Starting phenix.real_space_refine
on Tue Feb  3 18:04:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9loe_63246/02_2026/9loe_63246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9loe_63246/02_2026/9loe_63246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9loe_63246/02_2026/9loe_63246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9loe_63246/02_2026/9loe_63246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9loe_63246/02_2026/9loe_63246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9loe_63246/02_2026/9loe_63246.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.172
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    3664      2.51       5
     N     988      2.21       5
     O    1172      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5865
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2444
          Classifications: {'peptide': 318}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 299}
    Chain: "B"
      Number of atoms: 1723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1723
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 219}
    Chain: "C"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1612
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'MAN': 4, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.42, per 1000 atoms: 0.24
  Number of scatterers: 5865
  At special positions: 0
  Unit cell: (65.22, 71.742, 148.919, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1172      8.00
     N     988      7.00
     C    3664      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  49 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 143 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 206 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 258 " - pdb=" SG  CYS A 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 303 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 292 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 159 " - pdb=" SG  CYS B 215 " distance=1.93
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 138 " - pdb=" SG  CYS C 197 " distance=1.95

  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
      " MAN D   3 " - " MAN D   6 "
      " MAN D   4 " - " MAN D   5 "
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
    ALPHA1-6
      " MAN D   3 " - " MAN D   4 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A1001 " - " ASN A  33 "
      " NAG D   1 " - " ASN A  63 "
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 324.1 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1374

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 17 sheets defined
      15.7% alpha, 39.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 53
      removed outlier: 3.643A  pdb=" N   LYS A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 65
      removed outlier: 3.686A  pdb=" N   SER A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 3.763A  pdb=" N   SER A  78 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A  80 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 104
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 187 through 202
      removed outlier: 3.764A  pdb=" N   PHE A 191 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 277
    Processing helix  chain 'A' and resid 283 through 288
    Processing helix  chain 'B' and resid 89 through 93
      removed outlier: 3.674A  pdb=" N   THR B  93 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 148
      No H-bonds generated for 'chain 'B' and resid 146 through 148'
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 220 through 223
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 4.139A  pdb=" N   GLU C  85 " --> pdb=" O   ALA C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 131
    Processing helix  chain 'C' and resid 185 through 192
      removed outlier: 3.693A  pdb=" N   HIS C 192 " --> pdb=" O   GLN C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 215
    Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83
      removed outlier: 6.759A  pdb=" N   SER A  81 " --> pdb=" O   TRP A 174 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   PHE A 129 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   ILE A 175 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   GLU A 131 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   LYS A 110 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   GLY A 142 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149
    Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 180
      removed outlier: 7.172A  pdb=" N   MET A 334 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   ILE A 208 " --> pdb=" O   MET A 334 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   THR A 336 " --> pdb=" O   CYS A 206 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   CYS A 206 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180
      removed outlier: 4.151A  pdb=" N   ALA A 228 " --> pdb=" O   MET A 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 248
    Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 265
      removed outlier: 3.620A  pdb=" N   GLY A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12
      removed outlier: 4.180A  pdb=" N   ASP B 101 " --> pdb=" O   TRP B  33 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   TRP B  33 " --> pdb=" O   ASP B 101 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 143
