Starting phenix.real_space_refine
on Tue Mar  3 16:42:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d85_27247/03_2026/8d85_27247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d85_27247/03_2026/8d85_27247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2026/8d85_27247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2026/8d85_27247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2026/8d85_27247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2026/8d85_27247.cif"
  }
  resolution = 3.81
  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=   0.019
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      31      5.16       5
     C    4527      2.51       5
     N    1197      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7093
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 178}
    Chain: "D"
      Number of atoms: 1452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1452
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 9, 'TRANS': 167}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1524
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 172}
    Chain: "B"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2373
          Classifications: {'peptide': 296}
          Link IDs: {'PTRANS': 16, 'TRANS': 279}
    Chain: "E"
      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: "F"
      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: "G"
      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: "C"
      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
    Chain: "A"
      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
    Chain: "B"
      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: 0.23
  Number of scatterers: 7093
  At special positions: 0
  Unit cell: (107.5, 104.06, 139.32, 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      31     16.00
     O    1338      8.00
     N    1197      7.00
     C    4527      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  35 " - pdb=" SG  CYS C  46 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  79 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B  54 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 182 " 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 E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A  76 "
      " NAG B 701 " - " ASN B 227 "
      " NAG B 702 " - " ASN B 157 "
      " NAG B 703 " - " ASN B 131 "
      " NAG C 301 " - " ASN C 105 "
      " NAG E   1 " - " ASN A  51 "
      " NAG F   1 " - " ASN B  83 "
      " NAG G   1 " - " ASN B  43 "
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 261.5 milliseconds
  

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1646

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 18 sheets defined
      17.8% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'D' and resid 42 through 73
    Processing helix  chain 'D' and resid 93 through 100
    Processing helix  chain 'D' and resid 103 through 124
      Proline residue:  D 115  - end of helix
    Processing helix  chain 'D' and resid 130 through 158
    Processing helix  chain 'D' and resid 166 through 179
    Processing helix  chain 'D' and resid 196 through 225
    Processing helix  chain 'B' and resid 51 through 58
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 4.305A  pdb=" N   SER B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.643A  pdb=" N   ALA B 278 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46
      removed outlier: 4.160A  pdb=" N   CYS C  46 " --> pdb=" O   CYS C  89 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS C  89 " --> pdb=" O   CYS C  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.649A  pdb=" N   ILE C  63 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL C 103 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE C 121 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138
      removed outlier: 3.686A  pdb=" N   LEU C 145 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 183
      removed outlier: 6.205A  pdb=" N   TYR C 165 " --> pdb=" O   PRO C 182 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66
      removed outlier: 3.674A  pdb=" N   GLU A  65 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A 108 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105
      removed outlier: 3.526A  pdb=" N   VAL A 105 " --> pdb=" O   VAL A 118 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 118 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 139
      removed outlier: 3.829A  pdb=" N   ARG A 132 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   HIS A 150 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ASP A 136 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   THR A 148 " --> pdb=" O   ASP A 136 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178
      removed outlier: 3.869A  pdb=" N   LEU A 183 " --> pdb=" O   CYS A 164 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 204
      removed outlier: 3.561A  pdb=" N   LEU A 224 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38
      removed outlier: 3.957A  pdb=" N   VAL B  38 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47
    Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 74
      removed outlier: 4.735A  pdb=" N   TRP B  67 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B  66 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ASN B 104 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN B 113 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183
      removed outlier: 4.364A  pdb=" N   CYS B 182 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   CYS B 144 " --> pdb=" O   CYS B 182 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B 143 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP B 147 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASN B 131 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 8.563A  pdb=" N   LYS B 221 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL B 136 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173
      removed outlier: 3.864A  pdb=" N   LYS B 161 " --> pdb=" O   TRP B 197 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 197 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173
      removed outlier: 3.864A  pdb=" N   LYS B 161 " --> pdb=" O   TRP B 197 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 197 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE B 194 " --> pdb=" O   PHE B 214 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   PHE B 214 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   VAL B 196 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE B 212 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.622A  pdb=" N   THR B 243 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS B 241 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 271
      removed outlier: 3.987A  pdb=" N   TYR B 295 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY B 319 " --> pdb=" O   TYR B 295 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B 317 " --> pdb=" O   PHE B 297 " (cutoff:3.500A)

    205 hydrogen bonds defined for protein.
