Starting phenix.real_space_refine
on Thu Jan 16 23:02:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjs_39348/01_2025/8yjs_39348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjs_39348/01_2025/8yjs_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_39348/01_2025/8yjs_39348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjs_39348/01_2025/8yjs_39348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjs_39348/01_2025/8yjs_39348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjs_39348/01_2025/8yjs_39348.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.29, per 1000 atoms: 0.64
  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: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 3.48
  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: 3.63

  Time building geometry restraints manager: 2.72 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=" CB  ASN B  24 "
       pdb=" CG  ASN B  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.75e+00
  bond pdb=" CB  GLN D 112 "
       pdb=" CG  GLN D 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.585 -0.065 3.00e-02 1.11e+03 4.72e+00
  bond pdb=" CA  ALA D 176 "
       pdb=" CB  ALA D 176 "
    ideal  model  delta    sigma   weight residual
    1.531  1.460  0.071 3.28e-02 9.30e+02 4.71e+00
  bond pdb=" CA  VAL D  52 "
       pdb=" CB  VAL D  52 "
    ideal  model  delta    sigma   weight residual
    1.540  1.570 -0.029 1.36e-02 5.41e+03 4.70e+00
  ... (remaining 10149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 13670
        3.09 -     6.18: 245
        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: 1504
       0.111 -    0.223: 93
       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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.220
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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  10154  Z= 0.403
  Angle     :  1.027  15.440  13963  Z= 0.536
  Chirality :  0.059   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.073   0.005   TRP D 274 
 HIS   0.005   0.001   HIS D 253 
 PHE   0.059   0.003   PHE B 214 
 TYR   0.028   0.003   TYR B 249 
 ARG   0.018   0.001   ARG D 129 

*********************** 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  : 1.018 
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: 0.2139
  time to fit residues: 43.8013
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  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0670
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
B  84 ASN
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 = 0.3845 r_free = 0.3845 target = 0.136676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.105230 restraints weight = 15170.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.108459 restraints weight = 10679.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.109788 restraints weight = 6673.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10154  Z= 0.214
  Angle     :  0.599   7.216  13963  Z= 0.329
  Chirality :  0.043   0.235   1607
  Planarity :  0.005   0.069   1587
  Dihedral  : 20.837  86.750   1901
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.78 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.22), residues: 1103
  helix: -1.06 (0.25), residues: 329
  sheet: -1.85 (0.28), residues: 283
  loop : -1.85 (0.24), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 253 
 PHE   0.025   0.001   PHE B 214 
 TYR   0.008   0.001   TYR D 152 
 ARG   0.003   0.000   ARG B  53 

*********************** 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
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 1.083 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8820 (mm) cc_final: 0.8572 (mm)
REVERT: B  125 GLN cc_start: 0.5982 (pm20) cc_final: 0.5774 (pm20)
REVERT: B  199 MET cc_start: 0.5518 (tpt) cc_final: 0.5252 (mmm)
REVERT: A   91 ARG cc_start: 0.6683 (tpt90) cc_final: 0.5297 (mtm180)
REVERT: A  229 MET cc_start: 0.8081 (pmm) cc_final: 0.7727 (ptp)
  outliers start: 11
  outliers final: 8
  residues processed: 141
  average time/residue: 0.2091
  time to fit residues: 43.2307
Evaluate side-chains
  118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
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 2 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0570
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0060
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.5514

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C  49 GLN
B  38 GLN
B  49 GLN
B 108 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.134661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.102326 restraints weight = 15288.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105043 restraints weight = 11249.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.106553 restraints weight = 7262.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10154  Z= 0.210
  Angle     :  0.552   5.899  13963  Z= 0.301
  Chirality :  0.042   0.255   1607
  Planarity :  0.004   0.057   1587
  Dihedral  : 20.402  88.736   1901
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.58 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.23), residues: 1103
  helix: -0.12 (0.27), residues: 333
  sheet: -1.94 (0.27), residues: 296
  loop : -1.62 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.016   0.001   PHE B 214 
 TYR   0.012   0.001   TYR B 211 
 ARG   0.003   0.000   ARG B 210 

