Starting phenix.real_space_refine
on Wed Feb  4 06:10:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9y93_72687/02_2026/9y93_72687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9y93_72687/02_2026/9y93_72687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9y93_72687/02_2026/9y93_72687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9y93_72687/02_2026/9y93_72687.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9y93_72687/02_2026/9y93_72687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9y93_72687/02_2026/9y93_72687.map"
  }
  resolution = 2.42
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    5850      2.51       5
     N    1535      2.21       5
     O    1671      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9084
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2274
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 279, 2263
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
      Conformer: "B"
        Number of residues, atoms: 279, 2263
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
          bond proxies already assigned to first conformer: 2292
    Chain: "B"
      Number of atoms: 2263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2263
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
    Chain: "C"
      Number of atoms: 2284
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 279, 2263
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
      Conformer: "B"
        Number of residues, atoms: 279, 2263
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
          bond proxies already assigned to first conformer: 2280
    Chain: "D"
      Number of atoms: 2263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2263
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG A 350 " occ=0.49
      ... (20 atoms not shown)
      pdb=" NH2BARG A 350 " occ=0.51
    residue:
      pdb=" N  AARG C 350 " occ=0.43
      ... (20 atoms not shown)
      pdb=" NH2BARG C 350 " occ=0.57
    residue:
      pdb=" N  AHIS C 359 " occ=0.70
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 359 " occ=0.30
  Time building chain proxies: 2.84, per 1000 atoms: 0.31
  Number of scatterers: 9084
  At special positions: 0
  Unit cell: (91.52, 83.2, 129.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1671      8.00
     N    1535      7.00
     C    5850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.66
  Conformation dependent library (CDL) restraints added in 354.9 milliseconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2166

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 103
    Processing helix  chain 'A' and resid 108 through 119
    Processing helix  chain 'A' and resid 121 through 135
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 3.717A  pdb=" N   LYS A 145 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 180
      removed outlier: 4.930A  pdb=" N   LEU A 170 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LYS A 171 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 196
      removed outlier: 3.527A  pdb=" N   LEU A 186 " --> pdb=" O   LYS A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 215 through 233
    Processing helix  chain 'A' and resid 239 through 269
    Processing helix  chain 'A' and resid 270 through 275
      removed outlier: 3.643A  pdb=" N   LYS A 274 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 293
    Processing helix  chain 'A' and resid 296 through 306
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.924A  pdb=" N   LEU A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 331
    Processing helix  chain 'A' and resid 332 through 336
    Processing helix  chain 'A' and resid 340 through 360
    Processing helix  chain 'B' and resid 89 through 103
    Processing helix  chain 'B' and resid 107 through 119
      removed outlier: 3.870A  pdb=" N   PHE B 111 " --> pdb=" O   ALA B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 135
    Processing helix  chain 'B' and resid 139 through 156
    Processing helix  chain 'B' and resid 158 through 180
      removed outlier: 4.943A  pdb=" N   LEU B 170 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   LYS B 171 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 195
      removed outlier: 3.532A  pdb=" N   LEU B 186 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 215 through 232
    Processing helix  chain 'B' and resid 239 through 270
      removed outlier: 4.220A  pdb=" N   TYR B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 276
      removed outlier: 3.807A  pdb=" N   LYS B 274 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE B 276 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 293
    Processing helix  chain 'B' and resid 296 through 304
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 313 through 330
    Processing helix  chain 'B' and resid 332 through 336
    Processing helix  chain 'B' and resid 340 through 360
    Processing helix  chain 'C' and resid 89 through 103