    549 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: 0.91

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2263
        1.34 -     1.46: 1724
        1.46 -     1.58: 3259
        1.58 -     1.70: 0
        1.70 -     1.82: 43
  Bond restraints: 7289
  Sorted by residual:
  bond pdb=" C   ASP D 102 "
       pdb=" N   PRO D 103 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.08e-02 8.57e+03 3.24e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.83e+00
  ... (remaining 7284 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 9795
        2.03 -     4.05: 129
        4.05 -     6.08: 14
        6.08 -     8.10: 2
        8.10 -    10.13: 1
  Bond angle restraints: 9941
  Sorted by residual:
  angle pdb=" CA  LEU A  68 "
        pdb=" CB  LEU A  68 "
        pdb=" CG  LEU A  68 "
      ideal   model   delta    sigma   weight residual
     116.30  126.43  -10.13 3.50e+00 8.16e-02 8.37e+00
  angle pdb=" N   SER B  32 "
        pdb=" CA  SER B  32 "
        pdb=" C   SER B  32 "
      ideal   model   delta    sigma   weight residual
     109.81  115.62   -5.81 2.21e+00 2.05e-01 6.92e+00
  angle pdb=" C   VAL C 109 "
        pdb=" N   HIS C 110 "
        pdb=" CA  HIS C 110 "
      ideal   model   delta    sigma   weight residual
     121.80  116.20    5.60 2.44e+00 1.68e-01 5.28e+00
  angle pdb=" C   LEU A 198 "
        pdb=" N   ALA A 199 "
        pdb=" CA  ALA A 199 "
      ideal   model   delta    sigma   weight residual
     122.08  125.21   -3.13 1.47e+00 4.63e-01 4.53e+00
  angle pdb=" C   ILE B  31 "
        pdb=" N   SER B  32 "
        pdb=" CA  SER B  32 "
      ideal   model   delta    sigma   weight residual
     121.80  116.99    4.81 2.44e+00 1.68e-01 3.89e+00
  ... (remaining 9936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.69: 4205
       21.69 -    43.38: 204
       43.38 -    65.07: 46
       65.07 -    86.76: 21
       86.76 -   108.45: 52
  Dihedral angle restraints: 4528
    sinusoidal: 1995
      harmonic: 2533
  Sorted by residual:
  dihedral pdb=" CB  CYS C  35 "
           pdb=" SG  CYS C  35 "
           pdb=" SG  CYS C  46 "
           pdb=" CB  CYS C  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -43.34  -42.66     1      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CA  SER B  32 "
           pdb=" C   SER B  32 "
           pdb=" N   PRO B  33 "
           pdb=" CA  PRO B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" C1  NAG G   1 "
           pdb=" C2  NAG G   1 "
           pdb=" C3  NAG G   1 "
           pdb=" O3  NAG G   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -66.64 -108.45     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 4525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 891
       0.041 -    0.082: 136
       0.082 -    0.122: 92
       0.122 -    0.163: 7
       0.163 -    0.204: 2
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A  51 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C1  NAG C 301 "
            pdb=" ND2 ASN C 105 "
            pdb=" C2  NAG C 301 "
            pdb=" O5  NAG C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" C1  NAG B 701 "
            pdb=" ND2 ASN B 227 "
            pdb=" C2  NAG B 701 "
            pdb=" O5  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.44e-01
  ... (remaining 1125 not shown)

  Planarity restraints: 1264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 102 "   -0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO D 103 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  40 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO C  41 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO C  41 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  41 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 272 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO B 273 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2379
        2.87 -     3.37: 6114
        3.37 -     3.88: 10679
        3.88 -     4.39: 10827
        4.39 -     4.90: 19504
  Nonbonded interactions: 49503
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C  81 "
            pdb=" O   SER C  86 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" NH2 ARG C 168 "
            pdb=" OE1 GLN C 202 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" NE1 TRP C 166 "
            pdb=" OE1 GLN C 206 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" OE1 GLU B  34 "
            pdb=" OG  SER B  35 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" ND2 ASN B 246 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.381 3.120
  ... (remaining 49498 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
