Starting phenix.real_space_refine
on Tue Jan 14 02:23:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xm6_38465/01_2025/8xm6_38465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xm6_38465/01_2025/8xm6_38465.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xm6_38465/01_2025/8xm6_38465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xm6_38465/01_2025/8xm6_38465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xm6_38465/01_2025/8xm6_38465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xm6_38465/01_2025/8xm6_38465.cif"
  }
  resolution = 3.48
  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=  -0.001 sd=   0.102
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: 5
    Type Number    sf(0)   Gaussians
     Zn      6      6.06       5
     S      52      5.16       5
     C    3422      2.51       5
     N     827      2.21       5
     O     898      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5205
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2442
          Classifications: {'peptide': 322}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 12, 'TRANS': 309}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "A"
      Number of atoms: 2444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2444
          Classifications: {'peptide': 323}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 12, 'TRANS': 310}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 177
          Unusual residues: {' ZN': 3, 'AV0': 1, 'Y01': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "A"
      Number of atoms: 142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 142
          Unusual residues: {' ZN': 3, 'AV0': 1, 'Y01': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2338  SG  CYS B 433      39.864  24.143  26.658  1.00 72.85           S
  ATOM   4810  SG  CYS A 437      39.094  30.166  53.026  1.00 69.64           S
  ATOM   2436  SG  CYS B 446      37.845  32.662  27.780  1.00 49.37           S
  ATOM   2442  SG  CYS B 447      41.991  33.675  26.705  1.00 50.90           S
  ATOM   4782  SG  CYS A 433      30.984  24.325  45.844  1.00 71.84           S
  ATOM   2366  SG  CYS B 437      31.037  26.848  20.080  1.00 74.96           S
  ATOM   4880  SG  CYS A 446      31.054  33.460  43.352  1.00 57.72           S
  ATOM   4886  SG  CYS A 447      27.237  34.038  44.096  1.00 57.24           S

  Time building chain proxies: 4.19, per 1000 atoms: 0.80
  Number of scatterers: 5205
  At special positions: 0
  Unit cell: (65.728, 119.808, 68.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      6     29.99
     S      52     16.00
     O     898      8.00
     N     827      7.00
     C    3422      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 282 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 387 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 370 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 433 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS B 437 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A 413 "
        pdb="ZN    ZN A 602 " - pdb=" NE2 HIS A 408 "
      pdb="  ZN A 603 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS A 373 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 446 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 447 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS B 370 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B 387 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 433 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" ND1 HIS B 413 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS A 437 "
        pdb="ZN    ZN B 602 " - pdb=" ND1 HIS B 408 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B 373 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 447 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 446 "


  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      65.1% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 33
      removed outlier: 3.515A  pdb=" N   ARG B  10 " --> pdb=" O   ARG B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 42
      removed outlier: 3.858A  pdb=" N   PHE B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 63
      removed outlier: 4.137A  pdb=" N   ARG B  63 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 106
    Processing helix  chain 'B' and resid 112 through 135
    Processing helix  chain 'B' and resid 241 through 272
    Processing helix  chain 'B' and resid 289 through 293
    Processing helix  chain 'B' and resid 315 through 344
      Proline residue:  B 334  - end of helix
    Processing helix  chain 'B' and resid 352 through 362
    Processing helix  chain 'B' and resid 395 through 410
      removed outlier: 3.807A  pdb=" N   VAL B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   HIS B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 33
    Processing helix  chain 'A' and resid 34 through 44
      removed outlier: 3.691A  pdb=" N   LEU A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 62
      removed outlier: 3.809A  pdb=" N   ARG A  62 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 75
      No H-bonds generated for 'chain 'A' and resid 73 through 75'
    Processing helix  chain 'A' and resid 76 through 106
    Processing helix  chain 'A' and resid 112 through 136
      removed outlier: 3.637A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 112 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   HIS A 136 " --> pdb=" O   CYS A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 272
      removed outlier: 3.551A  pdb=" N   ASP A 255 " --> pdb=" O   HIS A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 293
    Processing helix  chain 'A' and resid 310 through 314
      removed outlier: 3.559A  pdb=" N   VAL A 313 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 344
      removed outlier: 4.029A  pdb=" N   THR A 319 " --> pdb=" O   TYR A 315 " (cutoff:3.500A)
      Proline residue:  A 334  - end of helix
    Processing helix  chain 'A' and resid 352 through 361
    Processing helix  chain 'A' and resid 396 through 409
      removed outlier: 3.645A  pdb=" N   THR A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 369 through 376
      removed outlier: 7.152A  pdb=" N   VAL B 369 " --> pdb=" O   LYS B 389 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   LYS B 389 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   GLU B 371 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   HIS B 387 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 376
      removed outlier: 6.872A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ILE A 382 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   THR A 416 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ALA A 384 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   GLN A 418 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ALA A 386 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)

