Starting phenix.real_space_refine
on Wed Sep 17 06:59:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jub_61826/09_2025/9jub_61826_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jub_61826/09_2025/9jub_61826.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jub_61826/09_2025/9jub_61826_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jub_61826/09_2025/9jub_61826_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jub_61826/09_2025/9jub_61826.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jub_61826/09_2025/9jub_61826.map"
  }
  resolution = 3.1
  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=  -0.000 sd=   0.021
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      29      5.16       5
     C    4127      2.51       5
     N    1059      2.21       5
     O    1264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6479
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3286
          Classifications: {'peptide': 406}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 382}
    Chain: "B"
      Number of atoms: 1561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1561
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1562
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.60, per 1000 atoms: 0.25
  Number of scatterers: 6479
  At special positions: 0
  Unit cell: (68.392, 73.04, 162.68, 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      29     16.00
     O    1264      8.00
     N    1059      7.00
     C    4127      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 351 " distance=2.26
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 238 " distance=0.71
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 387 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 381 " - pdb=" SG  CYS A 435 " distance=1.15
    Simple disulfide: pdb=" SG  CYS B  21 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 145 " - pdb=" SG  CYS B 198 " distance=1.78
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 137 " - pdb=" SG  CYS C 196 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 166 "
      " NAG A 502 " - " ASN A 235 "
      " NAG A 503 " - " ASN A 393 "
      " NAG D   1 " - " ASN A 368 "
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 368.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1540

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 15 sheets defined
      20.4% alpha, 28.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 135
      removed outlier: 3.602A  pdb=" N   MET A 135 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 176
      removed outlier: 3.821A  pdb=" N   SER A 168 " --> pdb=" O   TYR A 164 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   VAL A 172 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 189
      removed outlier: 3.696A  pdb=" N   LYS A 189 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 209
      removed outlier: 3.731A  pdb=" N   GLU A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY A 207 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LEU A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 249
      removed outlier: 3.605A  pdb=" N   ILE A 243 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 254
      removed outlier: 4.329A  pdb=" N   TRP A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASN A 254 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 254'
    Processing helix  chain 'A' and resid 270 through 288
    Processing helix  chain 'A' and resid 317 through 330
      removed outlier: 3.515A  pdb=" N   TYR A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   GLU A 327 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 361
    Processing helix  chain 'A' and resid 361 through 381
    Processing helix  chain 'A' and resid 422 through 432
      removed outlier: 3.607A  pdb=" N   LEU A 426 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 87
      removed outlier: 4.191A  pdb=" N   THR B  87 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 163
      No H-bonds generated for 'chain 'B' and resid 161 through 163'
    Processing helix  chain 'C' and resid 185 through 190
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 77
      removed outlier: 7.016A  pdb=" N   TRP A  51 " --> pdb=" O   PHE A  75 " (cutoff:3.500A)
      removed outlier: 8.518A  pdb=" N   GLY A  77 " --> pdb=" O   TRP A  51 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   TRP A  53 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   ALA A 302 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   TRP A 339 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   THR A 304 " --> pdb=" O   TRP A 339 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389
    Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 409
    Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.642A  pdb=" N   VAL B  36 " --> pdb=" O   PHE B  91 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ILE B  33 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   ILE B  49 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   TRP B  35 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 11
      removed outlier: 3.703A  pdb=" N   LEU B 107 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 129
    Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 129
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 159
    Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.557A  pdb=" N   ILE C  48 " --> pdb=" O   TRP C  35 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   GLN C  37 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   LEU C  46 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 16 through 24
      removed outlier: 7.500A  pdb=" N   GLY C  17 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   GLY C  77 " --> pdb=" O   GLY C  17 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   VAL C  19 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE C  75 " --> pdb=" O   VAL C  19 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER C  67 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 118 through 121
      removed outlier: 3.808A  pdb=" N   VAL C 136 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   THR C 134 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   LEU C 183 " --> pdb=" O   THR C 134 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   VAL C 136 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   LEU C 181 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   VAL C 138 " --> pdb=" O   SER C 179 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   SER C 179 " --> pdb=" O   VAL C 138 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   ASN C 140 " --> pdb=" O   LEU C 177 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   LEU C 177 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 152

    238 hydrogen bonds defined for protein.