*********************** 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
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.128 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8851 (t) cc_final: 0.8634 (m)
REVERT: C  199 MET cc_start: 0.7111 (tpp) cc_final: 0.5843 (mtm)
REVERT: D   10 ILE cc_start: 0.8862 (mm) cc_final: 0.8599 (mm)
REVERT: D  126 PHE cc_start: 0.7492 (m-80) cc_final: 0.7240 (m-10)
REVERT: D  259 ILE cc_start: 0.8008 (mm) cc_final: 0.7521 (mt)
REVERT: B  199 MET cc_start: 0.5790 (tpt) cc_final: 0.3656 (mtm)
REVERT: A   91 ARG cc_start: 0.6830 (tpt90) cc_final: 0.5371 (mtm-85)
  outliers start: 16
  outliers final: 12
  residues processed: 134
  average time/residue: 0.1950
  time to fit residues: 38.5888
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
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  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 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  203 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0270
   chunk 99 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 97 optimal weight:    0.4980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.136122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103043 restraints weight = 14979.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.106311 restraints weight = 10947.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.107933 restraints weight = 6806.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10154  Z= 0.192
  Angle     :  0.529   5.836  13963  Z= 0.290
  Chirality :  0.042   0.267   1607
  Planarity :  0.003   0.051   1587
  Dihedral  : 20.326  88.382   1901
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.28 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.24), residues: 1103
  helix:  0.39 (0.28), residues: 334
  sheet: -1.79 (0.27), residues: 303
  loop : -1.42 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.011   0.001   PHE B 215 
 TYR   0.015   0.001   TYR B 211 
 ARG   0.002   0.000   ARG B  53 

*********************** 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
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.076 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8845 (mm) cc_final: 0.8591 (mm)
REVERT: D  126 PHE cc_start: 0.7569 (m-80) cc_final: 0.7306 (m-10)
REVERT: D  214 GLN cc_start: 0.7277 (tm-30) cc_final: 0.7076 (tm-30)
REVERT: D  259 ILE cc_start: 0.8213 (mm) cc_final: 0.7592 (mt)
REVERT: D  274 TRP cc_start: 0.7936 (t60) cc_final: 0.7623 (t60)
REVERT: B   64 ARG cc_start: 0.8195 (tpt-90) cc_final: 0.7970 (tmt170)
REVERT: B   86 ASP cc_start: 0.7814 (m-30) cc_final: 0.7575 (m-30)
REVERT: B  199 MET cc_start: 0.5690 (tpt) cc_final: 0.3517 (mtm)
REVERT: A   91 ARG cc_start: 0.6733 (tpt90) cc_final: 0.5297 (mtm-85)
  outliers start: 17
  outliers final: 9
  residues processed: 133
  average time/residue: 0.2003
  time to fit residues: 38.9028
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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  167 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 108 optimal weight:    0.0970
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.7778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.132895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099390 restraints weight = 15049.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.102783 restraints weight = 11192.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.103779 restraints weight = 6877.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10154  Z= 0.256
  Angle     :  0.565   6.298  13963  Z= 0.303
  Chirality :  0.043   0.286   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.349  89.323   1901
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.00 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.24), residues: 1103
  helix:  0.68 (0.29), residues: 328
  sheet: -1.85 (0.27), residues: 303
  loop : -1.35 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 
 PHE   0.013   0.002   PHE B 215 
 TYR   0.023   0.002   TYR B 211 
 ARG   0.003   0.000   ARG A   5 

*********************** 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
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.006 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8907 (mm) cc_final: 0.8664 (mm)
REVERT: D   74 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8689 (mtp)
REVERT: D   77 ASN cc_start: 0.8673 (m-40) cc_final: 0.8450 (m110)
REVERT: D  126 PHE cc_start: 0.7583 (m-80) cc_final: 0.7310 (m-10)
REVERT: D  259 ILE cc_start: 0.8266 (mm) cc_final: 0.7646 (mt)
REVERT: D  274 TRP cc_start: 0.8032 (t60) cc_final: 0.7724 (t60)
REVERT: A   91 ARG cc_start: 0.6820 (tpt90) cc_final: 0.5327 (mtm180)
  outliers start: 20
  outliers final: 14
  residues processed: 130
  average time/residue: 0.2102
  time to fit residues: 40.0911
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
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  132 GLU
Chi-restraints excluded: chain C residue  167 VAL
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  253 HIS
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   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 31 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 80 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0980
   chunk 95 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
D  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.133001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.100714 restraints weight = 15325.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.103688 restraints weight = 11175.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104980 restraints weight = 7114.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10154  Z= 0.192
  Angle     :  0.537   6.854  13963  Z= 0.288
  Chirality :  0.042   0.306   1607
  Planarity :  0.003   0.044   1587
  Dihedral  : 20.248  87.870   1901
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.25 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.24), residues: 1103
  helix:  0.91 (0.29), residues: 328
  sheet: -1.77 (0.26), residues: 322
  loop : -1.14 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.015   0.001   PHE D  27 
 TYR   0.014   0.001   TYR B 211 
 ARG   0.003   0.000   ARG A   5 

