Starting phenix.real_space_refine
on Sat Aug 23 17:54:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jj5_36340/08_2025/8jj5_36340_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jj5_36340/08_2025/8jj5_36340.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jj5_36340/08_2025/8jj5_36340.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jj5_36340/08_2025/8jj5_36340.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jj5_36340/08_2025/8jj5_36340_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jj5_36340/08_2025/8jj5_36340_trim.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.124
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    4460      2.51       5
     N    1108      2.21       5
     O    1290      1.98       5
     H    6679      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13594
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 3893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 3893
          Classifications: {'peptide': 248}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 237}
    Chain: "B"
      Number of atoms: 2224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2224
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 135}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3253
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 15, 'TRANS': 202}
    Chain: "D"
      Number of atoms: 4040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 4040
          Classifications: {'peptide': 254}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 243}
    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: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "G"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 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: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.27, per 1000 atoms: 0.17
  Number of scatterers: 13594
  At special positions: 0
  Unit cell: (94.5, 78.3, 145.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1290      8.00
     N    1108      7.00
     C    4460      6.00
     H    6679      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 158 " - pdb=" SG  CYS A 217 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS A 189 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 204 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  51 " - pdb=" SG  CYS B  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  47 " - pdb=" SG  CYS C 110 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 152 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 218 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D 160 " - pdb=" SG  CYS D 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 191 " - pdb=" SG  CYS D 205 " distance=2.02

  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
    ALPHA1-3
      " BMA G   3 " - " MAN G   4 "
    ALPHA1-6
      " BMA G   3 " - " MAN G   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG B 201 " - " ASN B  28 "
      " NAG D 301 " - " ASN D 131 "
      " NAG E   1 " - " ASN A 169 "
      " NAG F   1 " - " ASN B  57 "
      " NAG G   1 " - " ASN C 139 "
      " NAG H   1 " - " ASN C 170 "
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 357.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      57.3% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 42
      removed outlier: 3.504A  pdb=" N   LEU A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.677A  pdb=" N   GLY A  52 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 87
      removed outlier: 4.061A  pdb=" N   ALA A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   PHE A  68 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 122
      removed outlier: 5.670A  pdb=" N   ILE A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ARG A 117 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 135
      removed outlier: 4.855A  pdb=" N   GLN A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET A 131 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 3.564A  pdb=" N   LEU A 148 " --> pdb=" O   GLU A 144 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 164
      No H-bonds generated for 'chain 'A' and resid 162 through 164'
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 172 through 178
      removed outlier: 4.109A  pdb=" N   ALA A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 190
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 217 through 257
      removed outlier: 3.623A  pdb=" N   ILE A 221 " --> pdb=" O   CYS A 217 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE A 235 " --> pdb=" O   GLY A 231 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
    Processing helix  chain 'B' and resid 50 through 54
    Processing helix  chain 'B' and resid 142 through 146
    Processing helix  chain 'B' and resid 153 through 182
      removed outlier: 3.705A  pdb=" N   VAL B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 75
      removed outlier: 3.921A  pdb=" N   ARG C  73 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 121
      removed outlier: 4.023A  pdb=" N   ARG C 120 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 132
    Processing helix  chain 'C' and resid 193 through 197
      removed outlier: 3.525A  pdb=" N   ILE C 197 " --> pdb=" O   TYR C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 236
