Starting phenix.real_space_refine
on Thu Jul  2 20:06:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjs_39348/07_2026/8yjs_39348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjs_39348/07_2026/8yjs_39348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2026/8yjs_39348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2026/8yjs_39348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2026/8yjs_39348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2026/8yjs_39348.cif"
  }
  resolution = 3.55
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 331 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      61      5.49       5
     S      61      5.16       5
     C    6031      2.51       5
     N    1657      2.21       5
     O    2070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9880
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1951
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "B"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "J"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 387
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "E"
      Number of atoms: 590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 590
          Classifications: {'DNA': 29}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "F"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 2.70, per 1000 atoms: 0.27
  Number of scatterers: 9880
  At special positions: 0
  Unit cell: (107.07, 98.77, 106.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      61     16.00
     P      61     15.00
     O    2070      8.00
     N    1657      7.00
     C    6031      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 322.6 milliseconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      30.7% alpha, 24.2% beta
      15 base pairs and 52 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.554A  pdb=" N   LYS C  20 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 140 through 155
      removed outlier: 4.066A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'D' and resid 6 through 14
    Processing helix  chain 'D' and resid 22 through 26
      removed outlier: 3.504A  pdb=" N   SER D  25 " --> pdb=" O   ASP D  22 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR D  26 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 22 through 26'
    Processing helix  chain 'D' and resid 35 through 45
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 90 through 92
      No H-bonds generated for 'chain 'D' and resid 90 through 92'
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 4.032A  pdb=" N   ALA D 116 " --> pdb=" O   GLN D 112 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA D 117 " --> pdb=" O   GLN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 129
    Processing helix  chain 'D' and resid 134 through 149
      removed outlier: 3.524A  pdb=" N   ASN D 138 " --> pdb=" O   THR D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
    Processing helix  chain 'D' and resid 181 through 186
    Processing helix  chain 'D' and resid 209 through 217
    Processing helix  chain 'D' and resid 219 through 231
    Processing helix  chain 'D' and resid 242 through 253
      removed outlier: 3.552A  pdb=" N   ALA D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 262
      removed outlier: 4.113A  pdb=" N   ARG D 262 " --> pdb=" O   GLU D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 285
      removed outlier: 3.533A  pdb=" N   ALA D 279 " --> pdb=" O   LEU D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 313
      removed outlier: 3.669A  pdb=" N   LEU D 306 " --> pdb=" O   ASN D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 334
      removed outlier: 4.006A  pdb=" N   GLY D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 20
    Processing helix  chain 'B' and resid 72 through 82
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 208 through 216
    Processing helix  chain 'B' and resid 217 through 222
      Proline residue:  B 220  - end of helix
      No H-bonds generated for 'chain 'B' and resid 217 through 222'
    Processing helix  chain 'A' and resid 8 through 20
      removed outlier: 4.146A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 60
      removed outlier: 3.721A  pdb=" N   PHE C   2 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 71
      removed outlier: 7.163A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY C 245 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR C 239 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU C 238 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 123 through 127
      removed outlier: 6.621A  pdb=" N   VAL C 123 " --> pdb=" O   SER D 349 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER D 349 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   GLN C 125 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS D 345 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 204 through 208