    Processing helix  chain 'C' and resid 107 through 119
    Processing helix  chain 'C' and resid 121 through 135
      removed outlier: 3.761A  pdb=" N   LEU C 125 " --> pdb=" O   ASP C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 157
    Processing helix  chain 'C' and resid 158 through 180
      removed outlier: 4.860A  pdb=" N   LEU C 170 " --> pdb=" O   ILE C 166 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   LYS C 171 " --> pdb=" O   ASN C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 195
      removed outlier: 3.524A  pdb=" N   LEU C 186 " --> pdb=" O   LYS C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 212
    Processing helix  chain 'C' and resid 215 through 232
    Processing helix  chain 'C' and resid 239 through 269
    Processing helix  chain 'C' and resid 270 through 275
      removed outlier: 3.626A  pdb=" N   LYS C 274 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 293
    Processing helix  chain 'C' and resid 296 through 306
    Processing helix  chain 'C' and resid 307 through 312
      removed outlier: 3.986A  pdb=" N   LEU C 311 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU C 312 " --> pdb=" O   ASN C 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 307 through 312'
    Processing helix  chain 'C' and resid 313 through 331
    Processing helix  chain 'C' and resid 332 through 336
    Processing helix  chain 'C' and resid 340 through 360
    Processing helix  chain 'D' and resid 89 through 103
    Processing helix  chain 'D' and resid 107 through 119
    Processing helix  chain 'D' and resid 121 through 135
      removed outlier: 3.759A  pdb=" N   LEU D 125 " --> pdb=" O   ASP D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 156
    Processing helix  chain 'D' and resid 158 through 180
      removed outlier: 4.940A  pdb=" N   LEU D 170 " --> pdb=" O   ILE D 166 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   LYS D 171 " --> pdb=" O   ASN D 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 196
      removed outlier: 3.522A  pdb=" N   LEU D 186 " --> pdb=" O   LYS D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 212
    Processing helix  chain 'D' and resid 215 through 232
      removed outlier: 3.661A  pdb=" N   ASP D 232 " --> pdb=" O   LEU D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 270
      removed outlier: 3.989A  pdb=" N   TYR D 270 " --> pdb=" O   THR D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 275
      removed outlier: 3.817A  pdb=" N   LYS D 274 " --> pdb=" O   TYR D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 279 through 293
    Processing helix  chain 'D' and resid 296 through 304
    Processing helix  chain 'D' and resid 313 through 331
    Processing helix  chain 'D' and resid 332 through 336
    Processing helix  chain 'D' and resid 340 through 360

    702 hydrogen bonds defined for protein.
    2079 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2953
        1.34 -     1.46: 1386
        1.46 -     1.57: 4869
        1.57 -     1.69: 0
        1.69 -     1.80: 44
  Bond restraints: 9252
  Sorted by residual:
  bond pdb=" N   ASN D 277 "
       pdb=" CA  ASN D 277 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.012 1.29e-02 6.01e+03 8.88e-01
  bond pdb=" CB  ASN A 277 "
       pdb=" CG  ASN A 277 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.42e-01
  bond pdb=" CA  ASN A 277 "
       pdb=" CB  ASN A 277 "
    ideal  model  delta    sigma   weight residual
    1.533  1.548 -0.015 1.66e-02 3.63e+03 7.76e-01
  bond pdb=" CG1 ILE C 355 "
       pdb=" CD1 ILE C 355 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.20e-01
  bond pdb=" CG1 ILE A 355 "
       pdb=" CD1 ILE A 355 "
    ideal  model  delta    sigma   weight residual
    1.513  1.487  0.026 3.90e-02 6.57e+02 4.34e-01
  ... (remaining 9247 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 12304
        1.44 -     2.88: 134
        2.88 -     4.31: 35
        4.31 -     5.75: 10
        5.75 -     7.19: 1
  Bond angle restraints: 12484
  Sorted by residual:
  angle pdb=" C   PHE B 276 "
        pdb=" N   ASN B 277 "
        pdb=" CA  ASN B 277 "
      ideal   model   delta    sigma   weight residual
     121.54  125.71   -4.17 1.91e+00 2.74e-01 4.76e+00
  angle pdb=" CA  LEU C 146 "
        pdb=" CB  LEU C 146 "
        pdb=" CG  LEU C 146 "
      ideal   model   delta    sigma   weight residual
     116.30  123.49   -7.19 3.50e+00 8.16e-02 4.22e+00
  angle pdb=" C   ALA A 107 "
        pdb=" N   LEU A 108 "
        pdb=" CA  LEU A 108 "
      ideal   model   delta    sigma   weight residual
     121.54  125.26   -3.72 1.91e+00 2.74e-01 3.80e+00
  angle pdb=" CA  ASN A 277 "
        pdb=" CB  ASN A 277 "
        pdb=" CG  ASN A 277 "
      ideal   model   delta    sigma   weight residual
     112.60  114.54   -1.94 1.00e+00 1.00e+00 3.75e+00
  angle pdb=" C   PHE A 276 "
        pdb=" N   ASN A 277 "
        pdb=" CA  ASN A 277 "