      removed outlier: 5.295A  pdb=" N   ALA B 156 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   VAL B 203 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   GLY B 158 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   VAL B 201 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   LEU B 160 " --> pdb=" O   SER B 199 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   SER B 199 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   LYS B 162 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU B 197 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 151
      removed outlier: 5.295A  pdb=" N   ALA B 156 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   VAL B 203 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   GLY B 158 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   VAL B 201 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   LEU B 160 " --> pdb=" O   SER B 199 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   SER B 199 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   LYS B 162 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU B 197 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 173
    Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 11
      removed outlier: 7.062A  pdb=" N   VAL C  10 " --> pdb=" O   THR C 108 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY C  86 " --> pdb=" O   VAL C 107 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   TRP C  37 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 17 through 23
    Processing sheet with id=AB6, first strand: chain 'C' and resid 118 through 122
      removed outlier: 5.597A  pdb=" N   TYR C 176 " --> pdb=" O   ASP C 142 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 118 through 122
      removed outlier: 5.597A  pdb=" N   TYR C 176 " --> pdb=" O   ASP C 142 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 157 through 159
      removed outlier: 4.196A  pdb=" N   TRP C 152 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)

    234 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.60

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1218
        1.33 -     1.45: 1524
        1.45 -     1.58: 3208
        1.58 -     1.70: 0
        1.70 -     1.83: 56
  Bond restraints: 6006
  Sorted by residual:
  bond pdb=" C   SER B 131 "
       pdb=" O   SER B 131 "
    ideal  model  delta    sigma   weight residual
    1.235  1.202  0.033 1.26e-02 6.30e+03 6.81e+00
  bond pdb=" N   SER B 131 "
       pdb=" CA  SER B 131 "
    ideal  model  delta    sigma   weight residual
    1.457  1.425  0.032 1.29e-02 6.01e+03 6.21e+00
  bond pdb=" CA  SER B 134 "
       pdb=" C   SER B 134 "
    ideal  model  delta    sigma   weight residual
    1.523  1.555 -0.032 1.34e-02 5.57e+03 5.56e+00
  bond pdb=" C1  MAN D   5 "
       pdb=" C2  MAN D   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.570 -0.044 2.00e-02 2.50e+03 4.83e+00
  bond pdb=" CA  PHE B 165 "
       pdb=" C   PHE B 165 "
    ideal  model  delta    sigma   weight residual
    1.517  1.541 -0.023 1.07e-02 8.73e+03 4.77e+00
  ... (remaining 6001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 7593
        2.13 -     4.26: 498
        4.26 -     6.39: 44
        6.39 -     8.52: 8
        8.52 -    10.65: 4
  Bond angle restraints: 8147
  Sorted by residual:
  angle pdb=" CA  TYR C  34 "
        pdb=" CB  TYR C  34 "
        pdb=" CG  TYR C  34 "
      ideal   model   delta    sigma   weight residual
     113.90  124.11  -10.21 1.80e+00 3.09e-01 3.22e+01
  angle pdb=" C   TYR C  33 "
        pdb=" N   TYR C  34 "
        pdb=" CA  TYR C  34 "
      ideal   model   delta    sigma   weight residual
     121.54  132.08  -10.54 1.91e+00 2.74e-01 3.05e+01
  angle pdb=" N   LYS A 260 "
        pdb=" CA  LYS A 260 "
        pdb=" C   LYS A 260 "
      ideal   model   delta    sigma   weight residual
     109.59  100.84    8.75 1.61e+00 3.86e-01 2.95e+01
  angle pdb=" N   SER B 132 "
        pdb=" CA  SER B 132 "
        pdb=" C   SER B 132 "
      ideal   model   delta    sigma   weight residual
     110.80  100.15   10.65 2.13e+00 2.20e-01 2.50e+01
  angle pdb=" N   GLU A 268 "
        pdb=" CA  GLU A 268 "
        pdb=" C   GLU A 268 "
      ideal   model   delta    sigma   weight residual
     111.07  116.18   -5.11 1.07e+00 8.73e-01 2.28e+01
  ... (remaining 8142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3408
       17.94 -    35.88: 206
       35.88 -    53.81: 46
       53.81 -    71.75: 14
       71.75 -    89.69: 8
  Dihedral angle restraints: 3682
    sinusoidal: 1516
      harmonic: 2166
  Sorted by residual:
  dihedral pdb=" CA  ASP C  52 "
           pdb=" C   ASP C  52 "
           pdb=" N   VAL C  53 "
           pdb=" CA  VAL C  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.94  -48.06     0      5.00e+00 4.00e-02 9.24e+01
  dihedral pdb=" CB  CYS A 287 "
           pdb=" SG  CYS A 287 "
           pdb=" SG  CYS A 292 "
           pdb=" CB  CYS A 292 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.30   61.70     1      1.00e+01 1.00e-02 5.05e+01
  dihedral pdb=" CB  CYS A 206 "
           pdb=" SG  CYS A 206 "
           pdb=" SG  CYS A 216 "
           pdb=" CB  CYS A 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.20   58.80     1      1.00e+01 1.00e-02 4.63e+01
  ... (remaining 3679 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 663
       0.063 -    0.126: 185
       0.126 -    0.190: 46
       0.190 -    0.253: 11
       0.253 -    0.316: 3
  Chirality restraints: 908
  Sorted by residual:
  chirality pdb=" CA  ASP C 142 "
            pdb=" N   ASP C 142 "