*********************** 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
  133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 1.083 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8911 (mm) cc_final: 0.8660 (mm)
REVERT: D   74 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8662 (mtp)
REVERT: D  126 PHE cc_start: 0.7604 (m-80) cc_final: 0.7297 (m-10)
REVERT: D  259 ILE cc_start: 0.8169 (mm) cc_final: 0.7698 (mt)
REVERT: D  274 TRP cc_start: 0.7984 (t60) cc_final: 0.7700 (t60)
REVERT: A   91 ARG cc_start: 0.6699 (tpt90) cc_final: 0.5258 (mtm180)
  outliers start: 18
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2051
  time to fit residues: 37.6387
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
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  167 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
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  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 30 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 66 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 59 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   overall best weight:    0.9760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.129315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.096856 restraints weight = 15561.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099774 restraints weight = 11460.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.100932 restraints weight = 7296.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10154  Z= 0.296
  Angle     :  0.601  10.459  13963  Z= 0.317
  Chirality :  0.044   0.326   1607
  Planarity :  0.003   0.043   1587
  Dihedral  : 20.342  89.290   1901
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.08 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.24), residues: 1103
  helix:  0.75 (0.29), residues: 328
  sheet: -1.90 (0.25), residues: 329
  loop : -1.16 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 193 
 PHE   0.014   0.002   PHE B 215 
 TYR   0.026   0.002   TYR B 211 
 ARG   0.003   0.000   ARG D 261 

*********************** 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
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.124 
Fit side-chains
REVERT: D  126 PHE cc_start: 0.7653 (m-80) cc_final: 0.7345 (m-10)
REVERT: D  259 ILE cc_start: 0.8176 (mm) cc_final: 0.7739 (mt)
REVERT: D  274 TRP cc_start: 0.8103 (t60) cc_final: 0.7824 (t60)
REVERT: B   75 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8196 (tmm)
REVERT: A   91 ARG cc_start: 0.6824 (tpt90) cc_final: 0.5357 (mtm180)
  outliers start: 21
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1963
  time to fit residues: 33.9180
Evaluate side-chains
  114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
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 D residue  177 THR
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 100 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.130114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.097078 restraints weight = 15202.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.100185 restraints weight = 11086.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.101554 restraints weight = 6913.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10154  Z= 0.301
  Angle     :  0.605   9.483  13963  Z= 0.318
  Chirality :  0.044   0.339   1607
  Planarity :  0.003   0.040   1587
  Dihedral  : 20.408  88.955   1901
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.70 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.24), residues: 1103
  helix:  0.70 (0.29), residues: 328
  sheet: -1.98 (0.25), residues: 342
  loop : -1.16 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 
 PHE   0.020   0.002   PHE B 215 
 TYR   0.028   0.002   TYR B 211 
 ARG   0.002   0.000   ARG D  47 

*********************** 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
  125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.051 
Fit side-chains
REVERT: C  156 ASP cc_start: 0.6887 (p0) cc_final: 0.6633 (p0)
REVERT: D  126 PHE cc_start: 0.7675 (m-80) cc_final: 0.7354 (m-10)
REVERT: D  259 ILE cc_start: 0.8153 (mm) cc_final: 0.7775 (mt)
REVERT: B   75 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8185 (tmm)
REVERT: B  215 PHE cc_start: 0.8519 (m-80) cc_final: 0.8246 (m-80)
REVERT: A   75 MET cc_start: 0.9027 (ttt) cc_final: 0.8654 (ttt)
REVERT: A   91 ARG cc_start: 0.6835 (tpt90) cc_final: 0.5333 (mtm180)
REVERT: A  117 LYS cc_start: 0.8120 (mttp) cc_final: 0.7404 (mmmm)
REVERT: A  156 ASP cc_start: 0.6622 (m-30) cc_final: 0.6096 (t70)
  outliers start: 18
  outliers final: 16
  residues processed: 119
  average time/residue: 0.2154
  time to fit residues: 36.6290
Evaluate side-chains
  117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
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 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  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   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 52 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 36 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.098210 restraints weight = 15094.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.101912 restraints weight = 10466.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.102610 restraints weight = 6274.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10154  Z= 0.252
  Angle     :  0.587   9.105  13963  Z= 0.311
  Chirality :  0.043   0.340   1607
  Planarity :  0.003   0.037   1587
  Dihedral  : 20.377  87.435   1901
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.49 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.24), residues: 1103
  helix:  0.80 (0.29), residues: 328
  sheet: -1.92 (0.25), residues: 342
  loop : -1.13 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.017   0.001   PHE B 215 
 TYR   0.025   0.002   TYR B 211 
 ARG   0.003   0.000   ARG D 262 

