Starting phenix.real_space_refine
on Fri Aug 22 20:16:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur6_42484/08_2025/8ur6_42484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur6_42484/08_2025/8ur6_42484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur6_42484/08_2025/8ur6_42484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur6_42484/08_2025/8ur6_42484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur6_42484/08_2025/8ur6_42484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur6_42484/08_2025/8ur6_42484.cif"
  }
  resolution = 3.03
  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=   0.022
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      36      5.16       5
     C    4826      2.51       5
     N    1214      2.21       5
     O    1464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7540
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3770
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 19, 'TRANS': 445}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 3770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3770
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 19, 'TRANS': 445}
          Chain breaks: 5
  Time building chain proxies: 1.88, per 1000 atoms: 0.25
  Number of scatterers: 7540
  At special positions: 0
  Unit cell: (103.356, 115.884, 72.036, 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      36     16.00
     O    1464      8.00
     N    1214      7.00
     C    4826      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: 0.59
  Conformation dependent library (CDL) restraints added in 408.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1780

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 8 sheets defined
      40.6% alpha, 14.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 11
      removed outlier: 3.638A  pdb=" N   PHE A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 44
    Processing helix  chain 'A' and resid 48 through 50
      No H-bonds generated for 'chain 'A' and resid 48 through 50'
    Processing helix  chain 'A' and resid 87 through 94
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 4.056A  pdb=" N   ASP A 162 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
      removed outlier: 3.524A  pdb=" N   PHE A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 176 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 171 through 176'
    Processing helix  chain 'A' and resid 177 through 187
    Processing helix  chain 'A' and resid 194 through 205
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 229 through 240
    Processing helix  chain 'A' and resid 313 through 324
      removed outlier: 3.511A  pdb=" N   ARG A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.862A  pdb=" N   GLY A 330 " --> pdb=" O   PRO A 327 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   ASN A 331 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 354 through 365
      removed outlier: 3.911A  pdb=" N   ILE A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 443
    Processing helix  chain 'A' and resid 449 through 457
      removed outlier: 3.734A  pdb=" N   LEU A 453 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 524
    Processing helix  chain 'B' and resid 6 through 11
      removed outlier: 3.647A  pdb=" N   PHE B  11 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 44
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 106 through 118
    Processing helix  chain 'B' and resid 143 through 156
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 4.024A  pdb=" N   ASP B 162 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 169
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.612A  pdb=" N   PHE B 175 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 187
    Processing helix  chain 'B' and resid 194 through 205
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 229 through 240
    Processing helix  chain 'B' and resid 313 through 326
      removed outlier: 3.865A  pdb=" N   GLN B 325 " --> pdb=" O   ASN B 321 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
      removed outlier: 3.772A  pdb=" N   GLY B 330 " --> pdb=" O   PRO B 327 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   ASN B 331 " --> pdb=" O   GLU B 328 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 327 through 331'
    Processing helix  chain 'B' and resid 332 through 337
      removed outlier: 3.551A  pdb=" N   GLN B 337 " --> pdb=" O   ASP B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 365
      removed outlier: 3.830A  pdb=" N   ILE B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 443
    Processing helix  chain 'B' and resid 449 through 456
      removed outlier: 3.642A  pdb=" N   LEU B 453 " --> pdb=" O   LYS B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 524
      removed outlier: 3.505A  pdb=" N   SER B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4
    Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245
      removed outlier: 6.378A  pdb=" N   ILE A  52 " --> pdb=" O   GLN A 243 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   GLU A 245 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ILE A  54 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   SER A  24 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   PHE A 287 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   TYR A  26 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133
      removed outlier: 4.316A  pdb=" N   MET A 389 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA A 413 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   VAL A 346 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257
      removed outlier: 5.594A  pdb=" N   VAL A 250 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASP A 270 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP A 256 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   ALA A 264 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4
    Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245
      removed outlier: 6.500A  pdb=" N   SER B  24 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   PHE B 287 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR B  26 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   THR B 289 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ILE B  28 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133
      removed outlier: 4.309A  pdb=" N   MET B 389 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ALA B 413 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   VAL B 346 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257
      removed outlier: 6.756A  pdb=" N   VAL B 248 " --> pdb=" O   ARG B 271 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ARG B 271 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL B 250 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE B 269 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASP B 252 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE B 267 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LYS B 254 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)

    288 hydrogen bonds defined for protein.
