Starting phenix.real_space_refine
on Thu Jun  5 06:20:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kus_62579/06_2025/9kus_62579.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kus_62579/06_2025/9kus_62579.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kus_62579/06_2025/9kus_62579.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kus_62579/06_2025/9kus_62579.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kus_62579/06_2025/9kus_62579.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kus_62579/06_2025/9kus_62579.cif"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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      50      5.16       5
     C    3532      2.51       5
     N     898      2.21       5
     O    1008      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5488
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2744
          Classifications: {'peptide': 355}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2744
          Classifications: {'peptide': 355}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Chain breaks: 1
  Time building chain proxies: 4.08, per 1000 atoms: 0.74
  Number of scatterers: 5488
  At special positions: 0
  Unit cell: (102.85, 95.2, 61.2, 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      50     16.00
     O    1008      8.00
     N     898      7.00
     C    3532      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: 1.12
  Conformation dependent library (CDL) restraints added in 953.4 milliseconds
  

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1316

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      57.9% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 40
      removed outlier: 3.637A  pdb=" N   PHE A  40 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 54
      removed outlier: 3.616A  pdb=" N   ALA A  50 " --> pdb=" O   MET A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 3.712A  pdb=" N   ILE A  59 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 76
    Processing helix  chain 'A' and resid 88 through 103
      removed outlier: 3.723A  pdb=" N   HIS A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 131
    Processing helix  chain 'A' and resid 140 through 144
      removed outlier: 3.641A  pdb=" N   TYR A 143 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 161
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 171 through 179
    Processing helix  chain 'A' and resid 181 through 188
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 198 through 222
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.898A  pdb=" N   GLN A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 252
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 4.123A  pdb=" N   LYS A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.565A  pdb=" N   LYS A 315 " --> pdb=" O   LYS A 311 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 337
      No H-bonds generated for 'chain 'A' and resid 335 through 337'
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 3.697A  pdb=" N   PHE A 342 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 344 " --> pdb=" O   GLY A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 371
    Processing helix  chain 'B' and resid 26 through 40
      removed outlier: 4.332A  pdb=" N   TYR B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE B  40 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 54
      removed outlier: 3.510A  pdb=" N   MET B  46 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 62
      removed outlier: 3.577A  pdb=" N   ILE B  59 " --> pdb=" O   GLN B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 78
    Processing helix  chain 'B' and resid 88 through 103
      removed outlier: 3.660A  pdb=" N   HIS B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 131
    Processing helix  chain 'B' and resid 140 through 144
      removed outlier: 3.584A  pdb=" N   TYR B 143 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 161
      removed outlier: 3.502A  pdb=" N   VAL B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 171 through 179
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 193 through 197
    Processing helix  chain 'B' and resid 198 through 222
      removed outlier: 3.583A  pdb=" N   GLU B 203 " --> pdb=" O   PRO B 199 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN B 206 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   MET B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 3.883A  pdb=" N   GLN B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 252
    Processing helix  chain 'B' and resid 262 through 267
      removed outlier: 4.033A  pdb=" N   LYS B 267 " --> pdb=" O   PRO B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 301
      removed outlier: 3.843A  pdb=" N   TRP B 301 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 317
    Processing helix  chain 'B' and resid 335 through 337
      No H-bonds generated for 'chain 'B' and resid 335 through 337'
    Processing helix  chain 'B' and resid 338 through 350
      removed outlier: 3.911A  pdb=" N   MET B 344 " --> pdb=" O   GLY B 340 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN B 347 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 371
    Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 110
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 279
      removed outlier: 7.054A  pdb=" N   ALA A 257 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   VAL A 278 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ASN A 259 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   LYS A 295 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE A 292 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL A 326 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   MET A 294 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   CYS A 379 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   GLU A 388 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   LEU A 377 " --> pdb=" O   GLU A 388 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR A 390 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   ILE A 375 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 110
    Processing sheet with id=AA4, first strand: chain 'B' and resid 276 through 279
      removed outlier: 6.712A  pdb=" N   ALA B 257 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   VAL B 278 " --> pdb=" O   ALA B 257 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   ASN B 259 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU B 234 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   PHE B 260 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   ASP B 236 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   LYS B 295 " --> pdb=" O   VAL B 237 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE B 292 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   VAL B 326 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   MET B 294 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   CYS B 379 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLU B 388 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   LEU B 377 " --> pdb=" O   GLU B 388 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   TYR B 390 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   ILE B 375 " --> pdb=" O   TYR B 390 " (cutoff:3.500A)

    258 hydrogen bonds defined for protein.