    328 hydrogen bonds defined for protein.
    969 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: 1.36

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 862
        1.32 -     1.45: 1277
        1.45 -     1.57: 3108
        1.57 -     1.69: 0
        1.69 -     1.82: 72
  Bond restraints: 5319
  Sorted by residual:
  bond pdb=" CAX Y01 B 606 "
       pdb=" OAF Y01 B 606 "
    ideal  model  delta    sigma   weight residual
    1.247  1.308 -0.061 2.00e-02 2.50e+03 9.40e+00
  bond pdb=" CAX Y01 B 607 "
       pdb=" OAF Y01 B 607 "
    ideal  model  delta    sigma   weight residual
    1.247  1.308 -0.061 2.00e-02 2.50e+03 9.28e+00
  bond pdb=" CAX Y01 A 605 "
       pdb=" OAH Y01 A 605 "
    ideal  model  delta    sigma   weight residual
    1.248  1.308 -0.060 2.00e-02 2.50e+03 9.07e+00
  bond pdb=" CAX Y01 B 605 "
       pdb=" OAH Y01 B 605 "
    ideal  model  delta    sigma   weight residual
    1.248  1.308 -0.060 2.00e-02 2.50e+03 9.05e+00
  bond pdb=" CAX Y01 A 606 "
       pdb=" OAF Y01 A 606 "
    ideal  model  delta    sigma   weight residual
    1.247  1.307 -0.060 2.00e-02 2.50e+03 8.98e+00
  ... (remaining 5314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6994
        1.55 -     3.10: 222
        3.10 -     4.65: 37
        4.65 -     6.20: 12
        6.20 -     7.75: 7
  Bond angle restraints: 7272
  Sorted by residual:
  angle pdb=" C   HIS A 408 "
        pdb=" CA  HIS A 408 "
        pdb=" CB  HIS A 408 "
      ideal   model   delta    sigma   weight residual
     110.67  103.96    6.71 1.92e+00 2.71e-01 1.22e+01
  angle pdb=" N   ILE B 412 "
        pdb=" CA  ILE B 412 "
        pdb=" C   ILE B 412 "
      ideal   model   delta    sigma   weight residual
     109.55  113.39   -3.84 1.38e+00 5.25e-01 7.75e+00
  angle pdb=" C   HIS B 413 "
        pdb=" CA  HIS B 413 "
        pdb=" CB  HIS B 413 "
      ideal   model   delta    sigma   weight residual
     110.42  115.83   -5.41 1.99e+00 2.53e-01 7.38e+00
  angle pdb=" C   ILE B 412 "
        pdb=" CA  ILE B 412 "
        pdb=" CB  ILE B 412 "
      ideal   model   delta    sigma   weight residual
     111.63  107.99    3.64 1.38e+00 5.25e-01 6.96e+00
  angle pdb=" CA  ILE B 412 "
        pdb=" C   ILE B 412 "
        pdb=" N   HIS B 413 "
      ideal   model   delta    sigma   weight residual
     115.82  119.77   -3.95 1.52e+00 4.33e-01 6.74e+00
  ... (remaining 7267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.10: 3287
       28.10 -    56.20: 164
       56.20 -    84.30: 44
       84.30 -   112.39: 41
      112.39 -   140.49: 18
  Dihedral angle restraints: 3554
    sinusoidal: 1687
      harmonic: 1867
  Sorted by residual:
  dihedral pdb=" CB  CYS B 276 "
           pdb=" SG  CYS B 276 "
           pdb=" SG  CYS B 282 "
           pdb=" CB  CYS B 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.33   90.33     1      1.00e+01 1.00e-02 9.66e+01
  dihedral pdb=" OAJ AV0 A 604 "
           pdb=" CBN AV0 A 604 "
           pdb=" CCD AV0 A 604 "
           pdb=" OBZ AV0 A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.90  -75.59  140.49     1      3.00e+01 1.11e-03 1.89e+01
  dihedral pdb=" CCO AV0 A 604 "
           pdb=" CBN AV0 A 604 "
           pdb=" CCD AV0 A 604 "
           pdb=" OAJ AV0 A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.12  -46.66 -139.22     1      3.00e+01 1.11e-03 1.87e+01
  ... (remaining 3551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 655
       0.042 -    0.083: 205
       0.083 -    0.125: 45
       0.125 -    0.166: 5
       0.166 -    0.208: 6
  Chirality restraints: 916
  Sorted by residual:
  chirality pdb=" CCV AV0 A 604 "
            pdb=" CCR AV0 A 604 "
            pdb=" CCT AV0 A 604 "
            pdb=" OAU AV0 A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.50    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CCV AV0 B 604 "
            pdb=" CCR AV0 B 604 "
            pdb=" CCT AV0 B 604 "
            pdb=" OAU AV0 B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.50    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CCW AV0 A 604 "
            pdb=" CCS AV0 A 604 "
            pdb=" CCU AV0 A 604 "
            pdb=" OAV AV0 A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.49    0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 913 not shown)