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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=0.00 max=1.00 mean=0.99
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:             3.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.270
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
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   0.041   7308  Z= 0.127
  Angle     :  0.538  10.127   9990  Z= 0.262
  Chirality :  0.040   0.204   1128
  Planarity :  0.003   0.039   1256
  Dihedral  : 19.549 108.448   2858
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.09 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    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: -2.45 (0.25), residues: 855
  helix:  0.17 (0.39), residues: 154
  sheet: -0.72 (0.39), residues: 174
  loop : -2.67 (0.22), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 152 
 TYR   0.005   0.000   TYR B  79 
 PHE   0.005   0.000   PHE D 116 
 TRP   0.007   0.000   TRP A 115 
 HIS   0.001   0.000   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7289)
  covalent geometry    : angle       0.53136 ( 9941)
  SS BOND              : bond        0.00108 (    8)
  SS BOND              : angle       0.59197 (   16)
  hydrogen bonds       : bond        0.23180 (  196)
  hydrogen bonds       : angle       7.44029 (  549)
  link_BETA1-4         : bond        0.00251 (    3)
  link_BETA1-4         : angle       0.72290 (    9)
  link_NAG-ASN         : bond        0.00444 (    8)
  link_NAG-ASN         : angle       1.80770 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   30 LEU cc_start: 0.8169 (pt) cc_final: 0.7777 (mt)
REVERT: C  110 HIS cc_start: 0.2159 (m170) cc_final: 0.1912 (m90)
REVERT: D  144 LEU cc_start: 0.8883 (tp) cc_final: 0.8468 (tt)
REVERT: B  146 TRP cc_start: 0.8176 (p90) cc_final: 0.7824 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1099
  time to fit residues: 26.3590
Evaluate side-chains
  108 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  75 HIS
D 126 GLN
D 150 HIS
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 159 HIS
A 167 HIS
B 114 ASN
B 193 ASN
B 211 HIS
B 258 ASN
B 260 GLN
B 271 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.174799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.152892 restraints weight = 14955.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.156143 restraints weight = 9120.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.158435 restraints weight = 6412.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.159948 restraints weight = 4955.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.160823 restraints weight = 4124.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4196 r_free = 0.4196    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4193 r_free = 0.4193    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7308  Z= 0.169
  Angle     :  0.772  13.755   9990  Z= 0.351
  Chirality :  0.050   0.425   1128
  Planarity :  0.006   0.090   1256
  Dihedral  : 17.133  86.854   1167
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.26 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.14 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.27), residues: 855
  helix:  1.71 (0.42), residues: 148
  sheet: -1.02 (0.35), residues: 195
  loop : -2.04 (0.24), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 105 
 TYR   0.017   0.002   TYR B  79 
 PHE   0.016   0.002   PHE C 188 
 TRP   0.019   0.002   TRP A 217 
 HIS   0.003   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7289)
  covalent geometry    : angle       0.74961 ( 9941)
  SS BOND              : bond        0.00432 (    8)
  SS BOND              : angle       1.47870 (   16)
  hydrogen bonds       : bond        0.04013 (  196)
  hydrogen bonds       : angle       5.00208 (  549)
  link_BETA1-4         : bond        0.00390 (    3)
  link_BETA1-4         : angle       2.57268 (    9)
  link_NAG-ASN         : bond        0.01091 (    8)
  link_NAG-ASN         : angle       3.33687 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6922 (mtm-85) cc_final: 0.6521 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8923 (tp) cc_final: 0.8648 (tt)
REVERT: B  146 TRP cc_start: 0.8722 (p90) cc_final: 0.8393 (p90)
REVERT: B  239 ILE cc_start: 0.7084 (mm) cc_final: 0.6814 (pt)
REVERT: B  302 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5797 (ptt)
  outliers start: 15
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1020
  time to fit residues: 17.4252
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain A residue   99 MET
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue  223 ASN
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  301 CYS