    717 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: 1.81

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1766
        1.35 -     1.46: 1192
        1.46 -     1.58: 2568
        1.58 -     1.70: 0
        1.70 -     1.81: 80
  Bond restraints: 5606
  Sorted by residual:
  bond pdb=" C   ASP B 198 "
       pdb=" O   ASP B 198 "
    ideal  model  delta    sigma   weight residual
    1.249  1.237  0.012 8.50e-03 1.38e+04 1.87e+00
  bond pdb=" CA  HIS B 352 "
       pdb=" CB  HIS B 352 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.27e-02 6.20e+03 9.62e-01
  bond pdb=" N   GLY A 188 "
       pdb=" CA  GLY A 188 "
    ideal  model  delta    sigma   weight residual
    1.449  1.462 -0.013 1.45e-02 4.76e+03 8.11e-01
  bond pdb=" C   VAL B 297 "
       pdb=" O   VAL B 297 "
    ideal  model  delta    sigma   weight residual
    1.241  1.232  0.009 1.06e-02 8.90e+03 7.19e-01
  bond pdb=" CB  ASP A 236 "
       pdb=" CG  ASP A 236 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 2.50e-02 1.60e+03 7.15e-01
  ... (remaining 5601 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 7431
        1.72 -     3.44: 132
        3.44 -     5.16: 22
        5.16 -     6.87: 4
        6.87 -     8.59: 1
  Bond angle restraints: 7590
  Sorted by residual:
  angle pdb=" N   LYS A  62 "
        pdb=" CA  LYS A  62 "
        pdb=" C   LYS A  62 "
      ideal   model   delta    sigma   weight residual
     112.57  108.84    3.73 1.13e+00 7.83e-01 1.09e+01
  angle pdb=" CB  MET B 221 "
        pdb=" CG  MET B 221 "
        pdb=" SD  MET B 221 "
      ideal   model   delta    sigma   weight residual
     112.70  121.29   -8.59 3.00e+00 1.11e-01 8.20e+00
  angle pdb=" N   GLY B 321 "
        pdb=" CA  GLY B 321 "
        pdb=" C   GLY B 321 "
      ideal   model   delta    sigma   weight residual
     110.90  114.57   -3.67 1.53e+00 4.27e-01 5.74e+00
  angle pdb=" CA  TYR A 272 "
        pdb=" CB  TYR A 272 "
        pdb=" CG  TYR A 272 "
      ideal   model   delta    sigma   weight residual
     113.90  117.44   -3.54 1.80e+00 3.09e-01 3.86e+00
  angle pdb=" CA  LYS B 256 "
        pdb=" CB  LYS B 256 "
        pdb=" CG  LYS B 256 "
      ideal   model   delta    sigma   weight residual
     114.10  117.90   -3.80 2.00e+00 2.50e-01 3.61e+00
  ... (remaining 7585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3024
       17.95 -    35.89: 297
       35.89 -    53.84: 63
       53.84 -    71.79: 8
       71.79 -    89.73: 8
  Dihedral angle restraints: 3400
    sinusoidal: 1352
      harmonic: 2048
  Sorted by residual:
  dihedral pdb=" CA  ARG B  84 "
           pdb=" C   ARG B  84 "
           pdb=" N   CYS B  85 "
           pdb=" CA  CYS B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.95   17.05     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU B  53 "
           pdb=" CG  GLU B  53 "
           pdb=" CD  GLU B  53 "
           pdb=" OE1 GLU B  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B 284 "
           pdb=" CG  GLU B 284 "
           pdb=" CD  GLU B 284 "
           pdb=" OE1 GLU B 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.67  -89.67     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 3397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 499
       0.032 -    0.063: 253
       0.063 -    0.095: 57
       0.095 -    0.127: 44
       0.127 -    0.158: 3
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CB  ILE A 368 "
            pdb=" CA  ILE A 368 "
            pdb=" CG1 ILE A 368 "
            pdb=" CG2 ILE A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  ILE A 323 "
            pdb=" N   ILE A 323 "
            pdb=" C   ILE A 323 "
            pdb=" CB  ILE A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL B 145 "
            pdb=" N   VAL B 145 "
            pdb=" C   VAL B 145 "
            pdb=" CB  VAL B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 853 not shown)

  Planarity restraints: 972
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 138 "    0.037 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO B 139 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 139 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 139 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 138 "   -0.037 5.00e-02 4.00e+02   5.60e-02 5.02e+00
        pdb=" N   PRO A 139 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 139 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 139 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 131 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.64e+00