    645 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: 0.98

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1052
        1.31 -     1.44: 1847
        1.44 -     1.57: 3697
        1.57 -     1.71: 0
        1.71 -     1.84: 38
  Bond restraints: 6634
  Sorted by residual:
  bond pdb=" C   CYS A 381 "
       pdb=" O   CYS A 381 "
    ideal  model  delta    sigma   weight residual
    1.236  1.177  0.059 1.28e-02 6.10e+03 2.16e+01
  bond pdb=" CZ  TYR A 225 "
       pdb=" OH  TYR A 225 "
    ideal  model  delta    sigma   weight residual
    1.376  1.282  0.094 2.10e-02 2.27e+03 2.00e+01
  bond pdb=" CA  CYS A 238 "
       pdb=" C   CYS A 238 "
    ideal  model  delta    sigma   weight residual
    1.524  1.470  0.054 1.26e-02 6.30e+03 1.83e+01
  bond pdb=" C   GLU A 148 "
       pdb=" O   GLU A 148 "
    ideal  model  delta    sigma   weight residual
    1.236  1.182  0.054 1.29e-02 6.01e+03 1.73e+01
  bond pdb=" N   ASP A 223 "
       pdb=" CA  ASP A 223 "
    ideal  model  delta    sigma   weight residual
    1.455  1.404  0.050 1.29e-02 6.01e+03 1.51e+01
  ... (remaining 6629 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 8835
        2.19 -     4.37: 184
        4.37 -     6.56: 21
        6.56 -     8.74: 8
        8.74 -    10.93: 3
  Bond angle restraints: 9051
  Sorted by residual:
  angle pdb=" N   ASN A 240 "
        pdb=" CA  ASN A 240 "
        pdb=" C   ASN A 240 "
      ideal   model   delta    sigma   weight residual
     111.28  119.85   -8.57 1.09e+00 8.42e-01 6.19e+01
  angle pdb=" N   LEU A 342 "
        pdb=" CA  LEU A 342 "
        pdb=" C   LEU A 342 "
      ideal   model   delta    sigma   weight residual
     113.89  102.96   10.93 1.58e+00 4.01e-01 4.79e+01
  angle pdb=" C   ARG A  95 "
        pdb=" CA  ARG A  95 "
        pdb=" CB  ARG A  95 "
      ideal   model   delta    sigma   weight residual
     112.44  102.93    9.51 2.07e+00 2.33e-01 2.11e+01
  angle pdb=" C   CYS A 224 "
        pdb=" N   TYR A 225 "
        pdb=" CA  TYR A 225 "
      ideal   model   delta    sigma   weight residual
     121.54  129.70   -8.16 1.91e+00 2.74e-01 1.82e+01
  angle pdb=" CB  ARG A  95 "
        pdb=" CG  ARG A  95 "
        pdb=" CD  ARG A  95 "
      ideal   model   delta    sigma   weight residual
     111.30  120.23   -8.93 2.30e+00 1.89e-01 1.51e+01
  ... (remaining 9046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.96: 3820
       19.96 -    39.91: 150
       39.91 -    59.87: 25
       59.87 -    79.83: 5
       79.83 -    99.79: 7
  Dihedral angle restraints: 4007
    sinusoidal: 1603
      harmonic: 2404
  Sorted by residual:
  dihedral pdb=" C   TYR A 225 "
           pdb=" N   TYR A 225 "
           pdb=" CA  TYR A 225 "
           pdb=" CB  TYR A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.99   17.39     0      2.50e+00 1.60e-01 4.84e+01
  dihedral pdb=" N   TYR A 225 "
           pdb=" C   TYR A 225 "
           pdb=" CA  TYR A 225 "
           pdb=" CB  TYR A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.54  -16.74     0      2.50e+00 1.60e-01 4.48e+01
  dihedral pdb=" CB  CYS A 381 "
           pdb=" SG  CYS A 381 "
           pdb=" SG  CYS A 435 "
           pdb=" CB  CYS A 435 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.74  -52.74     1      1.00e+01 1.00e-02 3.79e+01
  ... (remaining 4004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.165: 1045
       0.165 -    0.330: 6
       0.330 -    0.494: 0
       0.494 -    0.659: 0
       0.659 -    0.824: 2
  Chirality restraints: 1053
  Sorted by residual:
  chirality pdb=" CA  TYR A 225 "
            pdb=" N   TYR A 225 "
            pdb=" C   TYR A 225 "
            pdb=" CB  TYR A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.69    0.82 2.00e-01 2.50e+01 1.70e+01
  chirality pdb=" C1  NAG A 503 "
            pdb=" ND2 ASN A 393 "
            pdb=" C2  NAG A 503 "
            pdb=" O5  NAG A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.62   -0.78 2.00e-01 2.50e+01 1.51e+01
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.30   -0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 1050 not shown)

  Planarity restraints: 1144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 393 "   -0.230 2.00e-02 2.50e+03   2.93e-01 1.08e+03