      removed outlier: 5.199A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 19 through 21
      removed outlier: 3.680A  pdb=" N   GLU D 206 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ALA D 175 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP D  34 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61
    Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71
      removed outlier: 3.633A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71
      removed outlier: 5.337A  pdb=" N   SER A 230 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET A 229 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      30 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      52 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2513
        1.33 -     1.45: 1975
        1.45 -     1.57: 5443
        1.57 -     1.69: 125
        1.69 -     1.81: 98
  Bond restraints: 10154
  Sorted by residual:
  bond pdb=" C   THR C 219 "
       pdb=" N   PRO C 220 "
    ideal  model  delta    sigma   weight residual
    1.337  1.388 -0.052 9.80e-03 1.04e+04 2.79e+01
  bond pdb=" C1'  DT J  16 "
       pdb=" N1   DT J  16 "
    ideal  model  delta    sigma   weight residual
    1.468  1.521 -0.053 1.40e-02 5.10e+03 1.44e+01
  bond pdb=" C3'  DT E  17 "
       pdb=" C2'  DT E  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" C3'  DT J  15 "
       pdb=" C2'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.73e+00
  bond pdb=" C3'  DT J   4 "
       pdb=" C2'  DT J   4 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.63e+00
  ... (remaining 10149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 13671
        3.09 -     6.18: 244
        6.18 -     9.26: 40
        9.26 -    12.35: 7
       12.35 -    15.44: 1
  Bond angle restraints: 13963
  Sorted by residual:
  angle pdb=" C   ASP D  51 "
        pdb=" N   VAL D  52 "
        pdb=" CA  VAL D  52 "
      ideal   model   delta    sigma   weight residual
     121.97  131.68   -9.71 1.80e+00 3.09e-01 2.91e+01
  angle pdb=" CA  ARG B  64 "
        pdb=" CB  ARG B  64 "
        pdb=" CG  ARG B  64 "
      ideal   model   delta    sigma   weight residual
     114.10  124.27  -10.17 2.00e+00 2.50e-01 2.59e+01
  angle pdb=" N   VAL B  45 "
        pdb=" CA  VAL B  45 "
        pdb=" C   VAL B  45 "
      ideal   model   delta    sigma   weight residual
     113.71  109.21    4.50 9.50e-01 1.11e+00 2.24e+01
  angle pdb=" CA  VAL D  52 "
        pdb=" CB  VAL D  52 "
        pdb=" CG1 VAL D  52 "
      ideal   model   delta    sigma   weight residual
     110.40  118.35   -7.95 1.70e+00 3.46e-01 2.19e+01
  angle pdb=" CB  GLN D 112 "
        pdb=" CG  GLN D 112 "
        pdb=" CD  GLN D 112 "
      ideal   model   delta    sigma   weight residual
     112.60  120.51   -7.91 1.70e+00 3.46e-01 2.16e+01
  ... (remaining 13958 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5043
       17.89 -    35.79: 731
       35.79 -    53.68: 287
       53.68 -    71.57: 62
       71.57 -    89.46: 14
  Dihedral angle restraints: 6137
    sinusoidal: 2903
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CA  GLU B 198 "
           pdb=" C   GLU B 198 "
           pdb=" N   MET B 199 "
           pdb=" CA  MET B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.81  -27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  PHE D 126 "
           pdb=" C   PHE D 126 "
           pdb=" N   THR D 127 "
           pdb=" CA  THR D 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ASN C  95 "
           pdb=" C   ASN C  95 "
           pdb=" N   ALA C  96 "
           pdb=" CA  ALA C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.64  -22.36     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 6134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1502
       0.111 -    0.223: 95
       0.223 -    0.334: 9
       0.334 -    0.445: 0
       0.445 -    0.556: 1
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CB  VAL D  52 "
            pdb=" CA  VAL D  52 "
            pdb=" CG1 VAL D  52 "
            pdb=" CG2 VAL D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" CB  ILE C  23 "
            pdb=" CA  ILE C  23 "
            pdb=" CG1 ILE C  23 "
            pdb=" CG2 ILE C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL A 123 "
            pdb=" CA  VAL A 123 "
            pdb=" CG1 VAL A 123 "
            pdb=" CG2 VAL A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 201 "   -0.080 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO B 202 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO B 202 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO B 202 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 274 "    0.028 2.00e-02 2.50e+03   2.74e-02 1.88e+01