        pdb=" CG  ASP A 131 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 131 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 131 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 969 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1594
        2.82 -     3.34: 5041
        3.34 -     3.86: 8402
        3.86 -     4.38: 9465
        4.38 -     4.90: 16798
  Nonbonded interactions: 41300
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 361 "
            pdb=" OD1 ASP A 365 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NE2 GLN B 361 "
            pdb=" OD1 ASP B 365 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   LEU A  99 "
            pdb=" OG  SER A 102 "
     model   vdw
     2.411 3.040
  nonbonded pdb=" O   LEU B  99 "
            pdb=" OG  SER B 102 "
     model   vdw
     2.426 3.040
  nonbonded pdb=" N   ASP B  88 "
            pdb=" OD1 ASP B  88 "
     model   vdw
     2.427 3.120
  ... (remaining 41295 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     18.120
  Find NCS groups from input model:        0.190
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
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   0.023   5606  Z= 0.132
  Angle     :  0.605   8.592   7590  Z= 0.334
  Chirality :  0.043   0.158    856
  Planarity :  0.005   0.057    972
  Dihedral  : 15.106  89.731   2084
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 13.17 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.32), residues: 702
  helix:  0.39 (0.31), residues: 316
  sheet:  0.64 (0.49), residues: 112
  loop :  1.04 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.011   0.001   PHE A 216 
 TYR   0.016   0.001   TYR A 390 
 ARG   0.003   0.000   ARG B 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20964 (  258)
  hydrogen bonds       : angle       6.65796 (  717)
  covalent geometry    : bond        0.00258 ( 5606)
  covalent geometry    : angle       0.60494 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A   33 SER cc_start: 0.7748 (t) cc_final: 0.7485 (m)
REVERT: A  383 ASN cc_start: 0.7402 (t0) cc_final: 0.6954 (t0)
REVERT: B   46 MET cc_start: 0.8481 (mmt) cc_final: 0.8122 (mmt)
REVERT: B  251 LYS cc_start: 0.8331 (tttt) cc_final: 0.8111 (ttpt)
REVERT: B  383 ASN cc_start: 0.7396 (t0) cc_final: 0.7064 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1485
  time to fit residues: 22.0621
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.158735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.113726 restraints weight = 6184.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.57
r_work: 0.3070 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5606  Z= 0.150
  Angle     :  0.573  12.053   7590  Z= 0.275
  Chirality :  0.044   0.136    856
  Planarity :  0.006   0.060    972
  Dihedral  :  4.116  17.798    754
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.17 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.32), residues: 702
  helix:  0.69 (0.30), residues: 334
  sheet:  1.07 (0.51), residues: 104
  loop :  0.84 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.010   0.001   PHE A 364 
 TYR   0.016   0.002   TYR B 272 
 ARG   0.003   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05236 (  258)
  hydrogen bonds       : angle       4.86383 (  717)
  covalent geometry    : bond        0.00364 ( 5606)
  covalent geometry    : angle       0.57255 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A   33 SER cc_start: 0.7343 (t) cc_final: 0.7094 (m)
REVERT: A  139 PRO cc_start: 0.8328 (Cg_exo) cc_final: 0.7999 (Cg_endo)
REVERT: A  229 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7434 (mm-30)
REVERT: A  282 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7475 (mtp)
REVERT: A  383 ASN cc_start: 0.7486 (t0) cc_final: 0.6921 (t0)
REVERT: B  139 PRO cc_start: 0.8359 (Cg_exo) cc_final: 0.8014 (Cg_endo)
REVERT: B  251 LYS cc_start: 0.8269 (tttt) cc_final: 0.7900 (ttpt)
REVERT: B  264 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8274 (t70)
REVERT: B  282 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7215 (mtp)
REVERT: B  383 ASN cc_start: 0.7558 (t0) cc_final: 0.7037 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1360
  time to fit residues: 17.3455
Evaluate side-chains
  82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0000
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
B 103 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.159862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.115593 restraints weight = 6205.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.49
r_work: 0.3091 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5606  Z= 0.108
  Angle     :  0.522  13.562   7590  Z= 0.241
  Chirality :  0.042   0.136    856