  Planarity restraints: 853
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 408 "    0.031 2.00e-02 2.50e+03   2.99e-02 1.34e+01
        pdb=" CG  HIS A 408 "   -0.031 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 408 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 408 "   -0.034 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 408 "   -0.012 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 408 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 112 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.74e+00
        pdb=" N   PRO B 113 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 113 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 113 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 407 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" C   PHE B 407 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE B 407 "    0.011 2.00e-02 2.50e+03
        pdb=" N   HIS B 408 "    0.010 2.00e-02 2.50e+03
  ... (remaining 850 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 38
        2.58 -     3.16: 4337
        3.16 -     3.74: 8099
        3.74 -     4.32: 10241
        4.32 -     4.90: 17424
  Nonbonded interactions: 40139
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 420 "
            pdb="ZN    ZN B 601 "
     model   vdw
     2.004 2.230
  nonbonded pdb=" OE2 GLU A 371 "
            pdb="ZN    ZN A 603 "
     model   vdw
     2.004 2.230
  nonbonded pdb=" OE1 GLU B 371 "
            pdb="ZN    ZN B 603 "
     model   vdw
     2.051 2.230
  nonbonded pdb=" OE2 GLU A 420 "
            pdb="ZN    ZN A 601 "
     model   vdw
     2.110 2.230
  nonbonded pdb=" O   LEU B 341 "
            pdb=" OG1 THR B 346 "
     model   vdw
     2.329 3.040
  ... (remaining 40134 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 136 or (resid 240 through 242 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 243 through 357 or (resid 358 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 359 through 390  \ 
or (resid 391 through 392 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 393 through 397 or (resid 398 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 399 through 447 or resid 601 through 606))
  selection = (chain 'B' and (resid 6 through 110 or (resid 111 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 112 through 135 or (resid 136 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 240 through 353 or (resid 35 \ 
4 and (name N or name CA or name C or name O or name CB )) or resid 355 through  \ 
394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 396 through 400 or (resid 401 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 402 through 404 or (resid 405 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 406 through 429 or (resid 430 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 431 through 447 or resid 601 \ 
 through 606))
}

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:             2.380
  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:          0.560
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.200
  Find NCS groups from input model:        0.230
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
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      :  0.004   0.061   5319  Z= 0.295
  Angle     :  0.681   7.753   7272  Z= 0.319
  Chirality :  0.043   0.208    916
  Planarity :  0.004   0.048    853
  Dihedral  : 23.935 140.492   2330
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.70 (0.35), residues: 629
  helix:  3.21 (0.25), residues: 381
  sheet: -0.27 (0.92), residues: 43
  loop : -0.62 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 273 
 HIS   0.029   0.002   HIS A 408 
 PHE   0.011   0.001   PHE B  19 
 TYR   0.006   0.001   TYR A 270 
 ARG   0.004   0.000   ARG A  63 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: B  245 MET cc_start: 0.6134 (ttm) cc_final: 0.5895 (tpp)
REVERT: B  359 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7189 (mp0)
REVERT: A  245 MET cc_start: 0.6235 (tmm) cc_final: 0.6017 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1636
  time to fit residues: 25.9240
Evaluate side-chains
  110 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
B 111 GLN
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 410 HIS
A 108 HIS
A 127 ASN
** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.192689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.157494 restraints weight = 5264.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.14
r_work: 0.3571 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5319  Z= 0.191
  Angle     :  0.633   8.214   7272  Z= 0.279
  Chirality :  0.045   0.370    916
  Planarity :  0.004   0.034    853
  Dihedral  : 14.313 122.284   1282
  Min Nonbonded Distance : 1.554