        pdb=" CG  ASN A 393 "    0.085 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 393 "   -0.051 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 393 "    0.516 2.00e-02 2.50e+03
        pdb=" C1  NAG A 503 "   -0.319 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 235 "    0.069 2.00e-02 2.50e+03   6.91e-02 5.97e+01
        pdb=" CG  ASN A 235 "   -0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 235 "   -0.028 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 235 "   -0.103 2.00e-02 2.50e+03
        pdb=" C1  NAG A 502 "    0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 239 "    0.012 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   PHE A 239 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE A 239 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASN A 240 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1141 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 54
        2.53 -     3.12: 4869
        3.12 -     3.71: 9111
        3.71 -     4.31: 12877
        4.31 -     4.90: 21959
  Nonbonded interactions: 48870
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 223 "
            pdb=" ND2 ASN A 246 "
     model   vdw
     1.934 3.120
  nonbonded pdb=" OD1 ASN A 240 "
            pdb=" N   VAL A 241 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" O   ASN A 235 "
            pdb=" OD1 ASN A 235 "
     model   vdw
     2.083 3.040
  nonbonded pdb=" CD2 LEU A 398 "
            pdb=" CE2 PHE A 433 "
     model   vdw
     2.092 3.760
  nonbonded pdb=" CD2 LEU A 398 "
            pdb=" CZ  PHE A 433 "
     model   vdw
     2.120 3.760
  ... (remaining 48865 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
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      :  0.022   1.324   6648  Z= 1.078
  Angle     :  1.258  50.955   9084  Z= 0.636
  Chirality :  0.060   0.824   1053
  Planarity :  0.005   0.046   1140
  Dihedral  : 11.954  99.786   2440
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.57 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.56 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.75 (0.28), residues: 819
  helix: -0.91 (0.39), residues: 157
  sheet:  0.37 (0.37), residues: 217
  loop : -2.14 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 389 
 TYR   0.022   0.003   TYR A 277 
 PHE   0.022   0.002   PHE A 199 
 TRP   0.028   0.003   TRP A 339 
 HIS   0.004   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00718 ( 6634)
  covalent geometry    : angle       0.78793 ( 9051)
  SS BOND              : bond        0.54183 (    9)
  SS BOND              : angle      20.97989 (   18)
  hydrogen bonds       : bond        0.16463 (  219)
  hydrogen bonds       : angle       7.51514 (  645)
  link_BETA1-4         : bond        0.00396 (    1)
  link_BETA1-4         : angle       2.75137 (    3)
  link_NAG-ASN         : bond        0.16212 (    4)
  link_NAG-ASN         : angle       8.24597 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 PHE cc_start: 0.7696 (m-80) cc_final: 0.7320 (m-80)
REVERT: B   42 LYS cc_start: 0.7502 (mttp) cc_final: 0.6937 (mtpt)
REVERT: B   78 LYS cc_start: 0.7640 (tttt) cc_final: 0.7422 (ttpt)
  outliers start: 4
  outliers final: 3
  residues processed: 144
  average time/residue: 0.0810
  time to fit residues: 15.5564
Evaluate side-chains
  90 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  438 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0070
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 268 GLN
C  24 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.240752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.208337 restraints weight = 6681.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.4309 rms_B_bonded: 1.67
r_work: 0.3987 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6648  Z= 0.140
  Angle     :  0.675  12.698   9084  Z= 0.334
  Chirality :  0.047   0.274   1053
  Planarity :  0.005   0.043   1140
  Dihedral  :  7.422  59.959    998
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  7.51 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.41 (0.29), residues: 819
  helix: -0.52 (0.40), residues: 160
  sheet:  0.39 (0.37), residues: 219
  loop : -1.85 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.014   0.001   TYR A 323 
 PHE   0.014   0.002   PHE A 199 
 TRP   0.007   0.001   TRP C  35 
 HIS   0.003   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6634)