  Planarity :  0.005   0.057    972
  Dihedral  :  3.844  15.996    754
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.83 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.32), residues: 702
  helix:  0.97 (0.29), residues: 336
  sheet:  1.20 (0.52), residues: 104
  loop :  0.88 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.014   0.001   PHE A 216 
 TYR   0.017   0.001   TYR B 272 
 ARG   0.003   0.000   ARG B 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  258)
  hydrogen bonds       : angle       4.55422 (  717)
  covalent geometry    : bond        0.00249 ( 5606)
  covalent geometry    : angle       0.52206 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  282 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7486 (mtp)
REVERT: A  383 ASN cc_start: 0.7486 (t0) cc_final: 0.6885 (t0)
REVERT: B  264 HIS cc_start: 0.8829 (OUTLIER) cc_final: 0.8345 (t70)
REVERT: B  282 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7276 (mtp)
REVERT: B  383 ASN cc_start: 0.7580 (t0) cc_final: 0.7050 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 80
  average time/residue: 0.1313
  time to fit residues: 15.1026
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   chunk 36 optimal weight:    0.0670
   overall best weight:    0.3714

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.162931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.118736 restraints weight = 6307.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.49
r_work: 0.3129 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5606  Z= 0.085
  Angle     :  0.505  13.774   7590  Z= 0.226
  Chirality :  0.041   0.134    856
  Planarity :  0.005   0.054    972
  Dihedral  :  3.615  13.527    754
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.17 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.32), residues: 702
  helix:  1.28 (0.29), residues: 344
  sheet:  1.26 (0.53), residues: 104
  loop :  1.11 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 385 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.013   0.001   PHE A 216 
 TYR   0.017   0.001   TYR B 272 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03382 (  258)
  hydrogen bonds       : angle       4.32557 (  717)
  covalent geometry    : bond        0.00180 ( 5606)
  covalent geometry    : angle       0.50453 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8647 (tpp) cc_final: 0.8435 (mmm)
REVERT: A  229 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7590 (mm-30)
REVERT: A  383 ASN cc_start: 0.7375 (t0) cc_final: 0.6940 (t0)
REVERT: B  264 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8360 (t70)
REVERT: B  282 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7316 (mtp)
REVERT: B  383 ASN cc_start: 0.7497 (t0) cc_final: 0.6949 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1463
  time to fit residues: 16.6996
Evaluate side-chains
  87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.159185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115333 restraints weight = 6166.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.44
r_work: 0.3085 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5606  Z= 0.112
  Angle     :  0.539  14.633   7590  Z= 0.241
  Chirality :  0.043   0.137    856
  Planarity :  0.005   0.054    972
  Dihedral  :  3.664  13.470    754
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.83 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.32), residues: 702
  helix:  1.48 (0.29), residues: 336
  sheet:  1.27 (0.53), residues: 104
  loop :  1.02 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.011   0.001   PHE A 216 
 TYR   0.016   0.001   TYR B 272 
 ARG   0.003   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  258)
  hydrogen bonds       : angle       4.26068 (  717)
  covalent geometry    : bond        0.00270 ( 5606)
  covalent geometry    : angle       0.53921 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8251 (mmm160)
REVERT: A  282 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7476 (mtp)
REVERT: A  383 ASN cc_start: 0.7511 (t0) cc_final: 0.6839 (t0)
REVERT: B   48 MET cc_start: 0.8455 (tpt) cc_final: 0.8094 (tpt)
REVERT: B  232 GLU cc_start: 0.7290 (tp30) cc_final: 0.6545 (tm-30)
REVERT: B  383 ASN cc_start: 0.7585 (t0) cc_final: 0.6997 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1724
  time to fit residues: 18.9573
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.159440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.116765 restraints weight = 6209.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.36
r_work: 0.3105 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5606  Z= 0.100
  Angle     :  0.524  14.777   7590  Z= 0.232