      Proline residue:  C 219  - end of helix
    Processing helix  chain 'D' and resid 8 through 38
    Processing helix  chain 'D' and resid 43 through 48
    Processing helix  chain 'D' and resid 53 through 83
    Processing helix  chain 'D' and resid 84 through 114
      removed outlier: 4.611A  pdb=" N   ASP D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 129
      removed outlier: 3.784A  pdb=" N   TYR D 129 " --> pdb=" O   MET D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 157
      removed outlier: 3.802A  pdb=" N   GLY D 145 " --> pdb=" O   TRP D 141 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR D 147 " --> pdb=" O   ASN D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 170
    Processing helix  chain 'D' and resid 173 through 179
    Processing helix  chain 'D' and resid 187 through 191
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 218 through 257
      Proline residue:  D 225  - end of helix
      removed outlier: 3.606A  pdb=" N   ALA D 234 " --> pdb=" O   ALA D 230 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE D 236 " --> pdb=" O   GLY D 232 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 44 through 46
    Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 76
      removed outlier: 3.549A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 76
    Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 43
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 106
      removed outlier: 5.948A  pdb=" N   LYS C 101 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   VAL C  65 " --> pdb=" O   LYS C 101 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA C 103 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU C  60 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TYR C 166 " --> pdb=" O   GLN C 179 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   GLN C 179 " --> pdb=" O   TYR C 166 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LEU C 168 " --> pdb=" O   GLN C 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 106
      removed outlier: 5.948A  pdb=" N   LYS C 101 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   VAL C  65 " --> pdb=" O   LYS C 101 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA C 103 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU C  60 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1164 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: 2.41

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1444
        1.04 -     1.23: 6047
        1.23 -     1.43: 2326
        1.43 -     1.63: 3865
        1.63 -     1.82: 84
  Bond restraints: 13766
  Sorted by residual:
  bond pdb=" N   ARG D   9 "
       pdb=" H   ARG D   9 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.77e+01
  bond pdb=" CZ  ARG D   9 "
       pdb=" NH2 ARG D   9 "
    ideal  model  delta    sigma   weight residual
    1.330  1.231  0.099 1.30e-02 5.92e+03 5.75e+01
  bond pdb=" N   TRP D 246 "
       pdb=" H   TRP D 246 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" N   GLY C 225 "
       pdb=" H   GLY C 225 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" CD2 PHE C 220 "
       pdb=" HD2 PHE C 220 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.73e+01
  ... (remaining 13761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 19364
        2.53 -     5.07: 4088
        5.07 -     7.60: 1145
        7.60 -    10.13: 152
       10.13 -    12.67: 18
  Bond angle restraints: 24767
  Sorted by residual:
  angle pdb=" CA  PHE D  11 "
        pdb=" CB  PHE D  11 "
        pdb=" CG  PHE D  11 "
      ideal   model   delta    sigma   weight residual
     113.80  121.20   -7.40 1.00e+00 1.00e+00 5.47e+01
  angle pdb=" CA  PHE D  92 "
        pdb=" CB  PHE D  92 "
        pdb=" CG  PHE D  92 "
      ideal   model   delta    sigma   weight residual
     113.80  121.09   -7.29 1.00e+00 1.00e+00 5.31e+01
  angle pdb=" CA  PHE D 253 "
        pdb=" CB  PHE D 253 "
        pdb=" CG  PHE D 253 "
      ideal   model   delta    sigma   weight residual
     113.80  120.90   -7.10 1.00e+00 1.00e+00 5.04e+01
  angle pdb=" CA  ASN D  19 "
        pdb=" CB  ASN D  19 "
        pdb=" CG  ASN D  19 "
      ideal   model   delta    sigma   weight residual
     112.60  119.63   -7.03 1.00e+00 1.00e+00 4.94e+01
  angle pdb=" CA  ASN D  84 "
        pdb=" CB  ASN D  84 "
        pdb=" CG  ASN D  84 "
      ideal   model   delta    sigma   weight residual
     112.60  119.62   -7.02 1.00e+00 1.00e+00 4.92e+01
  ... (remaining 24762 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.65: 6150
       21.65 -    43.31: 377
       43.31 -    64.96: 185
       64.96 -    86.62: 44
       86.62 -   108.27: 10
  Dihedral angle restraints: 6766
    sinusoidal: 3739
      harmonic: 3027
  Sorted by residual:
  dihedral pdb=" C   SER D  42 "
           pdb=" N   SER D  42 "
           pdb=" CA  SER D  42 "
           pdb=" CB  SER D  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.41   15.81     0      2.50e+00 1.60e-01 4.00e+01
  dihedral pdb=" CA  ASP D  39 "
           pdb=" C   ASP D  39 "
           pdb=" N   GLN D  40 "
           pdb=" CA  GLN D  40 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.05  -29.95     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  TYR D  41 "