Chi-restraints excluded: chain B residue  302 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A  79 GLN
B 114 ASN
B 258 ASN
B 260 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.171332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.149612 restraints weight = 14793.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.152797 restraints weight = 8934.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.155037 restraints weight = 6310.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.156370 restraints weight = 4856.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.157545 restraints weight = 4074.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4161 r_free = 0.4161    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4161 r_free = 0.4161    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7308  Z= 0.134
  Angle     :  0.684  10.653   9990  Z= 0.308
  Chirality :  0.048   0.474   1128
  Planarity :  0.005   0.087   1256
  Dihedral  : 13.361  77.897   1167
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.26 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.86 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.28), residues: 855
  helix:  2.14 (0.42), residues: 148
  sheet: -0.88 (0.32), residues: 230
  loop : -1.89 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 300 
 TYR   0.016   0.001   TYR B 295 
 PHE   0.016   0.001   PHE C 188 
 TRP   0.014   0.002   TRP B 310 
 HIS   0.002   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7289)
  covalent geometry    : angle       0.66558 ( 9941)
  SS BOND              : bond        0.00309 (    8)
  SS BOND              : angle       1.23168 (   16)
  hydrogen bonds       : bond        0.04262 (  196)
  hydrogen bonds       : angle       4.58115 (  549)
  link_BETA1-4         : bond        0.00360 (    3)
  link_BETA1-4         : angle       1.89852 (    9)
  link_NAG-ASN         : bond        0.00936 (    8)
  link_NAG-ASN         : angle       2.94134 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   70 MET cc_start: 0.7739 (tmm) cc_final: 0.7396 (ttm)
REVERT: C  198 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6632 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7474 (tp40) cc_final: 0.7036 (tp40)
REVERT: D  144 LEU cc_start: 0.8914 (tp) cc_final: 0.8593 (tt)
REVERT: B   76 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6759 (tttp)
REVERT: B  146 TRP cc_start: 0.8743 (p90) cc_final: 0.8390 (p90)
REVERT: B  239 ILE cc_start: 0.7008 (mm) cc_final: 0.6716 (pt)
  outliers start: 22
  outliers final: 9
  residues processed: 125
  average time/residue: 0.0844
  time to fit residues: 13.9896
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  114 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0370
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0370
   overall best weight:    1.3740

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

Flipped N/Q/H residues before XYZ refinement:
D 154 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.163005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.141317 restraints weight = 14885.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.144422 restraints weight = 9064.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.146664 restraints weight = 6418.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.148156 restraints weight = 4965.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.149121 restraints weight = 4136.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7308  Z= 0.182
  Angle     :  0.745  10.847   9990  Z= 0.344
  Chirality :  0.049   0.403   1128
  Planarity :  0.005   0.091   1256
  Dihedral  : 11.108  64.363   1167
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.20 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.94 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.28), residues: 855
  helix:  2.25 (0.43), residues: 148
  sheet: -0.86 (0.31), residues: 239
  loop : -1.82 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 298 
 TYR   0.018   0.002   TYR B  79 
 PHE   0.017   0.002   PHE B  72 
 TRP   0.017   0.002   TRP A 217 
 HIS   0.005   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7289)
  covalent geometry    : angle       0.72307 ( 9941)
  SS BOND              : bond        0.00660 (    8)
  SS BOND              : angle       1.76924 (   16)
  hydrogen bonds       : bond        0.04924 (  196)
  hydrogen bonds       : angle       4.60153 (  549)
  link_BETA1-4         : bond        0.00291 (    3)
  link_BETA1-4         : angle       2.22046 (    9)
  link_NAG-ASN         : bond        0.00644 (    8)
  link_NAG-ASN         : angle       3.21105 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   70 MET cc_start: 0.7628 (tmm) cc_final: 0.7413 (ttt)