      ideal   model   delta    sigma   weight residual
     123.91  126.96   -3.05 1.66e+00 3.63e-01 3.38e+00
  ... (remaining 12479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.26: 4940
       15.26 -    30.53: 558
       30.53 -    45.79: 110
       45.79 -    61.06: 40
       61.06 -    76.32: 20
  Dihedral angle restraints: 5668
    sinusoidal: 2348
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" CA  ASP C 303 "
           pdb=" CB  ASP C 303 "
           pdb=" CG  ASP C 303 "
           pdb=" OD1 ASP C 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.68   57.68     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CG  ARG C 135 "
           pdb=" CD  ARG C 135 "
           pdb=" NE  ARG C 135 "
           pdb=" CZ  ARG C 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.20   43.20     2      1.50e+01 4.44e-03 1.00e+01
  dihedral pdb=" CB  LYS D 163 "
           pdb=" CG  LYS D 163 "
           pdb=" CD  LYS D 163 "
           pdb=" CE  LYS D 163 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.28  -55.28     3      1.50e+01 4.44e-03 9.34e+00
  ... (remaining 5665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1068
       0.032 -    0.064: 263
       0.064 -    0.095: 83
       0.095 -    0.127: 18
       0.127 -    0.159: 3
  Chirality restraints: 1435
  Sorted by residual:
  chirality pdb=" CA  ASN A 277 "
            pdb=" N   ASN A 277 "
            pdb=" C   ASN A 277 "
            pdb=" CB  ASN A 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CG  LEU C 133 "
            pdb=" CB  LEU C 133 "
            pdb=" CD1 LEU C 133 "
            pdb=" CD2 LEU C 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 1432 not shown)

  Planarity restraints: 1569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 243 "   -0.012 2.00e-02 2.50e+03   1.14e-02 2.26e+00
        pdb=" CG  PHE A 243 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 243 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 243 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 243 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 243 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 243 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 121 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO C 122 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C 122 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 122 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 243 "    0.011 2.00e-02 2.50e+03   1.10e-02 2.12e+00
        pdb=" CG  PHE C 243 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 243 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 243 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 243 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 243 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 243 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1566 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2524
        2.82 -     3.34: 9591
        3.34 -     3.86: 15903
        3.86 -     4.38: 18276
        4.38 -     4.90: 30265
  Nonbonded interactions: 76559
  Sorted by model distance:
  nonbonded pdb=" O   THR D 266 "
            pdb=" OG  SER D 269 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OD2 ASP A 230 "
            pdb=" OG  SER A 237 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   LEU D 262 "
            pdb=" OG1 THR D 266 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OE1 GLU D 131 "
            pdb=" NH1 ARG D 134 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   VAL B  85 "
            pdb=" NH2 ARG B 173 "
     model   vdw
     2.344 3.120
  ... (remaining 76554 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 82 through 349 or resid 351 through 358 or resid 360))
  selection = (chain 'B' and (resid 82 through 349 or resid 351 through 358 or resid 360))
  selection = (chain 'C' and (resid 82 through 349 or resid 351 through 358 or resid 360))
  selection = (chain 'D' and (resid 82 through 349 or resid 351 through 358 or resid 360))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.510
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  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:8.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9252  Z= 0.120
  Angle     :  0.445   7.191  12484  Z= 0.232
  Chirality :  0.033   0.159   1435
  Planarity :  0.003   0.037   1569
  Dihedral  : 14.307  76.323   3502
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.29 %
    Favored  : 97.61 %
  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:  3.08 (0.25), residues: 1116
  helix:  2.37 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop :  0.61 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 187 
 TYR   0.007   0.001   TYR B 190 
 PHE   0.026   0.002   PHE A 243 
 TRP   0.005   0.001   TRP A 283 
 HIS   0.002   0.000   HIS B 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9252)
  covalent geometry    : angle       0.44518 (12484)
  hydrogen bonds       : bond        0.12157 (  702)