           pdb=" C   TYR D  41 "
           pdb=" N   SER D  42 "
           pdb=" CA  SER D  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.16  -28.84     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 6763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.154: 877
       0.154 -    0.308: 156
       0.308 -    0.462: 33
       0.462 -    0.617: 55
       0.617 -    0.771: 22
  Chirality restraints: 1143
  Sorted by residual:
  chirality pdb=" C1  MAN G   5 "
            pdb=" O6  BMA G   3 "
            pdb=" C2  MAN G   5 "
            pdb=" O5  MAN G   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.09    0.31 2.00e-02 2.50e+03 2.33e+02
  chirality pdb=" C1  BMA F   3 "
            pdb=" O4  NAG F   2 "
            pdb=" C2  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.64    0.24 2.00e-02 2.50e+03 1.43e+02
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.59    0.19 2.00e-02 2.50e+03 9.27e+01
  ... (remaining 1140 not shown)

  Planarity restraints: 2014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 230 "    0.199 2.00e-02 2.50e+03   1.35e-01 7.34e+02
        pdb=" CG  TRP A 230 "    0.085 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 230 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 230 "    0.050 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 230 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 230 "    0.051 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 230 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 230 "    0.071 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 230 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 230 "    0.117 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 230 "    0.027 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 230 "   -0.340 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 230 "   -0.253 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 230 "    0.046 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 230 "   -0.124 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 230 "    0.136 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 113 "    0.909 9.50e-02 1.11e+02   3.41e-01 6.41e+02
        pdb=" NE  ARG D 113 "    0.133 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 113 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 113 "   -0.072 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 113 "   -0.093 2.00e-02 2.50e+03
        pdb="HH11 ARG D 113 "   -0.265 2.00e-02 2.50e+03
        pdb="HH12 ARG D 113 "    0.333 2.00e-02 2.50e+03
        pdb="HH21 ARG D 113 "    0.022 2.00e-02 2.50e+03
        pdb="HH22 ARG D 113 "   -0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  48 "    0.326 2.00e-02 2.50e+03   1.24e-01 4.60e+02
        pdb=" CG  TYR A  48 "   -0.108 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  48 "   -0.108 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  48 "   -0.121 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  48 "   -0.044 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  48 "   -0.044 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  48 "    0.019 2.00e-02 2.50e+03
        pdb=" OH  TYR A  48 "    0.166 2.00e-02 2.50e+03
        pdb=" HD1 TYR A  48 "   -0.055 2.00e-02 2.50e+03
        pdb=" HD2 TYR A  48 "   -0.066 2.00e-02 2.50e+03
        pdb=" HE1 TYR A  48 "    0.008 2.00e-02 2.50e+03
        pdb=" HE2 TYR A  48 "    0.027 2.00e-02 2.50e+03
  ... (remaining 2011 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 867
        2.18 -     2.78: 23757
        2.78 -     3.39: 38509
        3.39 -     3.99: 49776
        3.99 -     4.60: 72615
  Nonbonded interactions: 185524
  Sorted by model distance:
  nonbonded pdb=" HG  SER A 162 "
            pdb=" OD1 ASP A 166 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" HH  TYR D 129 "
            pdb=" OD1 ASP D 151 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" OE2 GLU C  43 "
            pdb=" HH  TYR C 132 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" HH  TYR A 135 "
            pdb=" OD1 ASP A 150 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" O   PHE D  35 "
            pdb=" HG  SER D  38 "
     model   vdw
     1.611 2.450
  ... (remaining 185519 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 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.580
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6280
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      :  0.021   0.170   7110  Z= 1.153
  Angle     :  2.212  14.724   9717  Z= 1.447
  Chirality :  0.194   0.771   1143
  Planarity :  0.021   0.278   1192
  Dihedral  : 17.067 108.270   2725
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.88 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.53 %
    Favored  : 90.26 %
  Cbeta Deviations :  4.87 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.93 (0.25), residues: 856
  helix: -1.78 (0.20), residues: 452
  sheet: -0.70 (0.66), residues: 47
  loop : -2.19 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG D 228 
 TYR   0.289   0.036   TYR A  48 
 PHE   0.054   0.012   PHE A  68 
 TRP   0.148   0.032   TRP A 185 