REVERT: C  198 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6764 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7761 (tp40) cc_final: 0.7370 (tp40)
REVERT: D  132 MET cc_start: 0.7537 (ppp) cc_final: 0.7255 (ppp)
REVERT: B   76 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6939 (tttp)
REVERT: B  146 TRP cc_start: 0.8824 (p90) cc_final: 0.8397 (p90)
  outliers start: 22
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0719
  time to fit residues: 11.9103
Evaluate side-chains
  102 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0570
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0040
   chunk 53 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0570
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5630

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

Flipped N/Q/H residues before XYZ refinement:
D  77 ASN
D 154 GLN
B 271 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.167826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.147052 restraints weight = 15440.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.150344 restraints weight = 9254.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.152592 restraints weight = 6428.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.154051 restraints weight = 4915.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.155068 restraints weight = 4063.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7308  Z= 0.113
  Angle     :  0.687  15.200   9990  Z= 0.304
  Chirality :  0.046   0.392   1128
  Planarity :  0.005   0.091   1256
  Dihedral  :  9.755  55.176   1167
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.50 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.36 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.28), residues: 855
  helix:  2.44 (0.42), residues: 148
  sheet: -0.72 (0.31), residues: 241
  loop : -1.73 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  67 
 TYR   0.016   0.001   TYR D 204 
 PHE   0.019   0.001   PHE B  72 
 TRP   0.022   0.001   TRP A  89 
 HIS   0.004   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7289)
  covalent geometry    : angle       0.66696 ( 9941)
  SS BOND              : bond        0.00350 (    8)
  SS BOND              : angle       1.51472 (   16)
  hydrogen bonds       : bond        0.04232 (  196)
  hydrogen bonds       : angle       4.31387 (  549)
  link_BETA1-4         : bond        0.00450 (    3)
  link_BETA1-4         : angle       2.36460 (    9)
  link_NAG-ASN         : bond        0.00654 (    8)
  link_NAG-ASN         : angle       2.95934 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6719 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7694 (tp40) cc_final: 0.7325 (tp40)
REVERT: D  140 MET cc_start: 0.8470 (tmm) cc_final: 0.8183 (tmm)
REVERT: A  217 TRP cc_start: 0.7828 (m100) cc_final: 0.6629 (m100)
REVERT: B   76 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6954 (tttp)
REVERT: B  146 TRP cc_start: 0.8772 (p90) cc_final: 0.8378 (p90)
REVERT: B  260 GLN cc_start: 0.6968 (mt0) cc_final: 0.6765 (mt0)
  outliers start: 24
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0788
  time to fit residues: 12.1959
Evaluate side-chains
  108 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   77 ASN
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  102 ASP
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0270
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.4442

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.166886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.146581 restraints weight = 15112.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.149285 restraints weight = 9712.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.151127 restraints weight = 7132.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.152301 restraints weight = 5727.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.153231 restraints weight = 4922.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.5129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7308  Z= 0.181
  Angle     :  0.750  10.958   9990  Z= 0.348
  Chirality :  0.050   0.542   1128
  Planarity :  0.006   0.093   1256
  Dihedral  :  8.706  58.747   1167
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.02 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 20.49 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.28), residues: 855
  helix:  2.24 (0.42), residues: 148
  sheet: -0.77 (0.31), residues: 233
  loop : -1.79 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 105 
 TYR   0.021   0.002   TYR D 204 
 PHE   0.020   0.002   PHE B  72 