        pdb=" CG  TRP D 274 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 274 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 274 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 274 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 274 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 274 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 136 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   VAL B 136 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   VAL B 136 "    0.024 2.00e-02 2.50e+03
        pdb=" N   VAL B 137 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 3071
        2.86 -     3.37: 8455
        3.37 -     3.88: 17488
        3.88 -     4.39: 19562
        4.39 -     4.90: 32794
  Nonbonded interactions: 81370
  Sorted by model distance:
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   THR B 216 "
            pdb=" OG1 THR B 219 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   THR A 216 "
            pdb=" OG1 THR A 219 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OE2 GLU D  76 "
            pdb=" NE  ARG D 327 "
     model   vdw
     2.383 3.120
  nonbonded pdb=" OG  SER B 222 "
            pdb=" O   THR B 224 "
     model   vdw
     2.392 3.040
  ... (remaining 81365 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'B' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'C' and resid 2 through 254)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.060
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
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      :  0.006   0.071  10157  Z= 0.362
  Angle     :  1.054  15.440  13969  Z= 0.635
  Chirality :  0.061   0.556   1607
  Planarity :  0.008   0.119   1587
  Dihedral  : 19.677  89.464   4030
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.62 (0.20), residues: 1103
  helix: -2.73 (0.20), residues: 311
  sheet: -2.07 (0.26), residues: 312
  loop : -2.21 (0.23), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG D 129 
 TYR   0.028   0.003   TYR B 249 
 PHE   0.059   0.003   PHE B 214 
 TRP   0.073   0.005   TRP D 274 
 HIS   0.005   0.001   HIS D 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00649 /  0.36 (10154)
  covalent geometry    : angle       1.05457 /  0.64 (13963)
  SS BOND              : bond        0.00221 /  0.11 (    3)
  SS BOND              : angle       0.55622 /  0.29 (    6)
  hydrogen bonds       : bond        0.20336 / 13.04 (  460)
  hydrogen bonds       : angle      10.02207 /  6.98 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.366 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8766 (mm) cc_final: 0.8529 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0955
  time to fit residues: 19.8064
Evaluate side-chains
  108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  21 ASN
B  38 GLN
B 108 GLN
A 131 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.136471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104989 restraints weight = 15325.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.108241 restraints weight = 10687.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.109337 restraints weight = 6642.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.109700 restraints weight = 5779.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.110082 restraints weight = 5585.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10157  Z= 0.171
  Angle     :  0.667   8.575  13969  Z= 0.364
  Chirality :  0.047   0.242   1607
  Planarity :  0.005   0.067   1587
  Dihedral  : 21.019  82.930   1901
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.09 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.22), residues: 1103
  helix: -1.18 (0.25), residues: 325
  sheet: -2.00 (0.27), residues: 296
  loop : -1.90 (0.24), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  53 
 TYR   0.010   0.001   TYR C 211 
 PHE   0.027   0.002   PHE B 214 
 TRP   0.030   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 (10154)
  covalent geometry    : angle       0.66748 /  0.36 (13963)
  SS BOND              : bond        0.00131 /  0.07 (    3)
  SS BOND              : angle       0.56226 /  0.25 (    6)
  hydrogen bonds       : bond        0.05181 /  3.41 (  460)
  hydrogen bonds       : angle       7.25158 /  5.08 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.382 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8833 (mm) cc_final: 0.8591 (mm)
REVERT: B   53 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7807 (mtt-85)
REVERT: A  116 MET cc_start: 0.8581 (ttp) cc_final: 0.8369 (ttm)
REVERT: A  229 MET cc_start: 0.8046 (pmm) cc_final: 0.7549 (ptp)
  outliers start: 13
  outliers final: 8
  residues processed: 129
  average time/residue: 0.0968
  time to fit residues: 18.1580
Evaluate side-chains
  115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 74 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  38 GLN
C  49 GLN