  covalent geometry    : angle       0.63073 ( 9051)
  SS BOND              : bond        0.00384 (    9)
  SS BOND              : angle       1.12165 (   18)
  hydrogen bonds       : bond        0.03768 (  219)
  hydrogen bonds       : angle       5.75940 (  645)
  link_BETA1-4         : bond        0.00791 (    1)
  link_BETA1-4         : angle       1.17277 (    3)
  link_NAG-ASN         : bond        0.01136 (    4)
  link_NAG-ASN         : angle       6.54796 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6813 (mm-30)
REVERT: B   42 LYS cc_start: 0.7718 (mttp) cc_final: 0.7291 (mtpt)
REVERT: B   78 LYS cc_start: 0.8300 (tttt) cc_final: 0.8068 (ttpt)
REVERT: B  142 THR cc_start: 0.7627 (p) cc_final: 0.7388 (t)
  outliers start: 14
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0775
  time to fit residues: 10.6626
Evaluate side-chains
  91 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0170
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.8220

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

Flipped N/Q/H residues before XYZ refinement:
C  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.237936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.199816 restraints weight = 6667.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.4241 rms_B_bonded: 2.43
r_work: 0.4001 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6648  Z= 0.144
  Angle     :  0.661  11.861   9084  Z= 0.324
  Chirality :  0.048   0.332   1053
  Planarity :  0.005   0.046   1140
  Dihedral  :  6.465  59.892    995
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.57 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.11 (0.29), residues: 819
  helix: -0.26 (0.40), residues: 157
  sheet:  0.59 (0.38), residues: 219
  loop : -1.67 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 156 
 TYR   0.015   0.002   TYR A 323 
 PHE   0.017   0.002   PHE A 133 
 TRP   0.010   0.001   TRP C  35 
 HIS   0.004   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6634)
  covalent geometry    : angle       0.61419 ( 9051)
  SS BOND              : bond        0.00230 (    9)
  SS BOND              : angle       1.37567 (   18)
  hydrogen bonds       : bond        0.03478 (  219)
  hydrogen bonds       : angle       5.43054 (  645)
  link_BETA1-4         : bond        0.00595 (    1)
  link_BETA1-4         : angle       1.38477 (    3)
  link_NAG-ASN         : bond        0.00717 (    4)
  link_NAG-ASN         : angle       6.52697 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7695 (mttp) cc_final: 0.7279 (mtpt)
REVERT: B   78 LYS cc_start: 0.8173 (tttt) cc_final: 0.7880 (ttpt)
REVERT: B  142 THR cc_start: 0.7433 (p) cc_final: 0.7217 (t)
REVERT: C  135 ILE cc_start: 0.7830 (mm) cc_final: 0.7509 (mt)
  outliers start: 12
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0777
  time to fit residues: 9.8274
Evaluate side-chains
  86 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 399 HIS
C  22 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.231299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.194204 restraints weight = 6736.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 2.27
r_work: 0.3983 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6648  Z= 0.196
  Angle     :  0.726  11.312   9084  Z= 0.354
  Chirality :  0.050   0.351   1053
  Planarity :  0.005   0.046   1140
  Dihedral  :  6.513  57.900    993
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.68 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.22 (0.29), residues: 819
  helix: -0.40 (0.39), residues: 160
  sheet:  0.36 (0.37), residues: 223
  loop : -1.64 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 156 
 TYR   0.016   0.002   TYR A 323 
 PHE   0.021   0.002   PHE A 199 
 TRP   0.012   0.002   TRP A 154 
 HIS   0.003   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6634)
  covalent geometry    : angle       0.68169 ( 9051)
  SS BOND              : bond        0.00315 (    9)
  SS BOND              : angle       1.46307 (   18)
  hydrogen bonds       : bond        0.03750 (  219)
  hydrogen bonds       : angle       5.67645 (  645)
  link_BETA1-4         : bond        0.00424 (    1)
  link_BETA1-4         : angle       1.69739 (    3)
  link_NAG-ASN         : bond        0.00750 (    4)