    819 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: 1.09

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2408
        1.34 -     1.47: 1940
        1.47 -     1.59: 3312
        1.59 -     1.72: 0
        1.72 -     1.84: 58
  Bond restraints: 7718
  Sorted by residual:
  bond pdb=" CA  ILE B 461 "
       pdb=" C   ILE B 461 "
    ideal  model  delta    sigma   weight residual
    1.528  1.495  0.033 8.50e-03 1.38e+04 1.49e+01
  bond pdb=" N   ILE B 461 "
       pdb=" CA  ILE B 461 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.026 7.70e-03 1.69e+04 1.10e+01
  bond pdb=" N   PRO A 462 "
       pdb=" CD  PRO A 462 "
    ideal  model  delta    sigma   weight residual
    1.473  1.505 -0.032 1.40e-02 5.10e+03 5.31e+00
  bond pdb=" CA  GLU B 190 "
       pdb=" C   GLU B 190 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.017 1.02e-02 9.61e+03 2.90e+00
  bond pdb=" CA  GLU A 190 "
       pdb=" C   GLU A 190 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 9.90e-03 1.02e+04 2.25e+00
  ... (remaining 7713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 9866
        1.49 -     2.99: 549
        2.99 -     4.48: 57
        4.48 -     5.98: 4
        5.98 -     7.47: 2
  Bond angle restraints: 10478
  Sorted by residual:
  angle pdb=" C   LYS A 184 "
        pdb=" N   THR A 185 "
        pdb=" CA  THR A 185 "
      ideal   model   delta    sigma   weight residual
     122.09  117.49    4.60 1.79e+00 3.12e-01 6.60e+00
  angle pdb=" CA  TYR B 236 "
        pdb=" CB  TYR B 236 "
        pdb=" CG  TYR B 236 "
      ideal   model   delta    sigma   weight residual
     113.90  117.97   -4.07 1.80e+00 3.09e-01 5.10e+00
  angle pdb=" C   GLU A 501 "
        pdb=" N   ARG A 502 "
        pdb=" CA  ARG A 502 "
      ideal   model   delta    sigma   weight residual
     122.19  125.26   -3.07 1.41e+00 5.03e-01 4.73e+00
  angle pdb=" CA  VAL B 169 "
        pdb=" C   VAL B 169 "
        pdb=" N   PHE B 170 "
      ideal   model   delta    sigma   weight residual
     116.60  119.68   -3.08 1.45e+00 4.76e-01 4.52e+00
  angle pdb=" C   ILE A 255 "
        pdb=" N   ASP A 256 "
        pdb=" CA  ASP A 256 "
      ideal   model   delta    sigma   weight residual
     123.00  120.07    2.93 1.38e+00 5.25e-01 4.50e+00
  ... (remaining 10473 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.65: 4078
       15.65 -    31.30: 383
       31.30 -    46.95: 92
       46.95 -    62.60: 21
       62.60 -    78.25: 6
  Dihedral angle restraints: 4580
    sinusoidal: 1838
      harmonic: 2742
  Sorted by residual:
  dihedral pdb=" CA  VAL B 483 "
           pdb=" C   VAL B 483 "
           pdb=" N   VAL B 484 "
           pdb=" CA  VAL B 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.61   18.39     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ILE A 255 "
           pdb=" C   ILE A 255 "
           pdb=" N   ASP A 256 "
           pdb=" CA  ASP A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.19   16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ILE B 255 "
           pdb=" C   ILE B 255 "
           pdb=" N   ASP B 256 "
           pdb=" CA  ASP B 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.29   15.71     0      5.00e+00 4.00e-02 9.87e+00
  ... (remaining 4577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 691
       0.040 -    0.080: 336
       0.080 -    0.120: 108
       0.120 -    0.160: 19
       0.160 -    0.199: 4
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CA  ILE B 255 "
            pdb=" N   ILE B 255 "
            pdb=" C   ILE B 255 "
            pdb=" CB  ILE B 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.95e-01
  chirality pdb=" CA  ILE A 255 "
            pdb=" N   ILE A 255 "
            pdb=" C   ILE A 255 "
            pdb=" CB  ILE A 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CA  ILE B 411 "
            pdb=" N   ILE B 411 "
            pdb=" C   ILE B 411 "
            pdb=" CB  ILE B 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.16e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 461 "   -0.077 5.00e-02 4.00e+02   1.19e-01 2.25e+01
        pdb=" N   PRO A 462 "    0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO A 462 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO A 462 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 461 "   -0.042 5.00e-02 4.00e+02   6.47e-02 6.70e+00