 TRP   0.016   0.002   TRP A  89 
 HIS   0.005   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 7289)
  covalent geometry    : angle       0.72695 ( 9941)
  SS BOND              : bond        0.00480 (    8)
  SS BOND              : angle       1.97879 (   16)
  hydrogen bonds       : bond        0.05197 (  196)
  hydrogen bonds       : angle       4.53930 (  549)
  link_BETA1-4         : bond        0.00384 (    3)
  link_BETA1-4         : angle       2.60439 (    9)
  link_NAG-ASN         : bond        0.00820 (    8)
  link_NAG-ASN         : angle       3.20945 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7631 (mm-30)
REVERT: C  198 ARG cc_start: 0.7021 (mtm-85) cc_final: 0.6751 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7877 (tp40) cc_final: 0.7562 (tp40)
REVERT: D  132 MET cc_start: 0.7398 (ppp) cc_final: 0.6676 (ppp)
REVERT: D  140 MET cc_start: 0.8408 (tmm) cc_final: 0.8112 (tmm)
REVERT: A  182 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6295 (mm-30)
REVERT: A  217 TRP cc_start: 0.8035 (m100) cc_final: 0.6723 (m100)
REVERT: B   76 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7131 (tttp)
REVERT: B  146 TRP cc_start: 0.8779 (p90) cc_final: 0.8365 (p90)
REVERT: B  260 GLN cc_start: 0.6998 (mt0) cc_final: 0.6778 (mt0)
  outliers start: 31
  outliers final: 19
  residues processed: 115
  average time/residue: 0.0747
  time to fit residues: 11.8899
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 80 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 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.165983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.146203 restraints weight = 15017.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.148760 restraints weight = 9586.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.150581 restraints weight = 7042.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.151819 restraints weight = 5653.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.152596 restraints weight = 4832.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.5580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7308  Z= 0.169
  Angle     :  0.735  11.659   9990  Z= 0.342
  Chirality :  0.048   0.435   1128
  Planarity :  0.006   0.093   1256
  Dihedral  :  7.960  57.900   1167
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.32 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 21.66 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.28), residues: 855
  helix:  2.21 (0.42), residues: 148
  sheet: -0.81 (0.31), residues: 233
  loop : -1.81 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 105 
 TYR   0.017   0.002   TYR B 261 
 PHE   0.020   0.001   PHE B  72 
 TRP   0.018   0.002   TRP A 115 
 HIS   0.004   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 7289)
  covalent geometry    : angle       0.71206 ( 9941)
  SS BOND              : bond        0.00969 (    8)
  SS BOND              : angle       2.00563 (   16)
  hydrogen bonds       : bond        0.05211 (  196)
  hydrogen bonds       : angle       4.58198 (  549)
  link_BETA1-4         : bond        0.00347 (    3)
  link_BETA1-4         : angle       2.67324 (    9)
  link_NAG-ASN         : bond        0.00789 (    8)
  link_NAG-ASN         : angle       3.09517 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: C  198 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6728 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7882 (tp40) cc_final: 0.7620 (tp40)
REVERT: D   95 GLN cc_start: 0.8300 (mm110) cc_final: 0.7948 (mm-40)
REVERT: D  132 MET cc_start: 0.7359 (ppp) cc_final: 0.6671 (ppp)
REVERT: D  140 MET cc_start: 0.8420 (tmm) cc_final: 0.8156 (tmm)
REVERT: A  182 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6208 (mm-30)
REVERT: A  217 TRP cc_start: 0.8089 (m100) cc_final: 0.6791 (m100)
REVERT: B   76 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7340 (tttp)
REVERT: B  146 TRP cc_start: 0.8748 (p90) cc_final: 0.8310 (p90)
REVERT: B  250 LYS cc_start: 0.8211 (pttm) cc_final: 0.7068 (tttt)
REVERT: B  260 GLN cc_start: 0.7026 (mt0) cc_final: 0.5832 (mt0)
  outliers start: 34
  outliers final: 22
  residues processed: 121
  average time/residue: 0.0776
  time to fit residues: 12.7473
Evaluate side-chains
  114 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 80 optimal weight:    0.0030
   chunk 56 optimal weight:    0.4980
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0370
   chunk 7 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.4668

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

Flipped N/Q/H residues before XYZ refinement:
B 246 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.168104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.147785 restraints weight = 15188.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.150526 restraints weight = 9634.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.152485 restraints weight = 7007.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.153573 restraints weight = 5567.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.154603 restraints weight = 4786.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.5547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7308  Z= 0.119
  Angle     :  0.717  17.279   9990  Z= 0.327
  Chirality :  0.046   0.401   1128
  Planarity :  0.006   0.091   1256
  Dihedral  :  7.493  56.790   1167
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.32 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.09 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.96 (0.28), residues: 855
  helix:  2.45 (0.43), residues: 148
  sheet: -0.67 (0.31), residues: 243
  loop : -1.72 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 134 
 TYR   0.026   0.001   TYR B 295 
 PHE   0.024   0.001   PHE B  72 
 TRP   0.018   0.001   TRP A 115 
 HIS   0.005   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7289)
  covalent geometry    : angle       0.69621 ( 9941)
  SS BOND              : bond        0.00434 (    8)
  SS BOND              : angle       1.71049 (   16)
  hydrogen bonds       : bond        0.04601 (  196)
  hydrogen bonds       : angle       4.40126 (  549)
  link_BETA1-4         : bond        0.00394 (    3)
  link_BETA1-4         : angle       2.38863 (    9)
  link_NAG-ASN         : bond        0.00731 (    8)
  link_NAG-ASN         : angle       3.03907 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7667 (mm-30)
REVERT: C  198 ARG cc_start: 0.7063 (mtm-85) cc_final: 0.6794 (mtm-85)
REVERT: D   64 GLN cc_start: 0.7791 (tp40) cc_final: 0.7484 (tp40)
REVERT: D  140 MET cc_start: 0.8413 (tmm) cc_final: 0.8107 (tmm)
REVERT: A   53 SER cc_start: 0.4884 (OUTLIER) cc_final: 0.4676 (m)
REVERT: A  217 TRP cc_start: 0.8073 (m100) cc_final: 0.6865 (m100)
REVERT: B   76 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7249 (tttp)
REVERT: B  146 TRP cc_start: 0.8779 (p90) cc_final: 0.8394 (p90)
REVERT: B  260 GLN cc_start: 0.7475 (mt0) cc_final: 0.7207 (mt0)
  outliers start: 25
  outliers final: 23
  residues processed: 110
  average time/residue: 0.0804
  time to fit residues: 12.0867
Evaluate side-chains
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0570
   chunk 66 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0470
   chunk 39 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
D 154 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.172744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.153581 restraints weight = 15043.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.156310 restraints weight = 9364.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.158199 restraints weight = 6722.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.159344 restraints weight = 5307.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.160324 restraints weight = 4508.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.5555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7308  Z= 0.112
  Angle     :  0.681  10.716   9990  Z= 0.315
  Chirality :  0.045   0.386   1128
  Planarity :  0.005   0.093   1256
  Dihedral  :  7.071  55.893   1167
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.57 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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 (0.28), residues: 855
  helix:  2.53 (0.42), residues: 148
  sheet: -0.51 (0.31), residues: 238
  loop : -1.62 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 105 
 TYR   0.024   0.001   TYR B 295 
 PHE   0.022   0.001   PHE B  72 
 TRP   0.020   0.001   TRP A 115 
 HIS   0.005   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7289)
  covalent geometry    : angle       0.66128 ( 9941)
  SS BOND              : bond        0.00403 (    8)
  SS BOND              : angle       1.50357 (   16)
  hydrogen bonds       : bond        0.04072 (  196)
  hydrogen bonds       : angle       4.25400 (  549)
  link_BETA1-4         : bond        0.00324 (    3)
  link_BETA1-4         : angle       2.25962 (    9)
  link_NAG-ASN         : bond        0.00718 (    8)
  link_NAG-ASN         : angle       2.94742 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7619 (mm-30)
REVERT: D   64 GLN cc_start: 0.7759 (tp40) cc_final: 0.7424 (tp40)
REVERT: D  140 MET cc_start: 0.8419 (tmm) cc_final: 0.8115 (tmm)
REVERT: A  217 TRP cc_start: 0.8128 (m100) cc_final: 0.6948 (m100)
REVERT: B  146 TRP cc_start: 0.8758 (p90) cc_final: 0.8368 (p90)