            pdb=" C   ASP C 142 "
            pdb=" CB  ASP C 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CA  ASN C 174 "
            pdb=" N   ASN C 174 "
            pdb=" C   ASN C 174 "
            pdb=" CB  ASN C 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C4  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" C5  NAG D   2 "
            pdb=" O4  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.25   -0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 905 not shown)

  Planarity restraints: 1036
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 152 "   -0.057 2.00e-02 2.50e+03   3.13e-02 2.44e+01
        pdb=" CG  TRP C 152 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 152 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 152 "    0.037 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 152 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 152 "    0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 152 "    0.044 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 152 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 152 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 152 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  97 "    0.050 5.00e-02 4.00e+02   7.57e-02 9.18e+00
        pdb=" N   PRO A  98 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  98 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  98 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 183 "   -0.032 2.00e-02 2.50e+03   2.36e-02 8.34e+00
        pdb=" CG  HIS B 183 "    0.034 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 183 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 183 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 183 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 183 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1033 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 18
        2.50 -     3.10: 3719
        3.10 -     3.70: 8445
        3.70 -     4.30: 12556
        4.30 -     4.90: 21582
  Nonbonded interactions: 46320
  Sorted by model distance:
  nonbonded pdb=" O   SER B 134 "
            pdb=" OG1 THR B 135 "
     model   vdw
     1.897 3.040
  nonbonded pdb=" O   SER C  92 "
            pdb=" OG  SER C  92 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ASP C  28 "
            pdb=" OG  SER C  92 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OG  SER B 131 "
            pdb=" N   SER B 132 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   GLU A 293 "
            pdb=" OG  SER A 299 "
     model   vdw
     2.355 3.040
  ... (remaining 46315 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
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      :  0.007   0.104   6025  Z= 0.404
  Angle     :  1.104  12.292   8192  Z= 0.651
  Chirality :  0.066   0.316    908
  Planarity :  0.008   0.076   1034
  Dihedral  : 13.070  89.688   2272
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  5.67 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  3.72 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.28), residues: 758
  helix: -2.28 (0.39), residues: 84
  sheet: -0.49 (0.32), residues: 249
  loop : -1.88 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.040   0.003   TYR C  34 
 PHE   0.023   0.004   PHE B 165 
 TRP   0.057   0.004   TRP C 152 
 HIS   0.007   0.002   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00731 ( 6006)
  covalent geometry    : angle       1.08766 ( 8147)
  SS BOND              : bond        0.03766 (   12)
  SS BOND              : angle       1.46702 (   24)
  hydrogen bonds       : bond        0.13723 (  208)
  hydrogen bonds       : angle       6.89875 (  573)
  link_ALPHA1-3        : bond        0.00246 (    2)
  link_ALPHA1-3        : angle       1.57091 (    6)
  link_ALPHA1-4        : bond        0.00065 (    1)
  link_ALPHA1-4        : angle       7.41511 (    3)
  link_ALPHA1-6        : bond        0.00265 (    1)
  link_ALPHA1-6        : angle       1.19223 (    3)
  link_BETA1-4         : bond        0.00852 (    1)
  link_BETA1-4         : angle       4.74803 (    3)
  link_NAG-ASN         : bond        0.00365 (    2)
  link_NAG-ASN         : angle       2.51432 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   66 GLN cc_start: 0.7558 (mp-120) cc_final: 0.7295 (mm-40)
REVERT: A  192 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7212 (mm)
REVERT: A  241 ARG cc_start: 0.7598 (tpp80) cc_final: 0.6811 (ttt180)
REVERT: A  300 GLU cc_start: 0.7070 (pp20) cc_final: 0.5948 (tm-30)
REVERT: A  322 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7714 (ppt170)
REVERT: B   92 ASP cc_start: 0.7977 (m-30) cc_final: 0.7622 (m-30)
REVERT: C   47 LYS cc_start: 0.7574 (tttt) cc_final: 0.7282 (tttm)
REVERT: C   62 ASP cc_start: 0.7532 (t0) cc_final: 0.7313 (t0)
  outliers start: 10
  outliers final: 3
  residues processed: 111
  average time/residue: 0.4724
  time to fit residues: 54.5737
Evaluate side-chains
  73 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue    3 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   1 GLN
B 183 HIS
B 190 GLN
C  71 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.185050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.118780 restraints weight = 6671.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.36
r_work: 0.3243 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   6025  Z= 0.281
  Angle     :  0.786   8.943   8192  Z= 0.406
  Chirality :  0.049   0.280    908