        pdb=" N   PRO B 462 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 462 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 462 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 387 "   -0.001 2.00e-02 2.50e+03   1.18e-02 3.48e+00
        pdb=" CG  TRP B 387 "    0.005 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 387 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 387 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 387 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 387 "    0.026 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 387 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 387 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 387 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 387 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1029
        2.75 -     3.29: 7316
        3.29 -     3.83: 12832
        3.83 -     4.36: 15821
        4.36 -     4.90: 26519
  Nonbonded interactions: 63517
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 431 "
            pdb=" OD1 ASN A 433 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG  SER B 431 "
            pdb=" OD1 ASN B 433 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG  SER A 347 "
            pdb=" NE1 TRP A 410 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OG  SER B 347 "
            pdb=" NE1 TRP B 410 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   THR B 185 "
            pdb=" OH  TYR B 412 "
     model   vdw
     2.297 3.040
  ... (remaining 63512 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: 0.01
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:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.750
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   7718  Z= 0.302
  Angle     :  0.760   7.474  10478  Z= 0.419
  Chirality :  0.050   0.199   1158
  Planarity :  0.007   0.119   1336
  Dihedral  : 13.542  78.246   2800
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.26), residues: 906
  helix:  0.82 (0.29), residues: 284
  sheet: -0.15 (0.45), residues: 130
  loop : -0.48 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.003   ARG B 200 
 TYR   0.022   0.004   TYR B 236 
 PHE   0.017   0.004   PHE B 170 
 TRP   0.026   0.005   TRP B 387 
 HIS   0.011   0.003   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 ( 7718)
  covalent geometry    : angle       0.76050 (10478)
  hydrogen bonds       : bond        0.15042 (  288)
  hydrogen bonds       : angle       5.90831 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8463 (mmtm)
REVERT: A  157 ASN cc_start: 0.8604 (m-40) cc_final: 0.8180 (p0)
REVERT: A  202 LEU cc_start: 0.9582 (mp) cc_final: 0.9297 (mt)
REVERT: A  268 LEU cc_start: 0.8925 (mp) cc_final: 0.8647 (mp)
REVERT: A  272 ASN cc_start: 0.9197 (t0) cc_final: 0.8991 (p0)
REVERT: A  274 ASN cc_start: 0.8423 (m-40) cc_final: 0.8167 (p0)
REVERT: A  311 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7615 (tm-30)
REVERT: A  389 MET cc_start: 0.8892 (ttm) cc_final: 0.8661 (ttm)
REVERT: A  473 MET cc_start: 0.8935 (mmm) cc_final: 0.8678 (mmm)
REVERT: B   58 LEU cc_start: 0.9013 (mm) cc_final: 0.8713 (pp)
REVERT: B  104 ASN cc_start: 0.9364 (m-40) cc_final: 0.9104 (m-40)
REVERT: B  112 TYR cc_start: 0.8558 (t80) cc_final: 0.8019 (t80)
REVERT: B  159 GLU cc_start: 0.8754 (mp0) cc_final: 0.8518 (pm20)
REVERT: B  173 ASP cc_start: 0.8920 (m-30) cc_final: 0.8557 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0825
  time to fit residues: 14.8345
Evaluate side-chains
  75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
A 321 ASN
B 207 HIS
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 331 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.076521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.061850 restraints weight = 19149.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 3.24
r_work: 0.2813 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7718  Z= 0.212
  Angle     :  0.509   4.897  10478  Z= 0.280
  Chirality :  0.045   0.155   1158
  Planarity :  0.004   0.062   1336
  Dihedral  :  4.126  18.322    994
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  4.88 %
    Favored  : 94.05 %
  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 aren not related in a simple way.