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 ASN
D  77 ASN
B  84 ASN
B 108 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.134440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102407 restraints weight = 15269.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.105799 restraints weight = 10900.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.106613 restraints weight = 6678.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.107193 restraints weight = 5975.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.107445 restraints weight = 5732.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10157  Z= 0.167
  Angle     :  0.589   6.648  13969  Z= 0.324
  Chirality :  0.044   0.239   1607
  Planarity :  0.004   0.054   1587
  Dihedral  : 20.936  85.938   1901
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.00 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.23), residues: 1103
  helix: -0.39 (0.27), residues: 331
  sheet: -2.05 (0.27), residues: 288
  loop : -1.72 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.041   0.002   TYR B 211 
 PHE   0.028   0.002   PHE B 214 
 TRP   0.020   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 253 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.17 (10154)
  covalent geometry    : angle       0.58933 /  0.32 (13963)
  SS BOND              : bond        0.00058 /  0.03 (    3)
  SS BOND              : angle       0.51100 /  0.23 (    6)
  hydrogen bonds       : bond        0.04576 /  2.99 (  460)
  hydrogen bonds       : angle       6.51622 /  4.57 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.393 
Fit side-chains
REVERT: C  244 MET cc_start: 0.8240 (mpp) cc_final: 0.7990 (mpp)
REVERT: D   10 ILE cc_start: 0.8880 (mm) cc_final: 0.8633 (mm)
REVERT: D  126 PHE cc_start: 0.7486 (m-80) cc_final: 0.7202 (m-10)
REVERT: B   53 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7960 (mtt-85)
REVERT: B  199 MET cc_start: 0.5575 (tpt) cc_final: 0.3436 (mtm)
REVERT: A  229 MET cc_start: 0.8136 (pmm) cc_final: 0.7831 (ptp)
  outliers start: 18
  outliers final: 13
  residues processed: 129
  average time/residue: 0.0862
  time to fit residues: 16.7347
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  38 GLN
C 125 GLN
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 ASN
D  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.131157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.099268 restraints weight = 15445.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102155 restraints weight = 10718.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102949 restraints weight = 6886.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.103551 restraints weight = 6131.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103837 restraints weight = 5871.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10157  Z= 0.203
  Angle     :  0.610   8.073  13969  Z= 0.330
  Chirality :  0.045   0.266   1607
  Planarity :  0.004   0.053   1587
  Dihedral  : 20.871  87.458   1901
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.11 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.23), residues: 1103
  helix:  0.12 (0.28), residues: 331
  sheet: -2.13 (0.26), residues: 295
  loop : -1.55 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 327 
 TYR   0.013   0.002   TYR B 211 
 PHE   0.017   0.002   PHE D  27 
 TRP   0.015   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.20 (10154)
  covalent geometry    : angle       0.61004 /  0.33 (13963)
  SS BOND              : bond        0.00142 /  0.07 (    3)
  SS BOND              : angle       0.61369 /  0.28 (    6)
  hydrogen bonds       : bond        0.04306 /  2.84 (  460)
  hydrogen bonds       : angle       6.20215 /  4.36 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: D  126 PHE cc_start: 0.7550 (m-80) cc_final: 0.7283 (m-10)
REVERT: B  199 MET cc_start: 0.5846 (tpt) cc_final: 0.3750 (mtm)
REVERT: B  215 PHE cc_start: 0.8554 (m-80) cc_final: 0.8338 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 122
  average time/residue: 0.0784
  time to fit residues: 14.8658
Evaluate side-chains
  118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue   21 ASN
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  299 SER
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 111 optimal weight:    9.9990
   chunk 103 optimal weight:    0.4980
   chunk 57 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.133754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.100246 restraints weight = 15177.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103636 restraints weight = 11124.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.104825 restraints weight = 6811.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.105188 restraints weight = 5938.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105547 restraints weight = 5721.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10157  Z= 0.148