REVERT: B  250 LYS cc_start: 0.8212 (pttm) cc_final: 0.6941 (tttt)
REVERT: B  315 GLU cc_start: 0.7413 (mp0) cc_final: 0.7209 (pm20)
  outliers start: 26
  outliers final: 22
  residues processed: 114
  average time/residue: 0.0750
  time to fit residues: 11.9113
Evaluate side-chains
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0470
   chunk 58 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8082

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.168144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.147917 restraints weight = 15026.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.150649 restraints weight = 9523.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.152583 restraints weight = 6940.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.153895 restraints weight = 5525.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.154440 restraints weight = 4695.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7308  Z= 0.130
  Angle     :  0.706  10.021   9990  Z= 0.330
  Chirality :  0.046   0.384   1128
  Planarity :  0.006   0.090   1256
  Dihedral  :  7.241  56.908   1167
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.44 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -0.79 (0.28), residues: 855
  helix:  2.51 (0.42), residues: 148
  sheet: -0.51 (0.32), residues: 236
  loop : -1.60 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 105 
 TYR   0.020   0.001   TYR B 295 
 PHE   0.023   0.001   PHE B  72 
 TRP   0.020   0.002   TRP A 217 
 HIS   0.004   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7289)
  covalent geometry    : angle       0.68675 ( 9941)
  SS BOND              : bond        0.00463 (    8)
  SS BOND              : angle       1.65424 (   16)
  hydrogen bonds       : bond        0.04329 (  196)
  hydrogen bonds       : angle       4.35118 (  549)
  link_BETA1-4         : bond        0.00285 (    3)
  link_BETA1-4         : angle       2.13831 (    9)
  link_NAG-ASN         : bond        0.00665 (    8)
  link_NAG-ASN         : angle       2.95310 (   24)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7674 (mm-30)
REVERT: D   64 GLN cc_start: 0.7848 (tp40) cc_final: 0.7502 (tp40)
REVERT: D  140 MET cc_start: 0.8445 (tmm) cc_final: 0.8129 (tmm)
REVERT: A  217 TRP cc_start: 0.8117 (m100) cc_final: 0.6909 (m100)
REVERT: B  146 TRP cc_start: 0.8801 (p90) cc_final: 0.8417 (p90)
REVERT: B  250 LYS cc_start: 0.8241 (pttm) cc_final: 0.6956 (tttt)
  outliers start: 25
  outliers final: 24
  residues processed: 111
  average time/residue: 0.0701
  time to fit residues: 10.9741
Evaluate side-chains
  111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0970
   chunk 1 optimal weight:    0.1980
   chunk 81 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0970
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.172988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.153791 restraints weight = 14972.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.156575 restraints weight = 9369.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.158456 restraints weight = 6703.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.159738 restraints weight = 5283.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.160620 restraints weight = 4447.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.5639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7308  Z= 0.111
  Angle     :  0.684  10.390   9990  Z= 0.319
  Chirality :  0.045   0.370   1128
  Planarity :  0.005   0.092   1256
  Dihedral  :  6.933  55.900   1167
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.57 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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 (0.28), residues: 855
  helix:  2.55 (0.42), residues: 148
  sheet: -0.50 (0.31), residues: 240
  loop : -1.56 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 198 
 TYR   0.021   0.001   TYR B 295 
 PHE   0.023   0.001   PHE B  72 
 TRP   0.020   0.001   TRP A 115 
 HIS   0.005   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7289)
  covalent geometry    : angle       0.66630 ( 9941)
  SS BOND              : bond        0.00399 (    8)
  SS BOND              : angle       1.49137 (   16)
  hydrogen bonds       : bond        0.03911 (  196)
  hydrogen bonds       : angle       4.18740 (  549)
  link_BETA1-4         : bond        0.00382 (    3)
  link_BETA1-4         : angle       2.05308 (    9)
  link_NAG-ASN         : bond        0.00675 (    8)
  link_NAG-ASN         : angle       2.83129 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1326.80 seconds
wall clock time: 23 minutes 29.56 seconds (1409.56 seconds total)