  whole:  0.44 (0.27), residues: 906
  helix:  1.27 (0.30), residues: 300
  sheet: -0.11 (0.47), residues: 130
  loop : -0.14 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 324 
 TYR   0.017   0.001   TYR B 236 
 PHE   0.028   0.001   PHE A 506 
 TRP   0.009   0.001   TRP A 316 
 HIS   0.006   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 7718)
  covalent geometry    : angle       0.50916 (10478)
  hydrogen bonds       : bond        0.03421 (  288)
  hydrogen bonds       : angle       4.68498 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  157 ASN cc_start: 0.8579 (m-40) cc_final: 0.8285 (t0)
REVERT: A  249 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8779 (ttmm)
REVERT: A  272 ASN cc_start: 0.9270 (t0) cc_final: 0.9023 (p0)
REVERT: A  274 ASN cc_start: 0.8485 (m-40) cc_final: 0.8111 (p0)
REVERT: A  311 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: A  465 MET cc_start: 0.9228 (mtm) cc_final: 0.8943 (mtt)
REVERT: A  473 MET cc_start: 0.9153 (mmm) cc_final: 0.8854 (mmm)
REVERT: B   58 LEU cc_start: 0.9096 (mm) cc_final: 0.8768 (pp)
REVERT: B  159 GLU cc_start: 0.8919 (mp0) cc_final: 0.8544 (tp30)
REVERT: B  173 ASP cc_start: 0.8956 (m-30) cc_final: 0.8548 (t0)
REVERT: B  274 ASN cc_start: 0.8663 (m-40) cc_final: 0.8085 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 78
  average time/residue: 0.0740
  time to fit residues: 8.2824
Evaluate side-chains
  67 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 54 optimal weight:    0.3980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 486 HIS
B 207 HIS
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.063383 restraints weight = 19057.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 3.19
r_work: 0.2825 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7718  Z= 0.140
  Angle     :  0.455   4.530  10478  Z= 0.248
  Chirality :  0.043   0.153   1158
  Planarity :  0.003   0.048   1336
  Dihedral  :  3.888  18.484    994
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.43 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.28), residues: 906
  helix:  1.45 (0.30), residues: 302
  sheet: -0.14 (0.46), residues: 130
  loop :  0.09 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 265 
 TYR   0.013   0.001   TYR B 236 
 PHE   0.016   0.001   PHE A 506 
 TRP   0.005   0.001   TRP B 316 
 HIS   0.005   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7718)
  covalent geometry    : angle       0.45462 (10478)
  hydrogen bonds       : bond        0.03006 (  288)
  hydrogen bonds       : angle       4.36953 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  173 ASP cc_start: 0.8905 (m-30) cc_final: 0.8565 (t0)
REVERT: A  249 LYS cc_start: 0.8988 (tmtt) cc_final: 0.8765 (ttmm)
REVERT: A  272 ASN cc_start: 0.9259 (t0) cc_final: 0.8960 (p0)
REVERT: A  311 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: A  465 MET cc_start: 0.9210 (mtm) cc_final: 0.8939 (mtt)
REVERT: A  473 MET cc_start: 0.9115 (mmm) cc_final: 0.8820 (mmm)
REVERT: B   58 LEU cc_start: 0.9139 (mm) cc_final: 0.8764 (pp)
REVERT: B  157 ASN cc_start: 0.8128 (t0) cc_final: 0.7518 (t0)
REVERT: B  159 GLU cc_start: 0.8837 (mp0) cc_final: 0.8402 (pm20)
REVERT: B  173 ASP cc_start: 0.8924 (m-30) cc_final: 0.8514 (t0)
REVERT: B  274 ASN cc_start: 0.8670 (m-40) cc_final: 0.8179 (p0)
REVERT: B  506 PHE cc_start: 0.9008 (t80) cc_final: 0.8770 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0744
  time to fit residues: 7.5242
Evaluate side-chains
  63 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0970
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B 207 HIS
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.076838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.062022 restraints weight = 19243.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 3.29
r_work: 0.2834 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7718  Z= 0.108
  Angle     :  0.429   4.672  10478  Z= 0.234
  Chirality :  0.042   0.150   1158
  Planarity :  0.003   0.045   1336
  Dihedral  :  3.745  17.687    994
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.14 %
    Favored  : 92.02 %
  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 aren not related in a simple way.