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.51 %
    Favored  : 84.94 %
  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:  2.79 (0.36), residues: 629
  helix:  3.03 (0.25), residues: 392
  sheet: -0.46 (0.91), residues: 45
  loop : -0.13 (0.50), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 273 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.011   0.001   PHE B 407 
 TYR   0.006   0.001   TYR B 396 
 ARG   0.003   0.000   ARG A  63 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.586 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7496 (ttm)
REVERT: B  135 HIS cc_start: 0.7117 (p90) cc_final: 0.6908 (p90)
REVERT: B  245 MET cc_start: 0.7065 (ttm) cc_final: 0.6519 (tpp)
REVERT: B  359 GLU cc_start: 0.7829 (mt-10) cc_final: 0.6998 (mp0)
REVERT: B  397 MET cc_start: 0.6967 (mmm) cc_final: 0.6754 (tpp)
REVERT: A  125 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8244 (mm)
REVERT: A  245 MET cc_start: 0.6096 (tmm) cc_final: 0.5824 (tmm)
REVERT: A  409 ASN cc_start: 0.8024 (m-40) cc_final: 0.7720 (m-40)
  outliers start: 8
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1609
  time to fit residues: 24.9032
Evaluate side-chains
  114 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN
A 345 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.191077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.154982 restraints weight = 5339.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.16
r_work: 0.3582 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5319  Z= 0.192
  Angle     :  0.569   6.069   7272  Z= 0.261
  Chirality :  0.041   0.222    916
  Planarity :  0.004   0.035    853
  Dihedral  : 12.753 146.259   1282
  Min Nonbonded Distance : 1.628

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.25 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.35), residues: 629
  helix:  2.98 (0.25), residues: 392
  sheet: -0.46 (0.89), residues: 45
  loop : -0.18 (0.50), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.007   0.001   PHE B 104 
 TYR   0.006   0.001   TYR B 396 
 ARG   0.002   0.000   ARG A 361 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.599 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7587 (ttm)
REVERT: B  359 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7034 (mp0)
REVERT: B  409 ASN cc_start: 0.7973 (m-40) cc_final: 0.7668 (t0)
REVERT: B  434 GLU cc_start: 0.7530 (pt0) cc_final: 0.7269 (pt0)
REVERT: A  104 PHE cc_start: 0.7659 (m-10) cc_final: 0.7434 (m-80)
REVERT: A  112 GLN cc_start: 0.8029 (pt0) cc_final: 0.7103 (tp40)
REVERT: A  125 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8151 (mm)
REVERT: A  245 MET cc_start: 0.6096 (tmm) cc_final: 0.5666 (tmm)
REVERT: A  409 ASN cc_start: 0.8104 (m-40) cc_final: 0.7768 (m-40)
  outliers start: 19
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1568
  time to fit residues: 26.4989
Evaluate side-chains
  128 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  369 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN
** A 373 HIS ** 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 = 0.4149 r_free = 0.4149 target = 0.191610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.155553 restraints weight = 5427.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 2.16
r_work: 0.3592 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5319  Z= 0.180
  Angle     :  0.547   6.688   7272  Z= 0.251
  Chirality :  0.040   0.195    916
  Planarity :  0.003   0.035    853
  Dihedral  : 11.915 134.615   1282
  Min Nonbonded Distance : 1.651