  hydrogen bonds       : angle       4.51266 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 ASP cc_start: 0.8886 (t0) cc_final: 0.8522 (t0)
REVERT: A  285 LEU cc_start: 0.8682 (tp) cc_final: 0.8167 (mt)
REVERT: B  152 HIS cc_start: 0.8684 (t-90) cc_final: 0.8246 (t70)
REVERT: B  177 LYS cc_start: 0.8977 (tppt) cc_final: 0.8601 (tmtt)
REVERT: B  285 LEU cc_start: 0.8679 (mp) cc_final: 0.8313 (tp)
REVERT: B  315 LYS cc_start: 0.8561 (tttp) cc_final: 0.8159 (tppt)
REVERT: B  350 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7997 (mtt90)
REVERT: C  111 PHE cc_start: 0.8145 (m-10) cc_final: 0.7832 (m-80)
REVERT: C  158 ASP cc_start: 0.8862 (t0) cc_final: 0.8591 (t0)
REVERT: C  229 THR cc_start: 0.9278 (t) cc_final: 0.9038 (p)
REVERT: C  260 ASP cc_start: 0.7546 (m-30) cc_final: 0.7326 (m-30)
REVERT: C  285 LEU cc_start: 0.8720 (tp) cc_final: 0.8228 (mt)
REVERT: C  315 LYS cc_start: 0.9325 (ptmt) cc_final: 0.8880 (pmmt)
REVERT: C  352 MET cc_start: 0.8641 (mtp) cc_final: 0.8335 (mtp)
REVERT: D   95 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7671 (mtmp)
REVERT: D   99 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7839 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 161
  average time/residue: 0.3942
  time to fit residues: 68.3704
Evaluate side-chains
  125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 HIS
C 314 HIS
D 167 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.138784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.084841 restraints weight = 30152.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 3.84
r_work: 0.2877 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9252  Z= 0.119
  Angle     :  0.492  10.356  12484  Z= 0.246
  Chirality :  0.035   0.160   1435
  Planarity :  0.003   0.038   1569
  Dihedral  :  3.595  29.640   1226
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.57 %
    Favored  : 89.23 %
  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:  3.12 (0.25), residues: 1116
  helix:  2.42 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop :  0.44 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 143 
 TYR   0.006   0.001   TYR B 190 
 PHE   0.018   0.001   PHE B 263 
 TRP   0.006   0.001   TRP B 283 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9252)
  covalent geometry    : angle       0.49157 (12484)
  hydrogen bonds       : bond        0.03618 (  702)
  hydrogen bonds       : angle       3.95745 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8084 (mm-30)
REVERT: A  315 LYS cc_start: 0.9211 (ptmm) cc_final: 0.8645 (pmmt)
REVERT: B  152 HIS cc_start: 0.8692 (t70) cc_final: 0.8210 (t70)
REVERT: B  156 GLN cc_start: 0.9094 (mt0) cc_final: 0.8782 (mt0)
REVERT: B  177 LYS cc_start: 0.8958 (tppt) cc_final: 0.8499 (tmtt)
REVERT: B  315 LYS cc_start: 0.8505 (tttp) cc_final: 0.8239 (mmtm)
REVERT: C  111 PHE cc_start: 0.8160 (m-10) cc_final: 0.7825 (m-10)
REVERT: C  229 THR cc_start: 0.9027 (t) cc_final: 0.8738 (p)
REVERT: C  260 ASP cc_start: 0.7506 (m-30) cc_final: 0.7086 (m-30)
REVERT: C  315 LYS cc_start: 0.9381 (ptmt) cc_final: 0.8849 (pmmt)
REVERT: C  352 MET cc_start: 0.8366 (mtp) cc_final: 0.8104 (mtp)
REVERT: D   95 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7581 (mtmp)
REVERT: D   99 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7795 (mttp)
REVERT: D  355 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7583 (mp)
  outliers start: 12
  outliers final: 4
  residues processed: 139
  average time/residue: 0.3978
  time to fit residues: 59.4741
Evaluate side-chains
  123 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain D residue  355 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 2 optimal weight:   30.0000
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 195 GLN
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
C 314 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.136530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.082876 restraints weight = 21089.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 3.34
r_work: 0.2857 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9252  Z= 0.165
  Angle     :  0.499   8.844  12484  Z= 0.252
  Chirality :  0.036   0.157   1435
  Planarity :  0.003   0.037   1569
  Dihedral  :  4.079  64.095   1226
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.97 %
    Favored  : 87.84 %
  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:  3.00 (0.25), residues: 1116
  helix:  2.31 (0.17), residues: 928
  sheet:  None (None), residues: 0
  loop :  0.36 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 143 
 TYR   0.009   0.001   TYR B 190 
 PHE   0.019   0.002   PHE A 243 
 TRP   0.006   0.001   TRP B 283 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9252)
  covalent geometry    : angle       0.49942 (12484)
  hydrogen bonds       : bond        0.03756 (  702)
  hydrogen bonds       : angle       3.97738 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8697 (pm20)