  whole:  0.84 (0.28), residues: 906
  helix:  1.54 (0.30), residues: 302
  sheet: -0.12 (0.46), residues: 130
  loop :  0.23 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 324 
 TYR   0.011   0.001   TYR B 412 
 PHE   0.013   0.001   PHE A 506 
 TRP   0.004   0.001   TRP A 316 
 HIS   0.005   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7718)
  covalent geometry    : angle       0.42932 (10478)
  hydrogen bonds       : bond        0.02691 (  288)
  hydrogen bonds       : angle       4.21864 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8897 (m-30) cc_final: 0.8552 (t0)
REVERT: A  272 ASN cc_start: 0.9232 (t0) cc_final: 0.8947 (p0)
REVERT: A  311 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7936 (tm-30)
REVERT: A  465 MET cc_start: 0.9186 (mtm) cc_final: 0.8918 (mtt)
REVERT: A  473 MET cc_start: 0.9098 (mmm) cc_final: 0.8879 (mmm)
REVERT: B   58 LEU cc_start: 0.9189 (mm) cc_final: 0.8918 (pp)
REVERT: B  173 ASP cc_start: 0.8899 (m-30) cc_final: 0.8492 (t0)
REVERT: B  272 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8993 (m-40)
REVERT: B  274 ASN cc_start: 0.8579 (m-40) cc_final: 0.8107 (p0)
REVERT: B  365 CYS cc_start: 0.7707 (t) cc_final: 0.7504 (p)
  outliers start: 7
  outliers final: 1
  residues processed: 69
  average time/residue: 0.0666
  time to fit residues: 6.8650
Evaluate side-chains
  61 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 75 optimal weight:    0.3980
   chunk 88 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 2 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 207 HIS
B 207 HIS
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.077021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.062749 restraints weight = 19063.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 3.21
r_work: 0.2823 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7718  Z= 0.135
  Angle     :  0.444   4.651  10478  Z= 0.244
  Chirality :  0.042   0.152   1158
  Planarity :  0.003   0.043   1336
  Dihedral  :  3.766  17.257    994
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.74 %
    Favored  : 91.79 %
  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 aren not related in a simple way.
