
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0482
  time to fit residues: 5.0830
Evaluate side-chains
  77 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 36 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.092299 restraints weight = 10876.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094676 restraints weight = 6927.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.096425 restraints weight = 4985.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097569 restraints weight = 3837.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.098579 restraints weight = 3167.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5505  Z= 0.107
  Angle     :  0.490   5.941   7494  Z= 0.258
  Chirality :  0.040   0.132    862
  Planarity :  0.003   0.040    957
  Dihedral  :  3.548  14.771    775
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 12.96 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.75 (0.33), residues: 688
  helix:  2.47 (0.31), residues: 292
  sheet: -0.79 (0.48), residues: 124
  loop : -1.11 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 230 
 TYR   0.009   0.001   TYR B  77 
 PHE   0.009   0.001   PHE D 172 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.004   0.001   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5503)
  covalent geometry    : angle       0.48749 ( 7489)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.16725 (    2)
  hydrogen bonds       : bond        0.02939 (  248)
  hydrogen bonds       : angle       3.60690 (  723)
  link_NAG-ASN         : bond        0.00371 (    1)
  link_NAG-ASN         : angle       2.61506 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 GLN cc_start: 0.8022 (mp10) cc_final: 0.7808 (mp10)
REVERT: B  164 CYS cc_start: 0.8372 (t) cc_final: 0.8037 (t)
REVERT: B  261 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8012 (tp)
REVERT: D   91 SER cc_start: 0.9099 (m) cc_final: 0.8595 (p)
REVERT: D  267 THR cc_start: 0.8218 (m) cc_final: 0.7986 (t)
REVERT: D  352 MET cc_start: 0.8771 (mtm) cc_final: 0.8357 (mtt)
  outliers start: 18
  outliers final: 14
  residues processed: 73
  average time/residue: 0.0574
  time to fit residues: 5.8454
Evaluate side-chains
  77 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  105 ARG
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  202 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.091783 restraints weight = 10980.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.094092 restraints weight = 7039.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.095790 restraints weight = 5061.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097003 restraints weight = 3919.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.097920 restraints weight = 3213.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5505  Z= 0.117
  Angle     :  0.486   5.983   7494  Z= 0.256
  Chirality :  0.040   0.132    862
  Planarity :  0.003   0.040    957
  Dihedral  :  3.628  14.738    775
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.59 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.74 (0.33), residues: 688
  helix:  2.49 (0.31), residues: 292
  sheet: -0.84 (0.47), residues: 124
  loop : -1.12 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 230 
 TYR   0.009   0.001   TYR B  77 
 PHE   0.009   0.001   PHE D 172 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.004   0.001   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 5503)
  covalent geometry    : angle       0.48358 ( 7489)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.16796 (    2)
  hydrogen bonds       : bond        0.03112 (  248)
  hydrogen bonds       : angle       3.63179 (  723)
  link_NAG-ASN         : bond        0.00413 (    1)
  link_NAG-ASN         : angle       2.66015 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 GLN cc_start: 0.8004 (mp10) cc_final: 0.7802 (mp10)
REVERT: B  164 CYS cc_start: 0.8376 (t) cc_final: 0.8049 (t)
REVERT: B  261 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8042 (tp)
REVERT: D   91 SER cc_start: 0.9100 (m) cc_final: 0.8637 (p)
REVERT: D  257 GLU cc_start: 0.7815 (pm20) cc_final: 0.7493 (pm20)
REVERT: D  267 THR cc_start: 0.8144 (m) cc_final: 0.7923 (t)
REVERT: D  352 MET cc_start: 0.8752 (mtm) cc_final: 0.8308 (mtt)
  outliers start: 17
  outliers final: 13
  residues processed: 73
  average time/residue: 0.0639
  time to fit residues: 6.5181
Evaluate side-chains
  76 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  105 ARG
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  202 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    0.0270
   chunk 31 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    0.3980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
D 328 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.092361 restraints weight = 11145.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094734 restraints weight = 7134.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.096505 restraints weight = 5128.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.097765 restraints weight = 3964.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.098590 restraints weight = 3243.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5505  Z= 0.095
  Angle     :  0.485   6.217   7494  Z= 0.254
  Chirality :  0.040   0.134    862
  Planarity :  0.003   0.040    957
  Dihedral  :  3.501  14.855    775
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.14 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.80 (0.33), residues: 688
  helix:  2.52 (0.31), residues: 292
  sheet: -0.72 (0.47), residues: 124
  loop : -1.11 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.008   0.001   TYR B  77 
 PHE   0.008   0.001   PHE D 172 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.005   0.001   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 5503)
  covalent geometry    : angle       0.48291 ( 7489)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.14039 (    2)
  hydrogen bonds       : bond        0.02756 (  248)
  hydrogen bonds       : angle       3.53486 (  723)
  link_NAG-ASN         : bond        0.00287 (    1)
  link_NAG-ASN         : angle       2.49582 (    3)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: B  164 CYS cc_start: 0.8322 (t) cc_final: 0.7986 (t)
REVERT: D  257 GLU cc_start: 0.7787 (pm20) cc_final: 0.7455 (pm20)
REVERT: D  352 MET cc_start: 0.8698 (mtm) cc_final: 0.8250 (mtt)
  outliers start: 15
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0649
  time to fit residues: 6.4320
Evaluate side-chains
  74 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   63 CYS
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  105 ARG
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  202 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  265 HIS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  373 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0970
   chunk 49 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
D 328 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.091083 restraints weight = 11036.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.093613 restraints weight = 6869.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.095344 restraints weight = 4847.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.096726 restraints weight = 3740.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.097691 restraints weight = 3030.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5505  Z= 0.105
  Angle     :  0.492   6.165   7494  Z= 0.257
  Chirality :  0.040   0.130    862
  Planarity :  0.003   0.039    957
  Dihedral  :  3.532  14.723    775
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.69 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.82 (0.33), residues: 688
  helix:  2.59 (0.31), residues: 292
  sheet: -0.82 (0.47), residues: 124
  loop : -1.09 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 230 
 TYR   0.009   0.001   TYR B  77 
 PHE   0.009   0.001   PHE D 172 
 TRP   0.022   0.001   TRP D 314 
 HIS   0.005   0.001   HIS D  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5503)
  covalent geometry    : angle       0.48893 ( 7489)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.17107 (    2)
  hydrogen bonds       : bond        0.02874 (  248)
  hydrogen bonds       : angle       3.53846 (  723)
  link_NAG-ASN         : bond        0.00344 (    1)
  link_NAG-ASN         : angle       2.58564 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 809.64 seconds
wall clock time: 14 minutes 35.25 seconds (875.25 seconds total)