  Angle     :  0.560   7.348  13969  Z= 0.305
  Chirality :  0.043   0.293   1607
  Planarity :  0.004   0.051   1587
  Dihedral  : 20.788  86.324   1901
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.32 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.24), residues: 1103
  helix:  0.45 (0.28), residues: 330
  sheet: -2.14 (0.26), residues: 295
  loop : -1.44 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 129 
 TYR   0.020   0.001   TYR B 211 
 PHE   0.016   0.001   PHE D  27 
 TRP   0.013   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.15 (10154)
  covalent geometry    : angle       0.56041 /  0.31 (13963)
  SS BOND              : bond        0.00111 /  0.06 (    3)
  SS BOND              : angle       0.45033 /  0.20 (    6)
  hydrogen bonds       : bond        0.04038 /  2.67 (  460)
  hydrogen bonds       : angle       6.07067 /  4.27 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.369 
Fit side-chains
REVERT: C  244 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8044 (mtp)
REVERT: D   10 ILE cc_start: 0.8891 (mm) cc_final: 0.8653 (mm)
REVERT: D  126 PHE cc_start: 0.7596 (m-80) cc_final: 0.7325 (m-10)
REVERT: D  259 ILE cc_start: 0.7981 (mm) cc_final: 0.7539 (mt)
REVERT: B   86 ASP cc_start: 0.7813 (m-30) cc_final: 0.7592 (m-30)
REVERT: B  199 MET cc_start: 0.5759 (tpt) cc_final: 0.3721 (mtm)
REVERT: B  215 PHE cc_start: 0.8590 (m-80) cc_final: 0.8387 (m-80)
REVERT: A  199 MET cc_start: 0.5440 (tpt) cc_final: 0.5199 (tpt)
  outliers start: 25
  outliers final: 16
  residues processed: 131
  average time/residue: 0.0779
  time to fit residues: 15.6457
Evaluate side-chains
  126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 38 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0570
   chunk 81 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.5898

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.133922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.100465 restraints weight = 15125.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.103906 restraints weight = 11090.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.105005 restraints weight = 6789.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105432 restraints weight = 5968.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.105755 restraints weight = 5715.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10157  Z= 0.148
  Angle     :  0.559   7.370  13969  Z= 0.302
  Chirality :  0.043   0.300   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.725  85.931   1901
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.15 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.24), residues: 1103
  helix:  0.75 (0.29), residues: 326
  sheet: -2.08 (0.26), residues: 295
  loop : -1.33 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 129 
 TYR   0.019   0.001   TYR B 211 
 PHE   0.014   0.001   PHE B 215 
 TRP   0.013   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.15 (10154)
  covalent geometry    : angle       0.55870 /  0.30 (13963)
  SS BOND              : bond        0.00052 /  0.03 (    3)
  SS BOND              : angle       0.45763 /  0.22 (    6)
  hydrogen bonds       : bond        0.03894 /  2.58 (  460)
  hydrogen bonds       : angle       5.93675 /  4.18 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.386 
Fit side-chains
REVERT: C  244 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8023 (mtt)
REVERT: D   10 ILE cc_start: 0.8895 (mm) cc_final: 0.8656 (mm)
REVERT: D  126 PHE cc_start: 0.7572 (m-80) cc_final: 0.7331 (m-10)
REVERT: D  214 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: D  259 ILE cc_start: 0.8001 (mm) cc_final: 0.7579 (mt)
REVERT: B   75 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8173 (tmm)
REVERT: B   86 ASP cc_start: 0.7862 (m-30) cc_final: 0.7650 (m-30)
REVERT: B  199 MET cc_start: 0.5794 (tpt) cc_final: 0.3749 (mtm)
  outliers start: 25
  outliers final: 18
  residues processed: 129
  average time/residue: 0.0750
  time to fit residues: 14.7321
Evaluate side-chains
  128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   40 MET
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  38 GLN
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.133479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.100290 restraints weight = 15079.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.103649 restraints weight = 10976.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.104896 restraints weight = 6735.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.105220 restraints weight = 5849.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105603 restraints weight = 5639.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10157  Z= 0.156
  Angle     :  0.560   7.839  13969  Z= 0.303