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.34 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.35), residues: 629
  helix:  2.95 (0.25), residues: 392
  sheet: -0.42 (0.89), residues: 45
  loop : -0.17 (0.51), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.009   0.001   PHE B  21 
 TYR   0.013   0.001   TYR B 396 
 ARG   0.002   0.000   ARG A  63 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.544 
Fit side-chains
REVERT: B   19 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8153 (t80)
REVERT: B   44 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7604 (ttm)
REVERT: B  359 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6995 (mp0)
REVERT: B  409 ASN cc_start: 0.7988 (m-40) cc_final: 0.7686 (t0)
REVERT: A   58 GLU cc_start: 0.8270 (tp30) cc_final: 0.8004 (tp30)
REVERT: A  104 PHE cc_start: 0.7639 (m-10) cc_final: 0.7425 (m-80)
REVERT: A  125 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8148 (mm)
REVERT: A  245 MET cc_start: 0.6135 (tmm) cc_final: 0.5675 (tmm)
REVERT: A  409 ASN cc_start: 0.8189 (m-40) cc_final: 0.7857 (m-40)
  outliers start: 15
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1814
  time to fit residues: 29.2942
Evaluate side-chains
  123 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  369 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 50 optimal weight:   40.0000
   chunk 53 optimal weight:    0.0470
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.6482

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 373 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 = 0.4158 r_free = 0.4158 target = 0.192440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156443 restraints weight = 5356.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.16
r_work: 0.3589 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5319  Z= 0.173
  Angle     :  0.534   7.092   7272  Z= 0.248
  Chirality :  0.039   0.190    916
  Planarity :  0.003   0.036    853
  Dihedral  : 11.395 122.925   1282
  Min Nonbonded Distance : 1.680

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.66 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.74 (0.35), residues: 629
  helix:  3.01 (0.25), residues: 391
  sheet: -0.25 (0.91), residues: 44
  loop : -0.23 (0.50), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.011   0.001   PHE B  21 
 TYR   0.007   0.001   TYR B 396 
 ARG   0.003   0.000   ARG A 361 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.559 
Fit side-chains
REVERT: B   19 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8132 (t80)
REVERT: B   44 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7527 (ttm)
REVERT: B  359 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7031 (mp0)
REVERT: B  409 ASN cc_start: 0.8055 (m-40) cc_final: 0.7760 (t0)
REVERT: A  112 GLN cc_start: 0.7638 (pt0) cc_final: 0.6820 (tp40)
REVERT: A  125 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8146 (mm)
REVERT: A  245 MET cc_start: 0.6053 (tmm) cc_final: 0.5339 (tmm)
REVERT: A  409 ASN cc_start: 0.8231 (m-40) cc_final: 0.7875 (m-40)
  outliers start: 15
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1732
  time to fit residues: 27.5005
Evaluate side-chains
  123 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  369 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0670
   chunk 41 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN
** A 373 HIS ** 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 = 0.4159 r_free = 0.4159 target = 0.192888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.156620 restraints weight = 5395.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 2.17
r_work: 0.3604 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5319  Z= 0.164
  Angle     :  0.533   6.516   7272  Z= 0.245
  Chirality :  0.039   0.192    916
  Planarity :  0.003   0.036    853
  Dihedral  : 10.889 108.969   1282
  Min Nonbonded Distance : 1.693

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.81 %
    Favored  : 74.52 %
  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:  2.79 (0.35), residues: 629
  helix:  3.05 (0.25), residues: 393
  sheet: -0.21 (0.91), residues: 44
  loop : -0.28 (0.50), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 375 
 HIS   0.007   0.001   HIS B 135 
 PHE   0.011   0.001   PHE B  21 
 TYR   0.005   0.001   TYR B 396 
 ARG   0.004   0.000   ARG A  63 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8098 (t80)
REVERT: B   44 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7464 (ttm)
REVERT: B  245 MET cc_start: 0.7004 (ttm) cc_final: 0.6771 (tpp)
REVERT: B  359 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7095 (mp0)
REVERT: B  397 MET cc_start: 0.6738 (mmm) cc_final: 0.5539 (mtp)
REVERT: B  409 ASN cc_start: 0.8128 (m-40) cc_final: 0.7813 (t0)
REVERT: A  112 GLN cc_start: 0.7594 (pt0) cc_final: 0.6789 (tp40)
REVERT: A  125 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (mm)
REVERT: A  245 MET cc_start: 0.6063 (tmm) cc_final: 0.5327 (tmm)
  outliers start: 19
  outliers final: 9
  residues processed: 124
  average time/residue: 0.1812
  time to fit residues: 28.8025
Evaluate side-chains
  122 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.192452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.156262 restraints weight = 5379.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.18
r_work: 0.3590 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5319  Z= 0.178
  Angle     :  0.554   7.942   7272  Z= 0.254
  Chirality :  0.039   0.193    916
  Planarity :  0.004   0.036    853
  Dihedral  : 10.630 104.251   1282
  Min Nonbonded Distance : 1.708