  link_NAG-ASN         : angle       6.65667 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 VAL cc_start: 0.7732 (m) cc_final: 0.7531 (p)
REVERT: B   78 LYS cc_start: 0.8130 (tttt) cc_final: 0.7802 (ttpt)
REVERT: B  142 THR cc_start: 0.7583 (p) cc_final: 0.7337 (t)
REVERT: C  135 ILE cc_start: 0.7951 (mm) cc_final: 0.7651 (mt)
  outliers start: 17
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0764
  time to fit residues: 9.3318
Evaluate side-chains
  90 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 160 ASN
C  22 ASN
C 127 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.231655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.194639 restraints weight = 6761.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 2.18
r_work: 0.3967 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6648  Z= 0.189
  Angle     :  0.699  11.124   9084  Z= 0.342
  Chirality :  0.049   0.347   1053
  Planarity :  0.005   0.046   1140
  Dihedral  :  6.357  57.952    993
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.66 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.29 (0.29), residues: 819
  helix: -0.35 (0.40), residues: 160
  sheet:  0.20 (0.37), residues: 229
  loop : -1.68 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 156 
 TYR   0.015   0.002   TYR A 323 
 PHE   0.019   0.002   PHE A 199 
 TRP   0.012   0.002   TRP C  35 
 HIS   0.002   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 6634)
  covalent geometry    : angle       0.65642 ( 9051)
  SS BOND              : bond        0.00310 (    9)
  SS BOND              : angle       1.40784 (   18)
  hydrogen bonds       : bond        0.03517 (  219)
  hydrogen bonds       : angle       5.61090 (  645)
  link_BETA1-4         : bond        0.00632 (    1)
  link_BETA1-4         : angle       1.66413 (    3)
  link_NAG-ASN         : bond        0.00723 (    4)
  link_NAG-ASN         : angle       6.45925 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6864 (mm-30)
REVERT: B   78 LYS cc_start: 0.8134 (tttt) cc_final: 0.7807 (ttpt)
REVERT: B  142 THR cc_start: 0.7560 (p) cc_final: 0.7273 (t)
REVERT: C  135 ILE cc_start: 0.7880 (mm) cc_final: 0.7559 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0776
  time to fit residues: 8.9361
Evaluate side-chains
  83 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 76 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
C 191 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.235786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.196531 restraints weight = 6826.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 2.60
r_work: 0.3998 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6648  Z= 0.127
  Angle     :  0.617  10.987   9084  Z= 0.300
  Chirality :  0.046   0.336   1053
  Planarity :  0.004   0.045   1140
  Dihedral  :  5.873  58.957    993
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.80 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.09 (0.29), residues: 819
  helix: -0.06 (0.41), residues: 160
  sheet:  0.41 (0.38), residues: 219
  loop : -1.63 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 156 
 TYR   0.014   0.002   TYR A 323 
 PHE   0.014   0.001   PHE A 199 
 TRP   0.009   0.001   TRP C  35 
 HIS   0.001   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6634)
  covalent geometry    : angle       0.57508 ( 9051)
  SS BOND              : bond        0.00293 (    9)
  SS BOND              : angle       1.08951 (   18)
  hydrogen bonds       : bond        0.02910 (  219)
  hydrogen bonds       : angle       5.31533 (  645)
  link_BETA1-4         : bond        0.00594 (    1)
  link_BETA1-4         : angle       1.41814 (    3)
  link_NAG-ASN         : bond        0.00776 (    4)
  link_NAG-ASN         : angle       6.05336 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.8073 (tttt) cc_final: 0.7454 (mtpt)
REVERT: B  142 THR cc_start: 0.7632 (p) cc_final: 0.7400 (t)
REVERT: C  135 ILE cc_start: 0.7892 (mm) cc_final: 0.7570 (mt)
  outliers start: 15
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0737
  time to fit residues: 8.8812
Evaluate side-chains
  86 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.233308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.196187 restraints weight = 6780.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 2.06
r_work: 0.3939 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6648  Z= 0.171