*********************** 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
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.136 
Fit side-chains
REVERT: C  156 ASP cc_start: 0.6887 (p0) cc_final: 0.6607 (p0)
REVERT: D  126 PHE cc_start: 0.7683 (m-80) cc_final: 0.7343 (m-10)
REVERT: D  259 ILE cc_start: 0.8181 (mm) cc_final: 0.7761 (mt)
REVERT: B   75 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8146 (tmm)
REVERT: A   91 ARG cc_start: 0.6772 (tpt90) cc_final: 0.5244 (mtm180)
REVERT: A  156 ASP cc_start: 0.6594 (m-30) cc_final: 0.6073 (t70)
  outliers start: 17
  outliers final: 14
  residues processed: 116
  average time/residue: 0.2225
  time to fit residues: 37.0977
Evaluate side-chains
  116 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
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 D residue  177 THR
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   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 79 optimal weight:    0.0270
   chunk 105 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 108 optimal weight:    0.2980
   chunk 30 optimal weight:    0.0670
   chunk 72 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0670
   chunk 107 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.1714

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.135789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.103522 restraints weight = 14928.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.107094 restraints weight = 10484.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.108389 restraints weight = 6393.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10154  Z= 0.156
  Angle     :  0.548   8.942  13963  Z= 0.292
  Chirality :  0.042   0.324   1607
  Planarity :  0.003   0.038   1587
  Dihedral  : 20.169  84.347   1901
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 17.12 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1103
  helix:  1.05 (0.29), residues: 329
  sheet: -1.61 (0.26), residues: 334
  loop : -1.10 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 274 
 HIS   0.003   0.001   HIS B 246 
 PHE   0.015   0.001   PHE D  27 
 TYR   0.010   0.001   TYR B 211 
 ARG   0.003   0.000   ARG A   5 

********************** 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
  144 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
REVERT: C   75 MET cc_start: 0.8595 (tpp) cc_final: 0.8265 (ttt)
REVERT: C  156 ASP cc_start: 0.6651 (p0) cc_final: 0.6343 (p0)
REVERT: D   10 ILE cc_start: 0.8937 (mm) cc_final: 0.8696 (mm)
REVERT: D  126 PHE cc_start: 0.7667 (m-80) cc_final: 0.7328 (m-10)
REVERT: D  259 ILE cc_start: 0.8089 (mm) cc_final: 0.7718 (mt)
REVERT: B   75 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8089 (tmm)
REVERT: A   91 ARG cc_start: 0.6763 (tpt90) cc_final: 0.5307 (mtm180)
REVERT: A  199 MET cc_start: 0.5449 (tpt) cc_final: 0.5023 (tpt)
  outliers start: 12
  outliers final: 8
  residues processed: 138
  average time/residue: 0.2188
  time to fit residues: 43.1799
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  177 THR
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   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   16 LEU
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 70 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0980
   chunk 35 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.100337 restraints weight = 15217.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.103618 restraints weight = 11067.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.104930 restraints weight = 6874.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10154  Z= 0.219
  Angle     :  0.578   9.254  13963  Z= 0.306
  Chirality :  0.043   0.331   1607
  Planarity :  0.003   0.028   1587
  Dihedral  : 20.177  87.083   1901
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 18.36 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.25), residues: 1103
  helix:  1.04 (0.29), residues: 329
  sheet: -1.61 (0.26), residues: 343
  loop : -1.03 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 276 
 PHE   0.014   0.001   PHE D  27 
 TYR   0.021   0.002   TYR B 211 
 ARG   0.002   0.000   ARG A   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2741.44 seconds
wall clock time: 50 minutes 18.96 seconds (3018.96 seconds total)