  Planarity :  0.006   0.066   1034
  Dihedral  :  7.319  49.498    963
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.60 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 11.32 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.29), residues: 758
  helix: -0.49 (0.52), residues: 85
  sheet:  0.18 (0.33), residues: 240
  loop : -1.52 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  63 
 TYR   0.045   0.003   TYR C  34 
 PHE   0.025   0.002   PHE C 101 
 TRP   0.014   0.002   TRP B  33 
 HIS   0.010   0.002   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 ( 6006)
  covalent geometry    : angle       0.76836 ( 8147)
  SS BOND              : bond        0.00575 (   12)
  SS BOND              : angle       1.51093 (   24)
  hydrogen bonds       : bond        0.04246 (  208)
  hydrogen bonds       : angle       5.25688 (  573)
  link_ALPHA1-3        : bond        0.00452 (    2)
  link_ALPHA1-3        : angle       1.98462 (    6)
  link_ALPHA1-4        : bond        0.00746 (    1)
  link_ALPHA1-4        : angle       5.22604 (    3)
  link_ALPHA1-6        : bond        0.00266 (    1)
  link_ALPHA1-6        : angle       1.80991 (    3)
  link_BETA1-4         : bond        0.00168 (    1)
  link_BETA1-4         : angle       3.84960 (    3)
  link_NAG-ASN         : bond        0.00353 (    2)
  link_NAG-ASN         : angle       2.65606 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   66 GLN cc_start: 0.7741 (mp-120) cc_final: 0.7524 (mm-40)
REVERT: A  192 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7156 (mm)
REVERT: A  241 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7103 (ttt180)
REVERT: A  300 GLU cc_start: 0.7416 (pp20) cc_final: 0.6106 (tm-30)
REVERT: A  310 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8536 (pttt)
REVERT: A  322 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8061 (ppt170)
REVERT: B   92 ASP cc_start: 0.8119 (m-30) cc_final: 0.7658 (m-30)
REVERT: C   47 LYS cc_start: 0.7957 (tttt) cc_final: 0.7648 (tttm)
REVERT: C   62 ASP cc_start: 0.8021 (t0) cc_final: 0.7776 (t0)
REVERT: C   83 GLU cc_start: 0.7860 (pp20) cc_final: 0.7599 (tt0)
  outliers start: 21
  outliers final: 13
  residues processed: 94
  average time/residue: 0.4860
  time to fit residues: 47.8012
Evaluate side-chains
  88 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  310 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  126 THR
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue  100 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 73 optimal weight:   20.0000
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0670
   chunk 67 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.3122

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.187844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.122441 restraints weight = 6567.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.33
r_work: 0.3290 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6025  Z= 0.159
  Angle     :  0.667   8.332   8192  Z= 0.342
  Chirality :  0.045   0.246    908
  Planarity :  0.005   0.062   1034
  Dihedral  :  6.421  47.070    962
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.80 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 12.71 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.30), residues: 758
  helix:  0.41 (0.56), residues: 85
  sheet:  0.58 (0.34), residues: 240
  loop : -1.40 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  63 
 TYR   0.038   0.002   TYR C  34 
 PHE   0.026   0.002   PHE A 197 
 TRP   0.010   0.001   TRP A 141 
 HIS   0.006   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6006)
  covalent geometry    : angle       0.65046 ( 8147)
  SS BOND              : bond        0.00468 (   12)
  SS BOND              : angle       1.30803 (   24)
  hydrogen bonds       : bond        0.03285 (  208)
  hydrogen bonds       : angle       4.93894 (  573)
  link_ALPHA1-3        : bond        0.00534 (    2)
  link_ALPHA1-3        : angle       1.67861 (    6)
  link_ALPHA1-4        : bond        0.00120 (    1)
  link_ALPHA1-4        : angle       4.66156 (    3)
  link_ALPHA1-6        : bond        0.00609 (    1)
  link_ALPHA1-6        : angle       1.63293 (    3)
  link_BETA1-4         : bond        0.00316 (    1)
  link_BETA1-4         : angle       3.41714 (    3)
  link_NAG-ASN         : bond        0.00281 (    2)
  link_NAG-ASN         : angle       2.11167 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7651 (mp-120) cc_final: 0.7449 (mm-40)
REVERT: A  181 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8293 (pt0)
REVERT: A  192 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7119 (mm)
REVERT: A  197 PHE cc_start: 0.7262 (t80) cc_final: 0.7049 (t80)
REVERT: A  241 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7184 (ttt180)
REVERT: A  244 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7130 (ttmm)
REVERT: A  300 GLU cc_start: 0.7242 (pp20) cc_final: 0.6099 (tm-30)
REVERT: A  310 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (pttm)
REVERT: A  322 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7523 (ppt170)
REVERT: A  340 ASN cc_start: 0.4535 (OUTLIER) cc_final: 0.4335 (m-40)
REVERT: B   92 ASP cc_start: 0.8053 (m-30) cc_final: 0.7615 (m-30)
REVERT: C   47 LYS cc_start: 0.7954 (tttt) cc_final: 0.7669 (tttm)
REVERT: C   62 ASP cc_start: 0.7943 (t0) cc_final: 0.7728 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 92
  average time/residue: 0.4598
  time to fit residues: 44.2494
Evaluate side-chains