  Angle     :  0.670  10.450   9084  Z= 0.328
  Chirality :  0.048   0.347   1053
  Planarity :  0.004   0.045   1140
  Dihedral  :  6.151  57.681    993
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.07 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.21 (0.29), residues: 819
  helix: -0.09 (0.40), residues: 160
  sheet:  0.10 (0.37), residues: 229
  loop : -1.62 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 156 
 TYR   0.016   0.002   TYR C  49 
 PHE   0.020   0.002   PHE A 133 
 TRP   0.010   0.001   TRP A 154 
 HIS   0.002   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6634)
  covalent geometry    : angle       0.63005 ( 9051)
  SS BOND              : bond        0.00283 (    9)
  SS BOND              : angle       1.27553 (   18)
  hydrogen bonds       : bond        0.03378 (  219)
  hydrogen bonds       : angle       5.48716 (  645)
  link_BETA1-4         : bond        0.00556 (    1)
  link_BETA1-4         : angle       1.60209 (    3)
  link_NAG-ASN         : bond        0.00622 (    4)
  link_NAG-ASN         : angle       6.07943 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6827 (mm-30)
REVERT: B   42 LYS cc_start: 0.7705 (mttp) cc_final: 0.7336 (mtpt)
REVERT: B   78 LYS cc_start: 0.8151 (tttt) cc_final: 0.7862 (ttpt)
REVERT: C  135 ILE cc_start: 0.7971 (mm) cc_final: 0.7660 (mt)
  outliers start: 16
  outliers final: 14
  residues processed: 80
  average time/residue: 0.0720
  time to fit residues: 7.9123
Evaluate side-chains
  85 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.235265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.196075 restraints weight = 6745.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 2.65
r_work: 0.3990 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6648  Z= 0.135
  Angle     :  0.618  10.158   9084  Z= 0.302
  Chirality :  0.046   0.336   1053
  Planarity :  0.004   0.044   1140
  Dihedral  :  5.825  59.285    993
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.21 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.12 (0.29), residues: 819
  helix:  0.10 (0.41), residues: 160
  sheet:  0.12 (0.36), residues: 229
  loop : -1.58 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 156 
 TYR   0.012   0.002   TYR C  49 
 PHE   0.020   0.002   PHE A 133 
 TRP   0.009   0.001   TRP C  35 
 HIS   0.002   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6634)
  covalent geometry    : angle       0.57954 ( 9051)
  SS BOND              : bond        0.00267 (    9)
  SS BOND              : angle       1.09554 (   18)
  hydrogen bonds       : bond        0.02940 (  219)
  hydrogen bonds       : angle       5.31040 (  645)
  link_BETA1-4         : bond        0.00587 (    1)
  link_BETA1-4         : angle       1.44028 (    3)
  link_NAG-ASN         : bond        0.00697 (    4)
  link_NAG-ASN         : angle       5.80660 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.8049 (tttt) cc_final: 0.7743 (ttpt)
REVERT: C  135 ILE cc_start: 0.7876 (mm) cc_final: 0.7566 (mt)
  outliers start: 15
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0733
  time to fit residues: 8.5753
Evaluate side-chains
  80 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.4530 r_free = 0.4530 target = 0.233937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.193789 restraints weight = 6835.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 2.63
r_work: 0.3962 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6648  Z= 0.160
  Angle     :  0.651  10.270   9084  Z= 0.318
  Chirality :  0.047   0.342   1053
  Planarity :  0.004   0.044   1140
  Dihedral  :  6.011  58.535    993
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.49 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.14 (0.29), residues: 819
  helix:  0.03 (0.41), residues: 160
  sheet:  0.10 (0.37), residues: 229
  loop : -1.58 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 156 
 TYR   0.014   0.002   TYR A 219 
 PHE   0.019   0.002   PHE A 133 
 TRP   0.010   0.001   TRP C  35 
 HIS   0.002   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6634)
  covalent geometry    : angle       0.61353 ( 9051)
  SS BOND              : bond        0.00287 (    9)
  SS BOND              : angle       1.37923 (   18)
  hydrogen bonds       : bond        0.03225 (  219)