  Chirality :  0.044   0.344   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.684  86.556   1901
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.25 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.24), residues: 1103
  helix:  0.80 (0.29), residues: 327
  sheet: -2.08 (0.26), residues: 305
  loop : -1.20 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 262 
 TYR   0.024   0.002   TYR B 211 
 PHE   0.016   0.001   PHE D  27 
 TRP   0.013   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.16 (10154)
  covalent geometry    : angle       0.56054 /  0.30 (13963)
  SS BOND              : bond        0.00087 /  0.05 (    3)
  SS BOND              : angle       0.44732 /  0.21 (    6)
  hydrogen bonds       : bond        0.03899 /  2.59 (  460)
  hydrogen bonds       : angle       5.85143 /  4.12 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.238 
Fit side-chains
REVERT: C  244 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8049 (mtt)
REVERT: D   10 ILE cc_start: 0.8892 (mm) cc_final: 0.8649 (mm)
REVERT: D  126 PHE cc_start: 0.7645 (m-80) cc_final: 0.7324 (m-10)
REVERT: D  259 ILE cc_start: 0.8105 (mm) cc_final: 0.7699 (mt)
REVERT: B   75 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8155 (tmm)
REVERT: B  199 MET cc_start: 0.5911 (tpt) cc_final: 0.3779 (mtm)
  outliers start: 26
  outliers final: 19
  residues processed: 125
  average time/residue: 0.0800
  time to fit residues: 15.2564
Evaluate side-chains
  124 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   40 MET
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.132392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099133 restraints weight = 15027.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102476 restraints weight = 10972.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103531 restraints weight = 6762.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.103963 restraints weight = 5953.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.104274 restraints weight = 5733.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10157  Z= 0.170
  Angle     :  0.573   6.714  13969  Z= 0.309
  Chirality :  0.044   0.337   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.688  87.473   1901
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.87 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.24), residues: 1103
  helix:  0.83 (0.29), residues: 328
  sheet: -2.06 (0.26), residues: 303
  loop : -1.15 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 320 
 TYR   0.023   0.002   TYR B 211 
 PHE   0.016   0.002   PHE D  27 
 TRP   0.013   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.17 (10154)
  covalent geometry    : angle       0.57294 /  0.31 (13963)
  SS BOND              : bond        0.00099 /  0.05 (    3)
  SS BOND              : angle       0.50191 /  0.24 (    6)
  hydrogen bonds       : bond        0.03862 /  2.57 (  460)
  hydrogen bonds       : angle       5.82347 /  4.09 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: C  244 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8111 (mtp)
REVERT: D   10 ILE cc_start: 0.8920 (mm) cc_final: 0.8689 (mm)
REVERT: D  126 PHE cc_start: 0.7640 (m-80) cc_final: 0.7350 (m-10)
REVERT: D  259 ILE cc_start: 0.8172 (mm) cc_final: 0.7741 (mt)
REVERT: D  274 TRP cc_start: 0.8054 (t60) cc_final: 0.7663 (t60)
REVERT: B   75 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8203 (tmm)
REVERT: B  199 MET cc_start: 0.5850 (tpt) cc_final: 0.3725 (mtm)
  outliers start: 24
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0753
  time to fit residues: 13.7415
Evaluate side-chains
  127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   40 MET
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.132047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098896 restraints weight = 14964.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.102383 restraints weight = 10878.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103155 restraints weight = 6638.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.103788 restraints weight = 5954.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.104025 restraints weight = 5688.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10157  Z= 0.178
  Angle     :  0.580   6.442  13969  Z= 0.312
  Chirality :  0.044   0.356   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.640  87.904   1901
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.77 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.24), residues: 1103
  helix:  0.82 (0.29), residues: 328
  sheet: -2.06 (0.25), residues: 319
  loop : -1.11 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 210 
 TYR   0.029   0.002   TYR B 211 
 PHE   0.015   0.002   PHE D  27 
 TRP   0.013   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.18 (10154)
  covalent geometry    : angle       0.57982 /  0.31 (13963)