 HIS   0.014   0.004   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.02098 ( 7087)
  covalent geometry    : angle       2.18056 ( 9657)
  SS BOND              : bond        0.01332 (    9)
  SS BOND              : angle       1.80835 (   18)
  hydrogen bonds       : bond        0.17562 (  386)
  hydrogen bonds       : angle       7.63530 ( 1164)
  link_ALPHA1-3        : bond        0.01942 (    1)
  link_ALPHA1-3        : angle       2.07816 (    3)
  link_ALPHA1-6        : bond        0.02693 (    1)
  link_ALPHA1-6        : angle       8.98225 (    3)
  link_BETA1-4         : bond        0.02700 (    6)
  link_BETA1-4         : angle       7.42702 (   18)
  link_NAG-ASN         : bond        0.01119 (    6)
  link_NAG-ASN         : angle       4.09686 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 276
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.6820 (m100) cc_final: 0.6429 (m100)
REVERT: A   85 LEU cc_start: 0.8291 (mm) cc_final: 0.8022 (mm)
REVERT: A   90 SER cc_start: 0.8737 (p) cc_final: 0.8276 (p)
REVERT: A  211 TYR cc_start: 0.6570 (m-80) cc_final: 0.6128 (m-10)
REVERT: A  247 MET cc_start: 0.5128 (mtp) cc_final: 0.4470 (mtp)
REVERT: C   91 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5271 (tm-30)
REVERT: D   24 MET cc_start: 0.7650 (mtt) cc_final: 0.7104 (mmt)
  outliers start: 9
  outliers final: 2
  residues processed: 281
  average time/residue: 0.1680
  time to fit residues: 62.0598
Evaluate side-chains
  196 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 194
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   47 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
C  78 GLN
C 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.191670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.176646 restraints weight = 37088.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.181556 restraints weight = 16115.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.184532 restraints weight = 8594.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.186370 restraints weight = 5211.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.187568 restraints weight = 3479.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   7110  Z= 0.246
  Angle     :  0.914   9.720   9717  Z= 0.473
  Chirality :  0.049   0.316   1143
  Planarity :  0.007   0.077   1192
  Dihedral  : 12.897  86.288   1230
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.05 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.27), residues: 856
  helix: -0.59 (0.23), residues: 460
  sheet: -1.09 (0.54), residues: 61
  loop : -1.93 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 113 
 TYR   0.039   0.003   TYR A 114 
 PHE   0.022   0.002   PHE A  71 
 TRP   0.023   0.002   TRP A  39 
 HIS   0.009   0.002   HIS D 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 7087)
  covalent geometry    : angle       0.86997 ( 9657)
  SS BOND              : bond        0.00383 (    9)
  SS BOND              : angle       2.96003 (   18)
  hydrogen bonds       : bond        0.07245 (  386)
  hydrogen bonds       : angle       5.54045 ( 1164)
  link_ALPHA1-3        : bond        0.00353 (    1)
  link_ALPHA1-3        : angle       3.97641 (    3)
  link_ALPHA1-6        : bond        0.01088 (    1)
  link_ALPHA1-6        : angle       3.79242 (    3)
  link_BETA1-4         : bond        0.00889 (    6)
  link_BETA1-4         : angle       4.07087 (   18)
  link_NAG-ASN         : bond        0.00511 (    6)
  link_NAG-ASN         : angle       3.77854 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 204
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.6157 (mmm) cc_final: 0.5567 (mmm)
REVERT: A   64 TRP cc_start: 0.7210 (m100) cc_final: 0.6905 (m100)
REVERT: A   85 LEU cc_start: 0.7909 (mm) cc_final: 0.7683 (mm)
REVERT: A  175 ARG cc_start: 0.7090 (mtm180) cc_final: 0.6772 (mtm180)
REVERT: B  157 VAL cc_start: 0.4299 (t) cc_final: 0.3769 (t)
REVERT: C   91 GLU cc_start: 0.6180 (mt-10) cc_final: 0.5552 (tm-30)
REVERT: D   32 GLU cc_start: 0.0577 (mm-30) cc_final: 0.0122 (mt-10)
REVERT: D  255 TRP cc_start: 0.7254 (t60) cc_final: 0.6766 (t60)
  outliers start: 13
  outliers final: 10
  residues processed: 210
  average time/residue: 0.1487
  time to fit residues: 41.9215
Evaluate side-chains
  187 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 177
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain D residue  130 GLN
Chi-restraints excluded: chain D residue  137 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
D  19 ASN
D  40 GLN
D 130 GLN
D 229 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.192959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.177862 restraints weight = 36729.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.182793 restraints weight = 15690.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.185743 restraints weight = 8289.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.187599 restraints weight = 5037.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.188759 restraints weight = 3374.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7110  Z= 0.167
  Angle     :  0.794   8.666   9717  Z= 0.406
  Chirality :  0.044   0.253   1143
  Planarity :  0.005   0.061   1192
  Dihedral  : 11.175  78.233   1229