  88 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  310 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue  100 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0770
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   overall best weight:    1.7944

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.185612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119849 restraints weight = 6662.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.36
r_work: 0.3258 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6025  Z= 0.195
  Angle     :  0.693   8.634   8192  Z= 0.352
  Chirality :  0.046   0.249    908
  Planarity :  0.006   0.064   1034
  Dihedral  :  6.110  47.179    960
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.60 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.80 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.31), residues: 758
  helix:  0.77 (0.58), residues: 85
  sheet:  0.70 (0.34), residues: 242
  loop : -1.29 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  91 
 TYR   0.041   0.002   TYR C  34 
 PHE   0.019   0.002   PHE A  67 
 TRP   0.011   0.001   TRP A 141 
 HIS   0.007   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 6006)
  covalent geometry    : angle       0.67647 ( 8147)
  SS BOND              : bond        0.00537 (   12)
  SS BOND              : angle       1.36710 (   24)
  hydrogen bonds       : bond        0.03406 (  208)
  hydrogen bonds       : angle       4.74928 (  573)
  link_ALPHA1-3        : bond        0.00466 (    2)
  link_ALPHA1-3        : angle       1.76423 (    6)
  link_ALPHA1-4        : bond        0.00156 (    1)
  link_ALPHA1-4        : angle       4.65079 (    3)
  link_ALPHA1-6        : bond        0.00285 (    1)
  link_ALPHA1-6        : angle       1.75425 (    3)
  link_BETA1-4         : bond        0.00273 (    1)
  link_BETA1-4         : angle       3.81822 (    3)
  link_NAG-ASN         : bond        0.00331 (    2)
  link_NAG-ASN         : angle       2.20327 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7707 (mp-120) cc_final: 0.7498 (mm-40)
REVERT: A  181 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8297 (pt0)
REVERT: A  192 LEU cc_start: 0.7571 (mp) cc_final: 0.7171 (mm)
REVERT: A  197 PHE cc_start: 0.7356 (t80) cc_final: 0.7000 (t80)
REVERT: A  241 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7203 (ttt180)
REVERT: A  300 GLU cc_start: 0.7351 (pp20) cc_final: 0.6251 (tm-30)
REVERT: A  310 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8569 (pttt)
REVERT: A  322 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7410 (tmt170)
REVERT: B   92 ASP cc_start: 0.8159 (m-30) cc_final: 0.7688 (m-30)
REVERT: C   47 LYS cc_start: 0.8005 (tttt) cc_final: 0.7695 (tttm)
  outliers start: 22
  outliers final: 14
  residues processed: 88
  average time/residue: 0.4747
  time to fit residues: 43.8261
Evaluate side-chains
  83 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  310 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue   87 ASP
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 46 optimal weight:   40.0000
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.187958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.137008 restraints weight = 6721.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 3.32
r_work: 0.3241 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6025  Z= 0.127
  Angle     :  0.630   7.829   8192  Z= 0.319
  Chirality :  0.044   0.230    908
  Planarity :  0.005   0.061   1034
  Dihedral  :  5.443  47.322    957
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.54 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.50 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.31), residues: 758
  helix:  0.96 (0.58), residues: 85
  sheet:  0.80 (0.33), residues: 245
  loop : -1.16 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.035   0.002   TYR C  34 
 PHE   0.014   0.001   PHE A  67 
 TRP   0.011   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6006)
  covalent geometry    : angle       0.61426 ( 8147)
  SS BOND              : bond        0.00418 (   12)
  SS BOND              : angle       1.26918 (   24)
  hydrogen bonds       : bond        0.02873 (  208)
  hydrogen bonds       : angle       4.62930 (  573)
  link_ALPHA1-3        : bond        0.00534 (    2)
  link_ALPHA1-3        : angle       1.63315 (    6)
  link_ALPHA1-4        : bond        0.00039 (    1)
  link_ALPHA1-4        : angle       4.51791 (    3)
  link_ALPHA1-6        : bond        0.00661 (    1)
  link_ALPHA1-6        : angle       1.59064 (    3)
  link_BETA1-4         : bond        0.00217 (    1)
  link_BETA1-4         : angle       3.30295 (    3)
  link_NAG-ASN         : bond        0.00296 (    2)
  link_NAG-ASN         : angle       1.84334 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7628 (mp-120) cc_final: 0.7418 (mm-40)
REVERT: A  192 LEU cc_start: 0.7572 (mp) cc_final: 0.7334 (mm)
REVERT: A  197 PHE cc_start: 0.7181 (t80) cc_final: 0.6957 (t80)
REVERT: A  241 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7276 (ttm-80)
REVERT: A  244 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6545 (ttmm)
REVERT: A  300 GLU cc_start: 0.7177 (pp20) cc_final: 0.6218 (tm-30)
REVERT: A  322 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7368 (tmt170)
REVERT: B   92 ASP cc_start: 0.8043 (m-30) cc_final: 0.7593 (m-30)
REVERT: C   47 LYS cc_start: 0.7888 (tttt) cc_final: 0.7590 (tttm)