  whole:  0.93 (0.28), residues: 906
  helix:  1.52 (0.30), residues: 302
  sheet: -0.08 (0.47), residues: 130
  loop :  0.36 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  95 
 TYR   0.013   0.001   TYR B 412 
 PHE   0.018   0.001   PHE B 506 
 TRP   0.005   0.001   TRP A 316 
 HIS   0.006   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7718)
  covalent geometry    : angle       0.44438 (10478)
  hydrogen bonds       : bond        0.02774 (  288)
  hydrogen bonds       : angle       4.19883 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8920 (m-30) cc_final: 0.8568 (t0)
REVERT: A  272 ASN cc_start: 0.9256 (t0) cc_final: 0.8954 (p0)
REVERT: A  311 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: A  473 MET cc_start: 0.9094 (mmm) cc_final: 0.8863 (mmm)
REVERT: B   58 LEU cc_start: 0.9192 (mm) cc_final: 0.8895 (pp)
REVERT: B  173 ASP cc_start: 0.8900 (m-30) cc_final: 0.8491 (t0)
REVERT: B  272 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9032 (m-40)
REVERT: B  274 ASN cc_start: 0.8613 (m-40) cc_final: 0.8159 (p0)
  outliers start: 4
  outliers final: 2
  residues processed: 62
  average time/residue: 0.0643
  time to fit residues: 6.0908
Evaluate side-chains
  57 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.073614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.059316 restraints weight = 19228.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 3.18
r_work: 0.2756 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7718  Z= 0.250
  Angle     :  0.513   4.814  10478  Z= 0.283
  Chirality :  0.044   0.139   1158
  Planarity :  0.003   0.043   1336
  Dihedral  :  4.039  18.170    994
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.10 %
    Favored  : 91.19 %
  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 aren not related in a simple way.
  whole:  0.83 (0.28), residues: 906
  helix:  1.36 (0.31), residues: 302
  sheet: -0.16 (0.48), residues: 130
  loop :  0.37 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  95 
 TYR   0.018   0.001   TYR B 236 
 PHE   0.025   0.001   PHE B 506 
 TRP   0.006   0.001   TRP A 316 
 HIS   0.003   0.001   HIS B 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 7718)
  covalent geometry    : angle       0.51337 (10478)
  hydrogen bonds       : bond        0.03227 (  288)
  hydrogen bonds       : angle       4.44287 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  173 ASP cc_start: 0.8977 (m-30) cc_final: 0.8622 (t0)
REVERT: A  272 ASN cc_start: 0.9313 (t0) cc_final: 0.9011 (p0)
REVERT: A  311 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: A  326 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8496 (p)
REVERT: B   58 LEU cc_start: 0.9218 (mm) cc_final: 0.8852 (pp)
REVERT: B  159 GLU cc_start: 0.8923 (mp0) cc_final: 0.8663 (tp30)
REVERT: B  173 ASP cc_start: 0.8964 (m-30) cc_final: 0.8551 (t0)
REVERT: B  272 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9048 (m-40)
REVERT: B  274 ASN cc_start: 0.8644 (m-40) cc_final: 0.8074 (p0)
  outliers start: 6
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0512
  time to fit residues: 4.8227
Evaluate side-chains
  57 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0000
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0470
   overall best weight:    0.5082

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

Flipped N/Q/H residues before XYZ refinement:
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.074842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.060645 restraints weight = 19146.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 3.23
r_work: 0.2819 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7718  Z= 0.098
  Angle     :  0.444   5.469  10478  Z= 0.242
  Chirality :  0.042   0.147   1158
  Planarity :  0.003   0.042   1336
  Dihedral  :  3.764  17.100    994
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  7.98 %
    Favored  : 90.95 %
  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 aren not related in a simple way.