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.27 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.27), residues: 856
  helix: -0.15 (0.24), residues: 452
  sheet: -0.77 (0.59), residues: 60
  loop : -1.71 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 257 
 TYR   0.028   0.002   TYR A 114 
 PHE   0.024   0.002   PHE A  34 
 TRP   0.019   0.002   TRP A 230 
 HIS   0.004   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7087)
  covalent geometry    : angle       0.76087 ( 9657)
  SS BOND              : bond        0.00276 (    9)
  SS BOND              : angle       2.18713 (   18)
  hydrogen bonds       : bond        0.06385 (  386)
  hydrogen bonds       : angle       5.13834 ( 1164)
  link_ALPHA1-3        : bond        0.00782 (    1)
  link_ALPHA1-3        : angle       2.46515 (    3)
  link_ALPHA1-6        : bond        0.02228 (    1)
  link_ALPHA1-6        : angle       3.33016 (    3)
  link_BETA1-4         : bond        0.00841 (    6)
  link_BETA1-4         : angle       3.76558 (   18)
  link_NAG-ASN         : bond        0.00371 (    6)
  link_NAG-ASN         : angle       2.78533 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.5004 (t80)
REVERT: A   51 MET cc_start: 0.6025 (mmm) cc_final: 0.5633 (mmm)
REVERT: A  106 GLU cc_start: 0.6996 (tp30) cc_final: 0.6768 (tp30)
REVERT: C   91 GLU cc_start: 0.6327 (mt-10) cc_final: 0.5503 (tm-30)
REVERT: D   32 GLU cc_start: 0.0905 (mm-30) cc_final: 0.0506 (mt-10)
REVERT: D  246 TRP cc_start: 0.6433 (m-10) cc_final: 0.6134 (m100)
  outliers start: 16
  outliers final: 11
  residues processed: 189
  average time/residue: 0.1409
  time to fit residues: 36.3166
Evaluate side-chains
  177 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   41 TYR
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  130 GLN
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
D  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.189988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.175909 restraints weight = 37313.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.180386 restraints weight = 16431.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.183080 restraints weight = 8886.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.184780 restraints weight = 5478.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.185850 restraints weight = 3728.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.4630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6596
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093   7110  Z= 0.268
  Angle     :  0.805   6.911   9717  Z= 0.421
  Chirality :  0.045   0.262   1143
  Planarity :  0.005   0.055   1192
  Dihedral  : 10.468  77.303   1229
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.76 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.28), residues: 856
  helix: -0.26 (0.24), residues: 451
  sheet: -1.12 (0.57), residues: 64
  loop : -1.77 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  46 
 TYR   0.027   0.003   TYR D  91 
 PHE   0.022   0.002   PHE A  34 
 TRP   0.028   0.003   TRP D 168 
 HIS   0.005   0.002   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 7087)
  covalent geometry    : angle       0.77911 ( 9657)
  SS BOND              : bond        0.00433 (    9)
  SS BOND              : angle       1.63539 (   18)
  hydrogen bonds       : bond        0.06401 (  386)
  hydrogen bonds       : angle       5.37241 ( 1164)
  link_ALPHA1-3        : bond        0.00539 (    1)
  link_ALPHA1-3        : angle       3.21737 (    3)
  link_ALPHA1-6        : bond        0.01323 (    1)
  link_ALPHA1-6        : angle       2.55012 (    3)
  link_BETA1-4         : bond        0.00691 (    6)
  link_BETA1-4         : angle       3.36886 (   18)
  link_NAG-ASN         : bond        0.00978 (    6)
  link_NAG-ASN         : angle       2.63258 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.5311 (t80)
REVERT: A   51 MET cc_start: 0.6703 (mmm) cc_final: 0.6314 (mmm)
REVERT: A   87 ARG cc_start: 0.6446 (ptp-110) cc_final: 0.6236 (ttp-110)
  outliers start: 25
  outliers final: 16
  residues processed: 188
  average time/residue: 0.1677
  time to fit residues: 41.7497
Evaluate side-chains
  181 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  119 TYR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
D  40 GLN
D 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.190509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.175469 restraints weight = 37213.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.180292 restraints weight = 16001.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.183183 restraints weight = 8518.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.184981 restraints weight = 5203.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.186177 restraints weight = 3518.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6582
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   7110  Z= 0.183
  Angle     :  0.728   7.119   9717  Z= 0.377
  Chirality :  0.043   0.263   1143
  Planarity :  0.005   0.054   1192
  Dihedral  :  9.435  76.658   1229
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.89 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.28), residues: 856
  helix:  0.03 (0.24), residues: 451