REVERT: C   62 ASP cc_start: 0.7703 (t0) cc_final: 0.7480 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 82
  average time/residue: 0.4986
  time to fit residues: 42.9087
Evaluate side-chains
  85 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    0.1980
   chunk 55 optimal weight:    0.2980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4129 r_free = 0.4129 target = 0.188657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.123589 restraints weight = 6624.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.33
r_work: 0.3318 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6025  Z= 0.119
  Angle     :  0.617   8.106   8192  Z= 0.310
  Chirality :  0.043   0.223    908
  Planarity :  0.005   0.060   1034
  Dihedral  :  5.214  46.268    957
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.33 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.66 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.31), residues: 758
  helix:  1.11 (0.58), residues: 85
  sheet:  0.92 (0.33), residues: 243
  loop : -1.08 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  91 
 TYR   0.033   0.001   TYR C  34 
 PHE   0.014   0.001   PHE A  67 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6006)
  covalent geometry    : angle       0.60134 ( 8147)
  SS BOND              : bond        0.00404 (   12)
  SS BOND              : angle       1.21469 (   24)
  hydrogen bonds       : bond        0.02736 (  208)
  hydrogen bonds       : angle       4.50117 (  573)
  link_ALPHA1-3        : bond        0.00547 (    2)
  link_ALPHA1-3        : angle       1.64842 (    6)
  link_ALPHA1-4        : bond        0.00059 (    1)
  link_ALPHA1-4        : angle       4.39207 (    3)
  link_ALPHA1-6        : bond        0.00437 (    1)
  link_ALPHA1-6        : angle       1.53731 (    3)
  link_BETA1-4         : bond        0.00208 (    1)
  link_BETA1-4         : angle       3.32588 (    3)
  link_NAG-ASN         : bond        0.00277 (    2)
  link_NAG-ASN         : angle       1.72514 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7671 (mp-120) cc_final: 0.7443 (mm-40)
REVERT: A  181 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8216 (pt0)
REVERT: A  192 LEU cc_start: 0.7544 (mp) cc_final: 0.7300 (mm)
REVERT: A  197 PHE cc_start: 0.7170 (t80) cc_final: 0.6907 (t80)
REVERT: A  241 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7267 (ttm-80)
REVERT: A  244 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6428 (ttmm)
REVERT: A  300 GLU cc_start: 0.7192 (pp20) cc_final: 0.6165 (tm-30)
REVERT: A  322 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7271 (tmt170)
REVERT: B   43 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6561 (tttt)
REVERT: B   92 ASP cc_start: 0.8083 (m-30) cc_final: 0.7630 (m-30)
REVERT: C   47 LYS cc_start: 0.7953 (tttt) cc_final: 0.7653 (tttm)
REVERT: C   62 ASP cc_start: 0.7852 (t0) cc_final: 0.7617 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 80
  average time/residue: 0.5001
  time to fit residues: 42.0664
Evaluate side-chains
  83 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   13 LYS
Chi-restraints excluded: chain B residue   43 LYS
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 56 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.4116 r_free = 0.4116 target = 0.186711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.122056 restraints weight = 6624.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.32
r_work: 0.3281 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6025  Z= 0.166
  Angle     :  0.654   8.245   8192  Z= 0.330
  Chirality :  0.045   0.238    908
  Planarity :  0.005   0.061   1034
  Dihedral  :  5.395  46.575    957
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.46 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.97 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.31), residues: 758
  helix:  1.05 (0.58), residues: 85
  sheet:  0.90 (0.33), residues: 242
  loop : -1.08 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 111 
 TYR   0.037   0.002   TYR C  34 
 PHE   0.017   0.001   PHE A  67 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.005   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6006)
  covalent geometry    : angle       0.63786 ( 8147)
  SS BOND              : bond        0.00479 (   12)
  SS BOND              : angle       1.31868 (   24)
  hydrogen bonds       : bond        0.03049 (  208)
  hydrogen bonds       : angle       4.48947 (  573)
  link_ALPHA1-3        : bond        0.00459 (    2)
  link_ALPHA1-3        : angle       1.70708 (    6)
  link_ALPHA1-4        : bond        0.00164 (    1)
  link_ALPHA1-4        : angle       4.52721 (    3)
  link_ALPHA1-6        : bond        0.00368 (    1)
  link_ALPHA1-6        : angle       1.70071 (    3)
  link_BETA1-4         : bond        0.00186 (    1)
  link_BETA1-4         : angle       3.72894 (    3)
  link_NAG-ASN         : bond        0.00329 (    2)
  link_NAG-ASN         : angle       1.84100 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7700 (mp-120) cc_final: 0.7480 (mm-40)
REVERT: A  181 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8171 (pt0)
REVERT: A  183 MET cc_start: 0.7554 (ttp) cc_final: 0.7014 (ttt)
REVERT: A  192 LEU cc_start: 0.7630 (mp) cc_final: 0.7357 (mm)
REVERT: A  197 PHE cc_start: 0.7337 (t80) cc_final: 0.7027 (t80)
REVERT: A  241 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7146 (ttm-80)
REVERT: A  244 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6535 (ttmm)
REVERT: A  300 GLU cc_start: 0.7299 (pp20) cc_final: 0.6266 (tm-30)