  Chirality :  0.042   0.135    856
  Planarity :  0.005   0.053    972
  Dihedral  :  3.603  13.179    754
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.00 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.32), residues: 702
  helix:  1.62 (0.29), residues: 336
  sheet:  1.54 (0.54), residues: 100
  loop :  0.94 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.021   0.001   PHE A 364 
 TYR   0.017   0.001   TYR B 272 
 ARG   0.003   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  258)
  hydrogen bonds       : angle       4.14396 (  717)
  covalent geometry    : bond        0.00235 ( 5606)
  covalent geometry    : angle       0.52403 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8220 (mmm160)
REVERT: A  282 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7414 (mtp)
REVERT: A  383 ASN cc_start: 0.7476 (t0) cc_final: 0.6732 (t0)
REVERT: B   48 MET cc_start: 0.8321 (tpt) cc_final: 0.8005 (tpt)
REVERT: B  282 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7240 (mtp)
REVERT: B  383 ASN cc_start: 0.7599 (t0) cc_final: 0.7006 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1579
  time to fit residues: 16.5810
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.158555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.115809 restraints weight = 6230.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.37
r_work: 0.3095 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5606  Z= 0.105
  Angle     :  0.531  14.914   7590  Z= 0.234
  Chirality :  0.042   0.136    856
  Planarity :  0.005   0.053    972
  Dihedral  :  3.613  12.830    754
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.33 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.32), residues: 702
  helix:  1.71 (0.29), residues: 336
  sheet:  1.57 (0.54), residues: 100
  loop :  0.93 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.017   0.001   PHE A 364 
 TYR   0.016   0.001   TYR B 272 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03757 (  258)
  hydrogen bonds       : angle       4.12193 (  717)
  covalent geometry    : bond        0.00253 ( 5606)
  covalent geometry    : angle       0.53075 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.582 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8231 (mmm160)
REVERT: A  282 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7509 (mtp)
REVERT: A  383 ASN cc_start: 0.7539 (t0) cc_final: 0.6818 (t0)
REVERT: B   48 MET cc_start: 0.8371 (tpt) cc_final: 0.8035 (tpt)
REVERT: B  232 GLU cc_start: 0.7368 (tp30) cc_final: 0.6568 (tm-30)
REVERT: B  276 GLU cc_start: 0.7076 (tp30) cc_final: 0.6631 (tm-30)
REVERT: B  282 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7318 (mtp)
REVERT: B  383 ASN cc_start: 0.7765 (t0) cc_final: 0.7097 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1499
  time to fit residues: 17.3064
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 46 optimal weight:    0.3980
   chunk 67 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.159713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.116037 restraints weight = 6230.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.47
r_work: 0.3096 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5606  Z= 0.095
  Angle     :  0.528  15.465   7590  Z= 0.230
  Chirality :  0.042   0.135    856
  Planarity :  0.005   0.053    972
  Dihedral  :  3.539  13.220    754
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.00 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.33), residues: 702
  helix:  1.68 (0.29), residues: 348
  sheet:  1.56 (0.54), residues: 100
  loop :  0.89 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.012   0.001   PHE A 216 
 TYR   0.015   0.001   TYR B 272 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  258)
  hydrogen bonds       : angle       4.07548 (  717)
  covalent geometry    : bond        0.00221 ( 5606)
  covalent geometry    : angle       0.52781 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8211 (mmm160)
REVERT: A  272 TYR cc_start: 0.6809 (t80) cc_final: 0.6577 (t80)
REVERT: A  282 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7480 (mtp)
REVERT: A  383 ASN cc_start: 0.7521 (t0) cc_final: 0.6783 (t0)
REVERT: B  232 GLU cc_start: 0.7299 (tp30) cc_final: 0.6474 (tm-30)
REVERT: B  276 GLU cc_start: 0.7094 (tp30) cc_final: 0.6641 (tm-30)
REVERT: B  282 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7182 (mtp)
REVERT: B  383 ASN cc_start: 0.7709 (t0) cc_final: 0.7062 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 80
  average time/residue: 0.1679
  time to fit residues: 17.9690