  sheet: -1.05 (0.58), residues: 64
  loop : -1.60 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 175 
 TYR   0.020   0.002   TYR D  91 
 PHE   0.017   0.002   PHE D  70 
 TRP   0.013   0.002   TRP D 186 
 HIS   0.004   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7087)
  covalent geometry    : angle       0.70420 ( 9657)
  SS BOND              : bond        0.00350 (    9)
  SS BOND              : angle       1.76970 (   18)
  hydrogen bonds       : bond        0.05949 (  386)
  hydrogen bonds       : angle       5.01381 ( 1164)
  link_ALPHA1-3        : bond        0.00896 (    1)
  link_ALPHA1-3        : angle       2.74832 (    3)
  link_ALPHA1-6        : bond        0.00896 (    1)
  link_ALPHA1-6        : angle       1.28391 (    3)
  link_BETA1-4         : bond        0.00608 (    6)
  link_BETA1-4         : angle       3.11075 (   18)
  link_NAG-ASN         : bond        0.00304 (    6)
  link_NAG-ASN         : angle       2.33008 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 178
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.4887 (t80)
REVERT: A   51 MET cc_start: 0.6374 (mmm) cc_final: 0.6052 (mmm)
  outliers start: 27
  outliers final: 18
  residues processed: 193
  average time/residue: 0.1528
  time to fit residues: 39.5253
Evaluate side-chains
  186 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0570
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    2.9904

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

Flipped N/Q/H residues before XYZ refinement:
B 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.190962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.175831 restraints weight = 37094.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.180706 restraints weight = 16039.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.183621 restraints weight = 8547.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.185455 restraints weight = 5231.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.186537 restraints weight = 3532.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.5661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7110  Z= 0.164
  Angle     :  0.687   6.578   9717  Z= 0.355
  Chirality :  0.042   0.225   1143
  Planarity :  0.004   0.049   1192
  Dihedral  :  8.864  75.328   1225
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.57 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.28), residues: 856
  helix:  0.18 (0.24), residues: 451
  sheet: -0.95 (0.59), residues: 64
  loop : -1.53 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.016   0.002   TYR A 114 
 PHE   0.021   0.002   PHE A  71 
 TRP   0.013   0.002   TRP D 186 
 HIS   0.004   0.001   HIS D 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7087)
  covalent geometry    : angle       0.66759 ( 9657)
  SS BOND              : bond        0.00360 (    9)
  SS BOND              : angle       1.42369 (   18)
  hydrogen bonds       : bond        0.05679 (  386)
  hydrogen bonds       : angle       4.85412 ( 1164)
  link_ALPHA1-3        : bond        0.00712 (    1)
  link_ALPHA1-3        : angle       2.54548 (    3)
  link_ALPHA1-6        : bond        0.00426 (    1)
  link_ALPHA1-6        : angle       1.25260 (    3)
  link_BETA1-4         : bond        0.00515 (    6)
  link_BETA1-4         : angle       2.83036 (   18)
  link_NAG-ASN         : bond        0.00333 (    6)
  link_NAG-ASN         : angle       2.14036 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 184
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.4867 (t80)
REVERT: D  246 TRP cc_start: 0.6392 (m-90) cc_final: 0.6190 (m100)
  outliers start: 23
  outliers final: 16
  residues processed: 195
  average time/residue: 0.1323
  time to fit residues: 36.1257
Evaluate side-chains
  191 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.192028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.177004 restraints weight = 36807.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.181843 restraints weight = 15866.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.184775 restraints weight = 8457.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.186605 restraints weight = 5175.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.187809 restraints weight = 3479.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.5870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7110  Z= 0.161
  Angle     :  0.686   7.570   9717  Z= 0.353
  Chirality :  0.042   0.222   1143
  Planarity :  0.004   0.050   1192
  Dihedral  :  8.653  73.880   1225
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.73 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.28), residues: 856
  helix:  0.21 (0.24), residues: 453
  sheet: -0.92 (0.59), residues: 64
  loop : -1.45 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.015   0.002   TYR D  91 
 PHE   0.016   0.001   PHE D  64 
 TRP   0.024   0.002   TRP D 168 
 HIS   0.009   0.002   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7087)
  covalent geometry    : angle       0.66739 ( 9657)
  SS BOND              : bond        0.00254 (    9)
  SS BOND              : angle       1.52205 (   18)
  hydrogen bonds       : bond        0.05568 (  386)
  hydrogen bonds       : angle       4.79935 ( 1164)