REVERT: A  214 GLN cc_start: 0.8389 (mp10) cc_final: 0.8144 (mp10)
REVERT: A  315 LYS cc_start: 0.9214 (ptmm) cc_final: 0.8646 (pmmt)
REVERT: B  152 HIS cc_start: 0.8676 (t70) cc_final: 0.8255 (t70)
REVERT: B  177 LYS cc_start: 0.8838 (tppt) cc_final: 0.8401 (tmtt)
REVERT: B  279 GLU cc_start: 0.7281 (pm20) cc_final: 0.7071 (pm20)
REVERT: B  315 LYS cc_start: 0.8528 (tttp) cc_final: 0.8263 (mmtm)
REVERT: C  111 PHE cc_start: 0.8188 (m-10) cc_final: 0.7831 (m-10)
REVERT: C  229 THR cc_start: 0.9043 (t) cc_final: 0.8738 (p)
REVERT: C  260 ASP cc_start: 0.7348 (m-30) cc_final: 0.6970 (m-30)
REVERT: C  315 LYS cc_start: 0.9362 (ptmt) cc_final: 0.8845 (pmmt)
REVERT: D   99 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7796 (mtmt)
REVERT: D  197 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8507 (pm20)
REVERT: D  279 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7047 (mp0)
REVERT: D  353 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7603 (p)
REVERT: D  355 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7598 (mp)
  outliers start: 21
  outliers final: 8
  residues processed: 136
  average time/residue: 0.3724
  time to fit residues: 54.5167
Evaluate side-chains
  125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  255 MET
Chi-restraints excluded: chain C residue  295 HIS
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  260 ASP
Chi-restraints excluded: chain D residue  353 THR
Chi-restraints excluded: chain D residue  355 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 167 ASN
C 314 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.137664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.083483 restraints weight = 39911.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 4.26
r_work: 0.2821 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9252  Z= 0.139
  Angle     :  0.487  10.348  12484  Z= 0.245
  Chirality :  0.035   0.155   1435
  Planarity :  0.003   0.037   1569
  Dihedral  :  3.429  14.755   1224
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.66 %
    Favored  : 85.24 %
  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:  3.00 (0.25), residues: 1116
  helix:  2.33 (0.17), residues: 926
  sheet:  None (None), residues: 0
  loop :  0.29 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 143 
 TYR   0.008   0.001   TYR B 190 
 PHE   0.017   0.002   PHE B 263 
 TRP   0.006   0.001   TRP B 283 
 HIS   0.003   0.001   HIS C 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9252)
  covalent geometry    : angle       0.48743 (12484)
  hydrogen bonds       : bond        0.03464 (  702)
  hydrogen bonds       : angle       3.90846 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8665 (pm20)
REVERT: A  214 GLN cc_start: 0.8430 (mp10) cc_final: 0.8168 (mp10)
REVERT: A  315 LYS cc_start: 0.9226 (ptmm) cc_final: 0.8634 (pmmt)
REVERT: B  152 HIS cc_start: 0.8623 (t70) cc_final: 0.8296 (t70)
REVERT: B  279 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7071 (pm20)
REVERT: B  315 LYS cc_start: 0.8535 (tttp) cc_final: 0.8251 (mmtm)
REVERT: C  111 PHE cc_start: 0.8170 (m-10) cc_final: 0.7794 (m-10)
REVERT: C  229 THR cc_start: 0.9038 (t) cc_final: 0.8749 (p)
REVERT: C  260 ASP cc_start: 0.7430 (m-30) cc_final: 0.7063 (m-30)
REVERT: C  315 LYS cc_start: 0.9360 (ptmt) cc_final: 0.8831 (pmmt)
REVERT: D   99 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7723 (mttp)
REVERT: D  279 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7008 (mp0)
REVERT: D  353 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7609 (p)
REVERT: D  355 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7532 (mp)
  outliers start: 20
  outliers final: 7
  residues processed: 125
  average time/residue: 0.3497
  time to fit residues: 47.6503
Evaluate side-chains
  125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  255 MET
Chi-restraints excluded: chain C residue  295 HIS
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  353 THR
Chi-restraints excluded: chain D residue  355 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 59 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 167 ASN
C 314 HIS

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 = 0.138123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.083625 restraints weight = 34788.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 4.05
r_work: 0.2853 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9252  Z= 0.116
  Angle     :  0.482  10.322  12484  Z= 0.239
  Chirality :  0.035   0.154   1435
  Planarity :  0.003   0.036   1569
  Dihedral  :  3.369  14.407   1224
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.26 %
    Favored  : 84.95 %
  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:  3.07 (0.25), residues: 1116
  helix:  2.38 (0.17), residues: 928
  sheet:  None (None), residues: 0
  loop :  0.29 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 143 
 TYR   0.007   0.001   TYR B 190 
 PHE   0.017   0.001   PHE B 263 