  SS BOND              : bond        0.00146 /  0.08 (    3)
  SS BOND              : angle       0.52035 /  0.25 (    6)
  hydrogen bonds       : bond        0.03909 /  2.63 (  460)
  hydrogen bonds       : angle       5.83057 /  4.09 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: C  244 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7963 (mtp)
REVERT: D   10 ILE cc_start: 0.8960 (mm) cc_final: 0.8740 (mm)
REVERT: D  126 PHE cc_start: 0.7667 (m-80) cc_final: 0.7374 (m-10)
REVERT: D  259 ILE cc_start: 0.8173 (mm) cc_final: 0.7762 (mt)
REVERT: D  274 TRP cc_start: 0.8057 (t60) cc_final: 0.7737 (t60)
REVERT: B   75 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8198 (tmm)
REVERT: A  199 MET cc_start: 0.5632 (tpt) cc_final: 0.5270 (tpt)
  outliers start: 26
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0798
  time to fit residues: 15.0743
Evaluate side-chains
  126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.130595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098663 restraints weight = 15246.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.101994 restraints weight = 10726.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.102645 restraints weight = 6623.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.103149 restraints weight = 6024.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103382 restraints weight = 5782.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10157  Z= 0.157
  Angle     :  0.573   6.622  13969  Z= 0.310
  Chirality :  0.044   0.372   1607
  Planarity :  0.003   0.050   1587
  Dihedral  : 20.588  87.614   1901
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.77 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.24), residues: 1103
  helix:  0.83 (0.29), residues: 328
  sheet: -2.03 (0.25), residues: 320
  loop : -1.07 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 129 
 TYR   0.019   0.002   TYR B 211 
 PHE   0.014   0.001   PHE D  27 
 TRP   0.016   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 (10154)
  covalent geometry    : angle       0.57338 /  0.31 (13963)
  SS BOND              : bond        0.00118 /  0.06 (    3)
  SS BOND              : angle       0.50417 /  0.24 (    6)
  hydrogen bonds       : bond        0.03785 /  2.54 (  460)
  hydrogen bonds       : angle       5.81570 /  4.08 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: C  244 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8266 (mtp)
REVERT: D   10 ILE cc_start: 0.8979 (mm) cc_final: 0.8769 (mm)
REVERT: D  126 PHE cc_start: 0.7628 (m-80) cc_final: 0.7342 (m-10)
REVERT: D  259 ILE cc_start: 0.8178 (mm) cc_final: 0.7767 (mt)
REVERT: D  274 TRP cc_start: 0.8109 (t60) cc_final: 0.7756 (t60)
REVERT: B   75 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8149 (tmm)
REVERT: A  199 MET cc_start: 0.5623 (tpt) cc_final: 0.5232 (tpt)
  outliers start: 25
  outliers final: 21
  residues processed: 122
  average time/residue: 0.0727
  time to fit residues: 13.6786
Evaluate side-chains
  131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  299 SER
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 104 optimal weight:    0.2980
   chunk 18 optimal weight:    0.3980
   chunk 42 optimal weight:    0.1980
   chunk 80 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.131461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.099240 restraints weight = 15376.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.102530 restraints weight = 10340.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.103462 restraints weight = 6335.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103940 restraints weight = 5649.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.104277 restraints weight = 5407.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10157  Z= 0.140
  Angle     :  0.561   6.689  13969  Z= 0.305
  Chirality :  0.043   0.349   1607
  Planarity :  0.003   0.050   1587
  Dihedral  : 20.523  87.108   1901
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.70 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.25), residues: 1103
  helix:  0.89 (0.29), residues: 328
  sheet: -1.97 (0.25), residues: 332
  loop : -1.00 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 339 
 TYR   0.027   0.002   TYR B 211 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.017   0.001   TRP D 274 
 HIS   0.004   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 (10154)
  covalent geometry    : angle       0.56084 /  0.30 (13963)
  SS BOND              : bond        0.00091 /  0.05 (    3)
  SS BOND              : angle       0.44583 /  0.21 (    6)
  hydrogen bonds       : bond        0.03707 /  2.49 (  460)
  hydrogen bonds       : angle       5.74868 /  4.04 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1489.85 seconds
wall clock time: 26 minutes 37.83 seconds (1597.83 seconds total)