REVERT: A  322 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7355 (tmt170)
REVERT: B   92 ASP cc_start: 0.8118 (m-30) cc_final: 0.7661 (m-30)
REVERT: C   47 LYS cc_start: 0.8002 (tttt) cc_final: 0.7696 (tttm)
  outliers start: 24
  outliers final: 19
  residues processed: 81
  average time/residue: 0.4676
  time to fit residues: 39.8330
Evaluate side-chains
  86 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   13 LYS
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue   87 ASP
Chi-restraints excluded: chain C residue   90 CYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 71 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.188501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.124294 restraints weight = 6532.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.31
r_work: 0.3312 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6025  Z= 0.119
  Angle     :  0.618   8.421   8192  Z= 0.310
  Chirality :  0.043   0.218    908
  Planarity :  0.005   0.059   1034
  Dihedral  :  5.090  45.588    957
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.80 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.90 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.31), residues: 758
  helix:  1.41 (0.60), residues: 79
  sheet:  0.97 (0.33), residues: 243
  loop : -1.04 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  63 
 TYR   0.030   0.001   TYR C  34 
 PHE   0.014   0.001   PHE A  67 
 TRP   0.011   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6006)
  covalent geometry    : angle       0.60276 ( 8147)
  SS BOND              : bond        0.00393 (   12)
  SS BOND              : angle       1.25370 (   24)
  hydrogen bonds       : bond        0.02630 (  208)
  hydrogen bonds       : angle       4.42174 (  573)
  link_ALPHA1-3        : bond        0.00518 (    2)
  link_ALPHA1-3        : angle       1.61886 (    6)
  link_ALPHA1-4        : bond        0.00076 (    1)
  link_ALPHA1-4        : angle       4.34499 (    3)
  link_ALPHA1-6        : bond        0.00616 (    1)
  link_ALPHA1-6        : angle       1.56326 (    3)
  link_BETA1-4         : bond        0.00247 (    1)
  link_BETA1-4         : angle       3.14770 (    3)
  link_NAG-ASN         : bond        0.00289 (    2)
  link_NAG-ASN         : angle       1.68845 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7781 (mp-120) cc_final: 0.7518 (mm-40)
REVERT: A  181 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8155 (pt0)
REVERT: A  183 MET cc_start: 0.7457 (ttp) cc_final: 0.6870 (ttt)
REVERT: A  192 LEU cc_start: 0.7544 (mp) cc_final: 0.7285 (mm)
REVERT: A  197 PHE cc_start: 0.7290 (t80) cc_final: 0.6905 (t80)
REVERT: A  241 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7217 (ttm-80)
REVERT: A  244 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6441 (ttmm)
REVERT: A  300 GLU cc_start: 0.7277 (pp20) cc_final: 0.6243 (tm-30)
REVERT: A  322 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7332 (tmt170)
REVERT: B   92 ASP cc_start: 0.8081 (m-30) cc_final: 0.7626 (m-30)
REVERT: C   47 LYS cc_start: 0.7958 (tttt) cc_final: 0.7661 (tttm)
  outliers start: 19
  outliers final: 16
  residues processed: 80
  average time/residue: 0.4624
  time to fit residues: 38.7177
Evaluate side-chains
  84 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0970
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0170
   chunk 70 optimal weight:    0.4980
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A 199 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.189492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.137199 restraints weight = 6543.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.54
r_work: 0.3334 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6025  Z= 0.111
  Angle     :  0.606   8.650   8192  Z= 0.304
  Chirality :  0.043   0.208    908
  Planarity :  0.005   0.059   1034
  Dihedral  :  4.888  44.458    957
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.05 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.31), residues: 758
  helix:  1.54 (0.61), residues: 79
  sheet:  0.99 (0.33), residues: 247
  loop : -1.01 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  63 
 TYR   0.029   0.001   TYR C  34 
 PHE   0.013   0.001   PHE A  67 
 TRP   0.010   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6006)
  covalent geometry    : angle       0.59132 ( 8147)
  SS BOND              : bond        0.00373 (   12)
  SS BOND              : angle       1.23755 (   24)
  hydrogen bonds       : bond        0.02596 (  208)
  hydrogen bonds       : angle       4.32619 (  573)
  link_ALPHA1-3        : bond        0.00482 (    2)
  link_ALPHA1-3        : angle       1.59361 (    6)
  link_ALPHA1-4        : bond        0.00104 (    1)
  link_ALPHA1-4        : angle       4.22863 (    3)
  link_ALPHA1-6        : bond        0.00500 (    1)
  link_ALPHA1-6        : angle       1.57813 (    3)
  link_BETA1-4         : bond        0.00227 (    1)
  link_BETA1-4         : angle       3.32245 (    3)
  link_NAG-ASN         : bond        0.00260 (    2)
  link_NAG-ASN         : angle       1.60989 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7813 (mp-120) cc_final: 0.7466 (mm-40)
REVERT: A  181 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8144 (pt0)
REVERT: A  183 MET cc_start: 0.7495 (ttp) cc_final: 0.6935 (ttt)
REVERT: A  192 LEU cc_start: 0.7563 (mp) cc_final: 0.7339 (mm)
REVERT: A  197 PHE cc_start: 0.7319 (t80) cc_final: 0.6940 (t80)