 TRP   0.005   0.001   TRP B 283 
 HIS   0.005   0.001   HIS D 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9252)
  covalent geometry    : angle       0.48156 (12484)
  hydrogen bonds       : bond        0.03251 (  702)
  hydrogen bonds       : angle       3.82867 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8631 (pm20)
REVERT: A  214 GLN cc_start: 0.8416 (mp10) cc_final: 0.8163 (mp10)
REVERT: A  315 LYS cc_start: 0.9192 (ptmm) cc_final: 0.8617 (pmmt)
REVERT: B  152 HIS cc_start: 0.8624 (t70) cc_final: 0.8291 (t70)
REVERT: B  214 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8433 (pm20)
REVERT: B  279 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7038 (pm20)
REVERT: B  315 LYS cc_start: 0.8521 (tttp) cc_final: 0.8259 (mmtm)
REVERT: C  111 PHE cc_start: 0.8126 (m-10) cc_final: 0.7720 (m-10)
REVERT: C  229 THR cc_start: 0.8987 (t) cc_final: 0.8707 (p)
REVERT: C  260 ASP cc_start: 0.7353 (m-30) cc_final: 0.6989 (m-30)
REVERT: C  315 LYS cc_start: 0.9346 (ptmt) cc_final: 0.8830 (pmmt)
REVERT: D   99 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7737 (mttp)
REVERT: D  353 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7551 (p)
  outliers start: 17
  outliers final: 5
  residues processed: 123
  average time/residue: 0.3837
  time to fit residues: 51.7016
Evaluate side-chains
  121 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain B residue  214 GLN
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  295 HIS
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  353 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 32 optimal weight:    0.2980
   chunk 75 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 192 GLN
C 314 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.136117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.081300 restraints weight = 36263.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 4.11
r_work: 0.2805 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9252  Z= 0.170
  Angle     :  0.507  10.143  12484  Z= 0.253
  Chirality :  0.036   0.152   1435
  Planarity :  0.003   0.036   1569
  Dihedral  :  3.464  17.821   1224
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.66 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.99 (0.25), residues: 1116
  helix:  2.31 (0.17), residues: 928
  sheet:  None (None), residues: 0
  loop :  0.32 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 143 
 TYR   0.009   0.001   TYR B 190 
 PHE   0.018   0.002   PHE B 263 
 TRP   0.005   0.001   TRP A 283 
 HIS   0.003   0.001   HIS C 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9252)
  covalent geometry    : angle       0.50679 (12484)
  hydrogen bonds       : bond        0.03632 (  702)
  hydrogen bonds       : angle       3.94986 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8690 (pm20)
REVERT: A  214 GLN cc_start: 0.8455 (mp10) cc_final: 0.8165 (mp10)
REVERT: A  315 LYS cc_start: 0.9206 (ptmm) cc_final: 0.8633 (pmmt)
REVERT: B  152 HIS cc_start: 0.8641 (t70) cc_final: 0.8230 (t70)
REVERT: B  279 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7121 (pm20)
REVERT: B  315 LYS cc_start: 0.8569 (tttp) cc_final: 0.8276 (mmtm)
REVERT: C  111 PHE cc_start: 0.8111 (m-10) cc_final: 0.7729 (m-10)
REVERT: C  229 THR cc_start: 0.9045 (t) cc_final: 0.8724 (p)
REVERT: C  315 LYS cc_start: 0.9338 (ptmt) cc_final: 0.8814 (pmmt)
REVERT: D   99 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7723 (mttt)
REVERT: D  167 ASN cc_start: 0.8766 (m-40) cc_final: 0.8308 (m110)
REVERT: D  353 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7570 (p)
  outliers start: 18
  outliers final: 7
  residues processed: 122
  average time/residue: 0.4011
  time to fit residues: 53.3614
Evaluate side-chains
  124 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  295 HIS
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  260 ASP
Chi-restraints excluded: chain D residue  353 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.137953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.083916 restraints weight = 32354.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 3.94
r_work: 0.2858 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9252  Z= 0.111
  Angle     :  0.482  10.203  12484  Z= 0.240
  Chirality :  0.035   0.155   1435
  Planarity :  0.003   0.038   1569
  Dihedral  :  3.380  19.252   1224
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.66 %
    Favored  : 83.85 %
  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:  3.05 (0.25), residues: 1116
  helix:  2.39 (0.17), residues: 926
  sheet:  None (None), residues: 0
  loop :  0.19 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 143 
 TYR   0.007   0.001   TYR B 190 
 PHE   0.017   0.001   PHE B 263 
 TRP   0.006   0.001   TRP C 283 
 HIS   0.003   0.000   HIS C 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9252)
  covalent geometry    : angle       0.48187 (12484)
  hydrogen bonds       : bond        0.03184 (  702)