  whole:  0.97 (0.28), residues: 906
  helix:  1.49 (0.31), residues: 302
  sheet: -0.05 (0.48), residues: 130
  loop :  0.44 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 324 
 TYR   0.013   0.001   TYR A 412 
 PHE   0.011   0.001   PHE B 506 
 TRP   0.006   0.001   TRP A 192 
 HIS   0.004   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7718)
  covalent geometry    : angle       0.44351 (10478)
  hydrogen bonds       : bond        0.02597 (  288)
  hydrogen bonds       : angle       4.20522 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  173 ASP cc_start: 0.8939 (m-30) cc_final: 0.8560 (t0)
REVERT: A  272 ASN cc_start: 0.9309 (t0) cc_final: 0.8991 (p0)
REVERT: A  311 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: A  326 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8592 (p)
REVERT: A  389 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.8010 (tpp)
REVERT: A  473 MET cc_start: 0.9053 (mmm) cc_final: 0.8803 (mmm)
REVERT: B   58 LEU cc_start: 0.9209 (mm) cc_final: 0.8831 (pp)
REVERT: B  173 ASP cc_start: 0.8960 (m-30) cc_final: 0.8505 (t0)
REVERT: B  272 ASN cc_start: 0.9371 (OUTLIER) cc_final: 0.9074 (m-40)
REVERT: B  274 ASN cc_start: 0.8566 (m-40) cc_final: 0.8052 (p0)
  outliers start: 9
  outliers final: 3
  residues processed: 62
  average time/residue: 0.0601
  time to fit residues: 5.8211
Evaluate side-chains
  60 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.073193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.058978 restraints weight = 19345.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 3.26
r_work: 0.2779 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7718  Z= 0.154
  Angle     :  0.459   5.651  10478  Z= 0.252
  Chirality :  0.043   0.143   1158
  Planarity :  0.003   0.042   1336
  Dihedral  :  3.794  16.707    994
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.10 %
    Favored  : 91.07 %
  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 aren not related in a simple way.
  whole:  1.01 (0.28), residues: 906
  helix:  1.55 (0.31), residues: 302
  sheet: -0.10 (0.48), residues: 130
  loop :  0.45 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  95 
 TYR   0.013   0.001   TYR B 236 
 PHE   0.017   0.001   PHE B 506 
 TRP   0.005   0.001   TRP B 316 
 HIS   0.004   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7718)
  covalent geometry    : angle       0.45928 (10478)
  hydrogen bonds       : bond        0.02779 (  288)
  hydrogen bonds       : angle       4.21556 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  173 ASP cc_start: 0.8980 (m-30) cc_final: 0.8594 (t0)
REVERT: A  272 ASN cc_start: 0.9344 (t0) cc_final: 0.8989 (p0)
REVERT: A  311 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: A  326 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8661 (p)
REVERT: A  473 MET cc_start: 0.9059 (mmm) cc_final: 0.8798 (mmm)
REVERT: B   58 LEU cc_start: 0.9199 (mm) cc_final: 0.8791 (pp)
REVERT: B  159 GLU cc_start: 0.8958 (mp0) cc_final: 0.8625 (tp30)
REVERT: B  173 ASP cc_start: 0.9002 (m-30) cc_final: 0.8548 (t0)
REVERT: B  272 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9088 (m-40)
REVERT: B  274 ASN cc_start: 0.8574 (m-40) cc_final: 0.8042 (p0)
REVERT: B  365 CYS cc_start: 0.7811 (t) cc_final: 0.7315 (p)
REVERT: B  389 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8141 (mtp)
  outliers start: 7
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0616
  time to fit residues: 5.4292
Evaluate side-chains
  56 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 321 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.071273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.056889 restraints weight = 19298.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 3.25
r_work: 0.2711 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7718  Z= 0.262
  Angle     :  0.526   6.106  10478  Z= 0.290
  Chirality :  0.044   0.138   1158
  Planarity :  0.003   0.044   1336
  Dihedral  :  4.061  18.192    994
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.21 %
    Favored  : 90.71 %
  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 aren not related in a simple way.