  link_ALPHA1-3        : bond        0.00769 (    1)
  link_ALPHA1-3        : angle       2.47162 (    3)
  link_ALPHA1-6        : bond        0.00595 (    1)
  link_ALPHA1-6        : angle       1.54812 (    3)
  link_BETA1-4         : bond        0.00540 (    6)
  link_BETA1-4         : angle       2.72531 (   18)
  link_NAG-ASN         : bond        0.00282 (    6)
  link_NAG-ASN         : angle       2.05720 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5046 (t80)
REVERT: A   51 MET cc_start: 0.6360 (mmm) cc_final: 0.5425 (tpp)
REVERT: B  156 MET cc_start: 0.5323 (tmm) cc_final: 0.5101 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 191
  average time/residue: 0.1316
  time to fit residues: 34.6839
Evaluate side-chains
  190 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 172
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
D  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.193126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.178105 restraints weight = 36500.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.183001 restraints weight = 15722.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.185962 restraints weight = 8346.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.187825 restraints weight = 5053.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.189014 restraints weight = 3366.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.4664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6575
moved from start:          0.6113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7110  Z= 0.148
  Angle     :  0.670   6.284   9717  Z= 0.343
  Chirality :  0.041   0.211   1143
  Planarity :  0.004   0.048   1192
  Dihedral  :  8.312  71.363   1225
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.00 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.28), residues: 856
  helix:  0.44 (0.24), residues: 453
  sheet: -0.79 (0.64), residues: 54
  loop : -1.39 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.015   0.001   TYR D  91 
 PHE   0.015   0.001   PHE D  64 
 TRP   0.013   0.002   TRP D 186 
 HIS   0.008   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7087)
  covalent geometry    : angle       0.65322 ( 9657)
  SS BOND              : bond        0.00240 (    9)
  SS BOND              : angle       1.30450 (   18)
  hydrogen bonds       : bond        0.05365 (  386)
  hydrogen bonds       : angle       4.69129 ( 1164)
  link_ALPHA1-3        : bond        0.00670 (    1)
  link_ALPHA1-3        : angle       2.28491 (    3)
  link_ALPHA1-6        : bond        0.00282 (    1)
  link_ALPHA1-6        : angle       1.55795 (    3)
  link_BETA1-4         : bond        0.00505 (    6)
  link_BETA1-4         : angle       2.57762 (   18)
  link_NAG-ASN         : bond        0.00272 (    6)
  link_NAG-ASN         : angle       1.92713 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5224 (t80)
REVERT: A   51 MET cc_start: 0.6213 (mmm) cc_final: 0.5352 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 188
  average time/residue: 0.1326
  time to fit residues: 35.0693
Evaluate side-chains
  188 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  242 TRP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0370
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    3.0066

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

Flipped N/Q/H residues before XYZ refinement:
C  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.193107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.178127 restraints weight = 37044.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.182972 restraints weight = 16047.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.185869 restraints weight = 8558.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.187694 restraints weight = 5244.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.188857 restraints weight = 3536.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.4653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.6306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7110  Z= 0.157
  Angle     :  0.667   6.239   9717  Z= 0.344
  Chirality :  0.041   0.214   1143
  Planarity :  0.004   0.048   1192
  Dihedral  :  8.098  68.855   1225
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 23.27 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.28), residues: 856
  helix:  0.43 (0.24), residues: 455
  sheet: -0.93 (0.58), residues: 65
  loop : -1.24 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  63 
 TYR   0.016   0.002   TYR A 228 
 PHE   0.016   0.001   PHE D  64 
 TRP   0.025   0.002   TRP D 168 
 HIS   0.008   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7087)
  covalent geometry    : angle       0.65147 ( 9657)
  SS BOND              : bond        0.00236 (    9)
  SS BOND              : angle       1.27890 (   18)
  hydrogen bonds       : bond        0.05295 (  386)
  hydrogen bonds       : angle       4.72305 ( 1164)
  link_ALPHA1-3        : bond        0.00508 (    1)
  link_ALPHA1-3        : angle       2.21194 (    3)
  link_ALPHA1-6        : bond        0.00188 (    1)
  link_ALPHA1-6        : angle       1.66762 (    3)
  link_BETA1-4         : bond        0.00466 (    6)
  link_BETA1-4         : angle       2.49453 (   18)