  hydrogen bonds       : angle       3.82424 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7671 (ttm110)
REVERT: A  197 GLU cc_start: 0.9128 (pt0) cc_final: 0.8643 (pm20)
REVERT: A  214 GLN cc_start: 0.8408 (mp10) cc_final: 0.8155 (mp10)
REVERT: A  315 LYS cc_start: 0.9202 (ptmm) cc_final: 0.8638 (pmmt)
REVERT: B   89 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8812 (mm-30)
REVERT: B  152 HIS cc_start: 0.8630 (t70) cc_final: 0.8265 (t70)
REVERT: B  279 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6979 (pm20)
REVERT: B  315 LYS cc_start: 0.8554 (tttp) cc_final: 0.8288 (mmtm)
REVERT: C  111 PHE cc_start: 0.8106 (m-10) cc_final: 0.7693 (m-10)
REVERT: C  229 THR cc_start: 0.9014 (t) cc_final: 0.8730 (p)
REVERT: C  315 LYS cc_start: 0.9333 (ptmt) cc_final: 0.8828 (pmmt)
REVERT: C  352 MET cc_start: 0.8375 (mtp) cc_final: 0.8157 (mtm)
REVERT: D   99 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7702 (mttp)
REVERT: D  315 LYS cc_start: 0.8736 (tptp) cc_final: 0.8223 (mmpt)
REVERT: D  353 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7539 (p)
  outliers start: 14
  outliers final: 5
  residues processed: 131
  average time/residue: 0.4167
  time to fit residues: 59.2895
Evaluate side-chains
  123 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  260 ASP
Chi-restraints excluded: chain D residue  353 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
C 314 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.137097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.082995 restraints weight = 32514.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 3.92
r_work: 0.2849 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9252  Z= 0.128
  Angle     :  0.489  10.155  12484  Z= 0.245
  Chirality :  0.035   0.154   1435
  Planarity :  0.003   0.041   1569
  Dihedral  :  3.382  15.773   1224
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.35 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.03 (0.25), residues: 1116
  helix:  2.37 (0.17), residues: 928
  sheet:  None (None), residues: 0
  loop :  0.17 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 143 
 TYR   0.008   0.001   TYR B 190 
 PHE   0.017   0.001   PHE B 263 
 TRP   0.005   0.001   TRP B 283 
 HIS   0.003   0.001   HIS C 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9252)
  covalent geometry    : angle       0.48883 (12484)
  hydrogen bonds       : bond        0.03300 (  702)
  hydrogen bonds       : angle       3.85776 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.9137 (pt0) cc_final: 0.8640 (pm20)
REVERT: A  214 GLN cc_start: 0.8417 (mp10) cc_final: 0.8163 (mp10)
REVERT: A  315 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8667 (pmmt)
REVERT: B  152 HIS cc_start: 0.8704 (t70) cc_final: 0.8331 (t70)
REVERT: B  279 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7034 (pm20)
REVERT: B  315 LYS cc_start: 0.8557 (tttp) cc_final: 0.8283 (mmtm)
REVERT: C  111 PHE cc_start: 0.8093 (m-10) cc_final: 0.7709 (m-80)
REVERT: C  124 ASP cc_start: 0.7941 (p0) cc_final: 0.7102 (m-30)
REVERT: C  229 THR cc_start: 0.9028 (t) cc_final: 0.8729 (p)
REVERT: C  315 LYS cc_start: 0.9317 (ptmt) cc_final: 0.8809 (pmmt)
REVERT: D   99 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7720 (mtmt)
REVERT: D  279 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6933 (mp0)
REVERT: D  315 LYS cc_start: 0.8741 (tptp) cc_final: 0.8231 (mmpt)
REVERT: D  353 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7534 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 118
  average time/residue: 0.3794
  time to fit residues: 48.9532
Evaluate side-chains
  122 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  295 HIS
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  260 ASP
Chi-restraints excluded: chain D residue  353 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
C 314 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.136749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.083698 restraints weight = 30546.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 3.86
r_work: 0.2835 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9252  Z= 0.153
  Angle     :  0.505  10.149  12484  Z= 0.253
  Chirality :  0.036   0.154   1435
  Planarity :  0.003   0.042   1569
  Dihedral  :  3.427  13.677   1224
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 15.35 %
    Favored  : 83.05 %
  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:  2.99 (0.25), residues: 1116
  helix:  2.34 (0.17), residues: 928
  sheet:  None (None), residues: 0
  loop :  0.19 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 143 
 TYR   0.009   0.001   TYR B 190 
 PHE   0.017   0.002   PHE B 263 
 TRP   0.005   0.001   TRP C 283 
 HIS   0.003   0.001   HIS C 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9252)
  covalent geometry    : angle       0.50532 (12484)
  hydrogen bonds       : bond        0.03480 (  702)
  hydrogen bonds       : angle       3.91750 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 PHE cc_start: 0.7991 (m-80) cc_final: 0.7595 (m-80)