  whole:  0.88 (0.28), residues: 906
  helix:  1.35 (0.31), residues: 302
  sheet: -0.24 (0.47), residues: 130
  loop :  0.47 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  95 
 TYR   0.018   0.001   TYR B 236 
 PHE   0.022   0.001   PHE B 506 
 TRP   0.006   0.001   TRP B 387 
 HIS   0.003   0.001   HIS A   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 7718)
  covalent geometry    : angle       0.52576 (10478)
  hydrogen bonds       : bond        0.03229 (  288)
  hydrogen bonds       : angle       4.44660 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8601 (t0)
REVERT: A  272 ASN cc_start: 0.9362 (t0) cc_final: 0.9055 (p0)
REVERT: A  311 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: A  326 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8780 (p)
REVERT: A  389 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (mtp)
REVERT: B  159 GLU cc_start: 0.8959 (mp0) cc_final: 0.8667 (tp30)
REVERT: B  173 ASP cc_start: 0.9024 (m-30) cc_final: 0.8596 (t0)
REVERT: B  272 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9078 (m-40)
REVERT: B  274 ASN cc_start: 0.8597 (m-40) cc_final: 0.7977 (p0)
REVERT: B  389 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8280 (mtp)
  outliers start: 9
  outliers final: 3
  residues processed: 54
  average time/residue: 0.0655
  time to fit residues: 5.4149
Evaluate side-chains
  55 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 489 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.073077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.058694 restraints weight = 19096.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 3.28
r_work: 0.2756 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7718  Z= 0.155
  Angle     :  0.474   6.456  10478  Z= 0.260
  Chirality :  0.043   0.143   1158
  Planarity :  0.003   0.042   1336
  Dihedral  :  3.872  17.238    994
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.69 %
    Favored  : 90.48 %
  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 aren not related in a simple way.
  whole:  0.97 (0.29), residues: 906
  helix:  1.48 (0.31), residues: 302
  sheet: -0.20 (0.48), residues: 130
  loop :  0.50 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  95 
 TYR   0.012   0.001   TYR B 236 
 PHE   0.014   0.001   PHE B 506 
 TRP   0.005   0.001   TRP A 192 
 HIS   0.002   0.001   HIS A   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7718)
  covalent geometry    : angle       0.47366 (10478)
  hydrogen bonds       : bond        0.02804 (  288)
  hydrogen bonds       : angle       4.27091 (  819)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  173 ASP cc_start: 0.8931 (m-30) cc_final: 0.8559 (t0)
REVERT: A  272 ASN cc_start: 0.9341 (t0) cc_final: 0.9029 (p0)
REVERT: A  311 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: A  326 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8827 (p)
REVERT: A  389 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8120 (mtp)
REVERT: B  159 GLU cc_start: 0.8973 (mp0) cc_final: 0.8649 (tp30)
REVERT: B  173 ASP cc_start: 0.8953 (m-30) cc_final: 0.8527 (t0)
REVERT: B  272 ASN cc_start: 0.9368 (OUTLIER) cc_final: 0.9086 (m-40)
REVERT: B  274 ASN cc_start: 0.8552 (m-40) cc_final: 0.7984 (p0)
REVERT: B  365 CYS cc_start: 0.7985 (t) cc_final: 0.7690 (p)
REVERT: B  389 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8130 (mtp)
  outliers start: 7
  outliers final: 3
  residues processed: 54
  average time/residue: 0.0685
  time to fit residues: 5.6831
Evaluate side-chains
  57 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  272 ASN
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0570
   chunk 35 optimal weight:    0.2980
   chunk 28 optimal weight:    0.0970
   chunk 6 optimal weight:    0.2980
   chunk 23 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.2896

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 GLN ** 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 = 0.3289 r_free = 0.3289 target = 0.075680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.061521 restraints weight = 19064.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 3.30
r_work: 0.2828 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7718  Z= 0.089
  Angle     :  0.445   6.307  10478  Z= 0.244
  Chirality :  0.042   0.146   1158
  Planarity :  0.003   0.041   1336
  Dihedral  :  3.648  16.252    994
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.57 %
    Favored  : 90.60 %
  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 aren not related in a simple way.
  whole:  1.07 (0.29), residues: 906
  helix:  1.63 (0.31), residues: 302
  sheet: -0.01 (0.47), residues: 130
  loop :  0.45 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 324 
 TYR   0.013   0.001   TYR A 412 
 PHE   0.008   0.001   PHE B 506 
 TRP   0.005   0.001   TRP A 192 
 HIS   0.003   0.000   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7718)
  covalent geometry    : angle       0.44549 (10478)
  hydrogen bonds       : bond        0.02408 (  288)
  hydrogen bonds       : angle       4.10552 (  819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1453.97 seconds
wall clock time: 25 minutes 56.28 seconds (1556.28 seconds total)