  link_NAG-ASN         : bond        0.00267 (    6)
  link_NAG-ASN         : angle       1.85581 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5219 (t80)
REVERT: A   51 MET cc_start: 0.6296 (mmm) cc_final: 0.5470 (tpp)
REVERT: C  200 TRP cc_start: 0.7946 (t-100) cc_final: 0.7642 (t-100)
REVERT: D  168 TRP cc_start: 0.7673 (m100) cc_final: 0.7410 (m100)
REVERT: D  193 MET cc_start: 0.4714 (mmt) cc_final: 0.3693 (pmm)
  outliers start: 20
  outliers final: 15
  residues processed: 184
  average time/residue: 0.1338
  time to fit residues: 34.3835
Evaluate side-chains
  186 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 78 optimal weight:    0.2980
   chunk 80 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.193317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.178325 restraints weight = 36771.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.183231 restraints weight = 15895.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.186162 restraints weight = 8439.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.188003 restraints weight = 5133.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.189034 restraints weight = 3440.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.6408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7110  Z= 0.136
  Angle     :  0.652   6.150   9717  Z= 0.334
  Chirality :  0.040   0.193   1143
  Planarity :  0.004   0.048   1192
  Dihedral  :  7.716  64.900   1225
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 23.82 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.29), residues: 856
  helix:  0.55 (0.24), residues: 460
  sheet: -0.83 (0.58), residues: 65
  loop : -1.17 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.016   0.001   TYR A 228 
 PHE   0.013   0.001   PHE D  64 
 TRP   0.022   0.002   TRP D 168 
 HIS   0.008   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7087)
  covalent geometry    : angle       0.63712 ( 9657)
  SS BOND              : bond        0.00226 (    9)
  SS BOND              : angle       1.22903 (   18)
  hydrogen bonds       : bond        0.05135 (  386)
  hydrogen bonds       : angle       4.66147 ( 1164)
  link_ALPHA1-3        : bond        0.00618 (    1)
  link_ALPHA1-3        : angle       2.05561 (    3)
  link_ALPHA1-6        : bond        0.00279 (    1)
  link_ALPHA1-6        : angle       1.68068 (    3)
  link_BETA1-4         : bond        0.00460 (    6)
  link_BETA1-4         : angle       2.41294 (   18)
  link_NAG-ASN         : bond        0.00268 (    6)
  link_NAG-ASN         : angle       1.75578 (   18)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 182
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.5197 (t80)
REVERT: A   51 MET cc_start: 0.6334 (mmm) cc_final: 0.5446 (tpp)
REVERT: C  200 TRP cc_start: 0.7982 (t-100) cc_final: 0.7666 (t-100)
REVERT: D  168 TRP cc_start: 0.7619 (m100) cc_final: 0.6945 (m100)
REVERT: D  193 MET cc_start: 0.4859 (mmt) cc_final: 0.3874 (pmm)
  outliers start: 15
  outliers final: 13
  residues processed: 190
  average time/residue: 0.1437
  time to fit residues: 37.5945
Evaluate side-chains
  194 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   78 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.4706 r_free = 0.4706 target = 0.192344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.177237 restraints weight = 36985.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.182183 restraints weight = 15978.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.185163 restraints weight = 8528.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.187036 restraints weight = 5173.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.188220 restraints weight = 3444.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.6569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7110  Z= 0.142
  Angle     :  0.655   6.066   9717  Z= 0.335
  Chirality :  0.041   0.203   1143
  Planarity :  0.004   0.047   1192
  Dihedral  :  7.462  60.791   1225
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 23.95 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.28), residues: 856
  helix:  0.51 (0.24), residues: 460
  sheet: -0.77 (0.58), residues: 65
  loop : -1.12 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.027   0.002   TYR A 228 
 PHE   0.020   0.001   PHE D  70 
 TRP   0.013   0.002   TRP D 186 
 HIS   0.007   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7087)
  covalent geometry    : angle       0.64084 ( 9657)
  SS BOND              : bond        0.00225 (    9)
  SS BOND              : angle       1.18704 (   18)
  hydrogen bonds       : bond        0.05091 (  386)
  hydrogen bonds       : angle       4.64657 ( 1164)
  link_ALPHA1-3        : bond        0.00587 (    1)
  link_ALPHA1-3        : angle       2.04517 (    3)
  link_ALPHA1-6        : bond        0.00190 (    1)
  link_ALPHA1-6        : angle       1.68038 (    3)
  link_BETA1-4         : bond        0.00405 (    6)
  link_BETA1-4         : angle       2.34874 (   18)
  link_NAG-ASN         : bond        0.00233 (    6)
  link_NAG-ASN         : angle       1.68144 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2004.77 seconds
wall clock time: 34 minutes 47.76 seconds (2087.76 seconds total)