REVERT: A  241 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7283 (ttm-80)
REVERT: A  244 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6440 (ttmm)
REVERT: A  300 GLU cc_start: 0.7281 (pp20) cc_final: 0.6251 (tm-30)
REVERT: A  322 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7330 (tmt170)
REVERT: B   92 ASP cc_start: 0.8102 (m-30) cc_final: 0.7646 (m-30)
REVERT: C   47 LYS cc_start: 0.7967 (tttt) cc_final: 0.7665 (tttm)
  outliers start: 20
  outliers final: 14
  residues processed: 86
  average time/residue: 0.4554
  time to fit residues: 41.0155
Evaluate side-chains
  84 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue   90 CYS
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    0.4980
   chunk 12 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 199 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.188891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.124945 restraints weight = 6568.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.30
r_work: 0.3319 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6025  Z= 0.122
  Angle     :  0.619   8.739   8192  Z= 0.310
  Chirality :  0.043   0.210    908
  Planarity :  0.005   0.059   1034
  Dihedral  :  4.893  44.028    957
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.52 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.31), residues: 758
  helix:  1.54 (0.60), residues: 79
  sheet:  1.06 (0.33), residues: 247
  loop : -0.94 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  99 
 TYR   0.030   0.001   TYR C  34 
 PHE   0.014   0.001   PHE A  67 
 TRP   0.010   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6006)
  covalent geometry    : angle       0.60418 ( 8147)
  SS BOND              : bond        0.00391 (   12)
  SS BOND              : angle       1.24131 (   24)
  hydrogen bonds       : bond        0.02674 (  208)
  hydrogen bonds       : angle       4.28901 (  573)
  link_ALPHA1-3        : bond        0.00462 (    2)
  link_ALPHA1-3        : angle       1.61127 (    6)
  link_ALPHA1-4        : bond        0.00003 (    1)
  link_ALPHA1-4        : angle       4.21439 (    3)
  link_ALPHA1-6        : bond        0.00468 (    1)
  link_ALPHA1-6        : angle       1.56687 (    3)
  link_BETA1-4         : bond        0.00218 (    1)
  link_BETA1-4         : angle       3.38741 (    3)
  link_NAG-ASN         : bond        0.00274 (    2)
  link_NAG-ASN         : angle       1.62646 (    6)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.7826 (mp-120) cc_final: 0.7463 (mm-40)
REVERT: A  181 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8132 (pt0)
REVERT: A  183 MET cc_start: 0.7483 (ttp) cc_final: 0.6924 (ttt)
REVERT: A  192 LEU cc_start: 0.7555 (mp) cc_final: 0.7330 (mm)
REVERT: A  197 PHE cc_start: 0.7300 (t80) cc_final: 0.6914 (t80)
REVERT: A  241 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7171 (ttm-80)
REVERT: A  244 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6431 (ttmm)
REVERT: A  300 GLU cc_start: 0.7318 (pp20) cc_final: 0.6253 (tm-30)
REVERT: A  322 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7350 (tmt170)
REVERT: B   92 ASP cc_start: 0.8111 (m-30) cc_final: 0.7654 (m-30)
REVERT: C   47 LYS cc_start: 0.7943 (tttt) cc_final: 0.7644 (tttm)
REVERT: C  109 VAL cc_start: 0.8800 (t) cc_final: 0.8382 (m)
  outliers start: 17
  outliers final: 15
  residues processed: 82
  average time/residue: 0.4337
  time to fit residues: 37.3447
Evaluate side-chains
  85 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue   90 CYS
Chi-restraints excluded: chain C residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 199 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.184990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.119834 restraints weight = 6604.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.36
r_work: 0.3260 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6025  Z= 0.225
  Angle     :  0.718   8.742   8192  Z= 0.360
  Chirality :  0.047   0.252    908
  Planarity :  0.006   0.062   1034
  Dihedral  :  5.454  45.735    957
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.86 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.36 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.31), residues: 758
  helix:  1.30 (0.59), residues: 79
  sheet:  0.95 (0.34), residues: 229
  loop : -0.98 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 116 
 TYR   0.040   0.002   TYR C  34 
 PHE   0.019   0.002   PHE A  67 
 TRP   0.008   0.001   TRP B  33 
 HIS   0.008   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 6006)
  covalent geometry    : angle       0.70175 ( 8147)
  SS BOND              : bond        0.00553 (   12)
  SS BOND              : angle       1.41689 (   24)
  hydrogen bonds       : bond        0.03391 (  208)
  hydrogen bonds       : angle       4.44850 (  573)
  link_ALPHA1-3        : bond        0.00375 (    2)
  link_ALPHA1-3        : angle       1.80604 (    6)
  link_ALPHA1-4        : bond        0.00378 (    1)
  link_ALPHA1-4        : angle       4.63987 (    3)
  link_ALPHA1-6        : bond        0.00198 (    1)
  link_ALPHA1-6        : angle       1.79260 (    3)
  link_BETA1-4         : bond        0.00186 (    1)
  link_BETA1-4         : angle       3.89099 (    3)
  link_NAG-ASN         : bond        0.00440 (    2)
  link_NAG-ASN         : angle       1.96641 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2122.16 seconds
wall clock time: 36 minutes 55.99 seconds (2215.99 seconds total)