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.156137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.113711 restraints weight = 6187.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.35
r_work: 0.3080 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5606  Z= 0.120
  Angle     :  0.561  15.951   7590  Z= 0.245
  Chirality :  0.043   0.137    856
  Planarity :  0.005   0.054    972
  Dihedral  :  3.633  12.817    754
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.17 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.33), residues: 702
  helix:  1.66 (0.29), residues: 348
  sheet:  1.57 (0.55), residues: 100
  loop :  0.81 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 385 
 HIS   0.003   0.001   HIS B 351 
 PHE   0.014   0.001   PHE A 216 
 TYR   0.016   0.001   TYR B 272 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  258)
  hydrogen bonds       : angle       4.11128 (  717)
  covalent geometry    : bond        0.00294 ( 5606)
  covalent geometry    : angle       0.56120 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8186 (mmm160)
REVERT: A  272 TYR cc_start: 0.6795 (t80) cc_final: 0.6559 (t80)
REVERT: A  282 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7484 (mtp)
REVERT: A  383 ASN cc_start: 0.7532 (t0) cc_final: 0.6780 (t0)
REVERT: B  232 GLU cc_start: 0.7327 (tp30) cc_final: 0.6444 (tm-30)
REVERT: B  251 LYS cc_start: 0.8075 (tttt) cc_final: 0.7799 (tttt)
REVERT: B  276 GLU cc_start: 0.7050 (tp30) cc_final: 0.6587 (tm-30)
REVERT: B  282 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7248 (mtp)
REVERT: B  383 ASN cc_start: 0.7750 (t0) cc_final: 0.7070 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 80
  average time/residue: 0.1547
  time to fit residues: 16.8612
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.158649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.115261 restraints weight = 6168.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.42
r_work: 0.3089 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5606  Z= 0.104
  Angle     :  0.556  15.775   7590  Z= 0.241
  Chirality :  0.042   0.135    856
  Planarity :  0.005   0.053    972
  Dihedral  :  3.588  12.963    754
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.33 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.33), residues: 702
  helix:  1.75 (0.29), residues: 346
  sheet:  1.53 (0.55), residues: 100
  loop :  0.85 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.014   0.001   PHE A 216 
 TYR   0.015   0.001   TYR B 272 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  258)
  hydrogen bonds       : angle       4.12082 (  717)
  covalent geometry    : bond        0.00248 ( 5606)
  covalent geometry    : angle       0.55593 ( 7590)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8195 (mmm160)
REVERT: A  221 MET cc_start: 0.6443 (mmm) cc_final: 0.6018 (tpt)
REVERT: A  272 TYR cc_start: 0.6778 (t80) cc_final: 0.6567 (t80)
REVERT: A  282 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7511 (mtp)
REVERT: A  383 ASN cc_start: 0.7535 (t0) cc_final: 0.6766 (t0)
REVERT: B  232 GLU cc_start: 0.7400 (tp30) cc_final: 0.6532 (tm-30)
REVERT: B  251 LYS cc_start: 0.8025 (tttt) cc_final: 0.7664 (tttt)
REVERT: B  276 GLU cc_start: 0.7044 (tp30) cc_final: 0.6582 (tm-30)
REVERT: B  282 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7239 (mtp)
REVERT: B  383 ASN cc_start: 0.7725 (t0) cc_final: 0.7052 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 81
  average time/residue: 0.1642
  time to fit residues: 18.0681
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    0.4980
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.158092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117224 restraints weight = 6249.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.56
r_work: 0.3082 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5606  Z= 0.114
  Angle     :  0.570  15.665   7590  Z= 0.249
  Chirality :  0.043   0.136    856
  Planarity :  0.005   0.059    972
  Dihedral  :  3.621  12.934    754
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.50 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.33), residues: 702
  helix:  1.75 (0.29), residues: 346
  sheet:  1.57 (0.55), residues: 100
  loop :  0.82 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.014   0.001   PHE A 216 
 TYR   0.015   0.001   TYR B 272 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  258)
  hydrogen bonds       : angle       4.25865 (  717)
  covalent geometry    : bond        0.00273 ( 5606)
  covalent geometry    : angle       0.56965 ( 7590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3246.92 seconds
wall clock time: 56 minutes 24.57 seconds (3384.57 seconds total)