REVERT: A  197 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8674 (pm20)
REVERT: A  214 GLN cc_start: 0.8419 (mp10) cc_final: 0.8156 (mp10)
REVERT: A  315 LYS cc_start: 0.9210 (ptmm) cc_final: 0.8672 (pmmt)
REVERT: B  152 HIS cc_start: 0.8688 (t70) cc_final: 0.8215 (t70)
REVERT: B  279 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7101 (pm20)
REVERT: C  111 PHE cc_start: 0.8094 (m-10) cc_final: 0.7709 (m-80)
REVERT: C  124 ASP cc_start: 0.7937 (p0) cc_final: 0.7100 (m-30)
REVERT: C  229 THR cc_start: 0.9055 (t) cc_final: 0.8735 (p)
REVERT: C  315 LYS cc_start: 0.9311 (ptmt) cc_final: 0.8805 (pmmt)
REVERT: D   99 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7637 (mtmt)
REVERT: D  167 ASN cc_start: 0.8783 (m-40) cc_final: 0.8337 (m110)
REVERT: D  279 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6962 (mp0)
REVERT: D  315 LYS cc_start: 0.8733 (tptp) cc_final: 0.8236 (mmpt)
REVERT: D  353 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7564 (p)
  outliers start: 15
  outliers final: 8
  residues processed: 122
  average time/residue: 0.3876
  time to fit residues: 51.4167
Evaluate side-chains
  121 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  295 HIS
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  260 ASP
Chi-restraints excluded: chain D residue  353 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.138151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.085564 restraints weight = 28731.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 3.76
r_work: 0.2868 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9252  Z= 0.116
  Angle     :  0.505  10.111  12484  Z= 0.249
  Chirality :  0.035   0.173   1435
  Planarity :  0.003   0.044   1569
  Dihedral  :  3.390  16.714   1224
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.05 %
    Favored  : 82.55 %
  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:  3.02 (0.25), residues: 1116
  helix:  2.37 (0.17), residues: 926
  sheet:  None (None), residues: 0
  loop :  0.14 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 143 
 TYR   0.007   0.001   TYR B 190 
 PHE   0.025   0.001   PHE B 119 
 TRP   0.006   0.001   TRP C 283 
 HIS   0.003   0.000   HIS C 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9252)
  covalent geometry    : angle       0.50530 (12484)
  hydrogen bonds       : bond        0.03189 (  702)
  hydrogen bonds       : angle       3.84134 ( 2079)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8633 (pm20)
REVERT: A  214 GLN cc_start: 0.8407 (mp10) cc_final: 0.8156 (mp10)
REVERT: B  152 HIS cc_start: 0.8667 (t70) cc_final: 0.8294 (t70)
REVERT: B  279 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6980 (pm20)
REVERT: C  111 PHE cc_start: 0.8094 (m-10) cc_final: 0.7710 (m-80)
REVERT: C  124 ASP cc_start: 0.7924 (p0) cc_final: 0.7103 (m-30)
REVERT: C  229 THR cc_start: 0.9011 (t) cc_final: 0.8718 (p)
REVERT: C  315 LYS cc_start: 0.9321 (ptmt) cc_final: 0.8820 (pmmt)
REVERT: D   99 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7652 (mttp)
REVERT: D  315 LYS cc_start: 0.8734 (tptp) cc_final: 0.8237 (mmpt)
REVERT: D  353 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7501 (p)
  outliers start: 13
  outliers final: 6
  residues processed: 118
  average time/residue: 0.4224
  time to fit residues: 53.9349
Evaluate side-chains
  121 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  260 ASP
Chi-restraints excluded: chain D residue  353 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0370
   chunk 7 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.7262

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 314 HIS
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 HIS
D 156 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.137983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.083977 restraints weight = 35680.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 4.07
r_work: 0.2858 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9252  Z= 0.112
  Angle     :  0.505  10.579  12484  Z= 0.249
  Chirality :  0.035   0.161   1435
  Planarity :  0.003   0.044   1569
  Dihedral  :  3.363  16.882   1224
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.45 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.04 (0.25), residues: 1116
  helix:  2.38 (0.17), residues: 926
  sheet:  None (None), residues: 0
  loop :  0.15 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 143 
 TYR   0.007   0.001   TYR B 190 
 PHE   0.021   0.001   PHE B 119 
 TRP   0.006   0.001   TRP C 283 
 HIS   0.004   0.001   HIS D 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9252)
  covalent geometry    : angle       0.50517 (12484)
  hydrogen bonds       : bond        0.03137 (  702)
  hydrogen bonds       : angle       3.81775 ( 2079)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3508.10 seconds
wall clock time: 60 minutes 20.46 seconds (3620.46 seconds total)