  hydrogen bonds       : angle       5.41235 (  645)
  link_BETA1-4         : bond        0.00609 (    1)
  link_BETA1-4         : angle       1.54411 (    3)
  link_NAG-ASN         : bond        0.00592 (    4)
  link_NAG-ASN         : angle       5.82141 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7681 (mttp) cc_final: 0.7286 (mtpt)
REVERT: B   78 LYS cc_start: 0.8110 (tttt) cc_final: 0.7790 (ttpt)
REVERT: C  135 ILE cc_start: 0.7814 (mm) cc_final: 0.7526 (mt)
  outliers start: 17
  outliers final: 16
  residues processed: 85
  average time/residue: 0.0820
  time to fit residues: 9.5385
Evaluate side-chains
  88 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 15 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4556 r_free = 0.4556 target = 0.237060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.197870 restraints weight = 6739.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 2.55
r_work: 0.4002 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6648  Z= 0.113
  Angle     :  0.591   9.876   9084  Z= 0.288
  Chirality :  0.045   0.326   1053
  Planarity :  0.004   0.043   1140
  Dihedral  :  5.568  58.058    993
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.60 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.08 (0.29), residues: 819
  helix:  0.02 (0.40), residues: 166
  sheet:  0.21 (0.37), residues: 221
  loop : -1.54 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 156 
 TYR   0.012   0.001   TYR C  49 
 PHE   0.023   0.001   PHE A 133 
 TRP   0.009   0.001   TRP A  53 
 HIS   0.001   0.000   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6634)
  covalent geometry    : angle       0.55338 ( 9051)
  SS BOND              : bond        0.00311 (    9)
  SS BOND              : angle       1.27036 (   18)
  hydrogen bonds       : bond        0.02736 (  219)
  hydrogen bonds       : angle       5.17007 (  645)
  link_BETA1-4         : bond        0.00641 (    1)
  link_BETA1-4         : angle       1.40474 (    3)
  link_NAG-ASN         : bond        0.00748 (    4)
  link_NAG-ASN         : angle       5.55302 (   12)

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

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

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1638 Ramachandran restraints generated.
    819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.8092 (tttt) cc_final: 0.7476 (mtpt)
REVERT: C  135 ILE cc_start: 0.7821 (mm) cc_final: 0.7533 (mt)
  outliers start: 12
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0751
  time to fit residues: 8.5159
Evaluate side-chains
  82 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain C residue   10 SER
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4540 r_free = 0.4540 target = 0.235099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.195496 restraints weight = 6772.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.4191 rms_B_bonded: 2.55
r_work: 0.3982 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6648  Z= 0.137
  Angle     :  0.619  10.102   9084  Z= 0.303
  Chirality :  0.046   0.333   1053
  Planarity :  0.004   0.044   1140
  Dihedral  :  5.741  59.513    993
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.46 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.87 %
    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 aren not related in a simple way.
  whole: -1.06 (0.29), residues: 819
  helix: -0.01 (0.40), residues: 166
  sheet:  0.20 (0.37), residues: 221
  loop : -1.50 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 156 
 TYR   0.015   0.002   TYR C  49 
 PHE   0.016   0.002   PHE A 199 
 TRP   0.010   0.001   TRP A 154 
 HIS   0.002   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6634)
  covalent geometry    : angle       0.58361 ( 9051)
  SS BOND              : bond        0.00274 (    9)
  SS BOND              : angle       1.25958 (   18)
  hydrogen bonds       : bond        0.03004 (  219)
  hydrogen bonds       : angle       5.25767 (  645)
  link_BETA1-4         : bond        0.00594 (    1)
  link_BETA1-4         : angle       1.45344 (    3)
  link_NAG-ASN         : bond        0.00591 (    4)
  link_NAG-ASN         : angle       5.51404 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1752.90 seconds
wall clock time: 30 minutes 46.00 seconds (1846.00 seconds total)