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.62 %
    Favored  : 74.32 %
  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:  2.75 (0.35), residues: 629
  helix:  3.00 (0.25), residues: 393
  sheet: -0.29 (0.91), residues: 44
  loop : -0.21 (0.50), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.008   0.001   PHE B 104 
 TYR   0.005   0.001   TYR B 396 
 ARG   0.006   0.001   ARG B 361 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8122 (t80)
REVERT: B   44 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7447 (ttm)
REVERT: B  106 GLU cc_start: 0.7127 (mp0) cc_final: 0.6682 (tp30)
REVERT: B  245 MET cc_start: 0.6998 (ttm) cc_final: 0.6762 (tpp)
REVERT: B  359 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7155 (mp0)
REVERT: B  397 MET cc_start: 0.6773 (mmm) cc_final: 0.5595 (mtp)
REVERT: B  409 ASN cc_start: 0.8184 (m-40) cc_final: 0.7823 (t0)
REVERT: A  112 GLN cc_start: 0.7634 (pt0) cc_final: 0.6635 (tp40)
REVERT: A  125 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8147 (mm)
REVERT: A  245 MET cc_start: 0.5987 (tmm) cc_final: 0.5309 (tmm)
  outliers start: 21
  outliers final: 13
  residues processed: 119
  average time/residue: 0.1690
  time to fit residues: 26.7092
Evaluate side-chains
  126 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  399 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    0.0010
   chunk 2 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0570
   chunk 41 optimal weight:    0.9980
   chunk 46 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.4304

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.194556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.158165 restraints weight = 5458.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.20
r_work: 0.3612 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5319  Z= 0.160
  Angle     :  0.541   7.382   7272  Z= 0.247
  Chirality :  0.039   0.192    916
  Planarity :  0.003   0.034    853
  Dihedral  : 10.091 104.435   1282
  Min Nonbonded Distance : 1.699

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.01 %
    Favored  : 74.52 %
  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:  2.79 (0.35), residues: 629
  helix:  3.04 (0.25), residues: 393
  sheet: -0.40 (0.91), residues: 45
  loop : -0.18 (0.51), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.018   0.001   PHE B  21 
 TYR   0.006   0.001   TYR B 396 
 ARG   0.007   0.000   ARG B 361 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8072 (t80)
REVERT: B   44 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7366 (ttm)
REVERT: B  106 GLU cc_start: 0.7119 (mp0) cc_final: 0.6649 (tp30)
REVERT: B  245 MET cc_start: 0.6986 (ttm) cc_final: 0.6755 (tpp)
REVERT: B  359 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7200 (mp0)
REVERT: B  397 MET cc_start: 0.6227 (mmm) cc_final: 0.5518 (mtp)
REVERT: B  409 ASN cc_start: 0.8262 (m-40) cc_final: 0.7858 (t0)
REVERT: A  112 GLN cc_start: 0.7626 (pt0) cc_final: 0.6793 (tp40)
REVERT: A  125 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8123 (mm)
REVERT: A  245 MET cc_start: 0.6010 (tmm) cc_final: 0.5342 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1676
  time to fit residues: 26.3907
Evaluate side-chains
  122 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 56 optimal weight:    0.0270
   chunk 24 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0980
   chunk 33 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 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 = 0.4192 r_free = 0.4192 target = 0.195914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.160135 restraints weight = 5382.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.19
r_work: 0.3640 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5319  Z= 0.153
  Angle     :  0.530   7.138   7272  Z= 0.244
  Chirality :  0.039   0.192    916
  Planarity :  0.003   0.034    853
  Dihedral  :  9.319 104.318   1282
  Min Nonbonded Distance : 1.707

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.20 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.93 (0.35), residues: 629
  helix:  3.13 (0.25), residues: 390
  sheet: -0.13 (0.91), residues: 44
  loop : -0.10 (0.50), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 375 
 HIS   0.007   0.001   HIS B 135 
 PHE   0.009   0.001   PHE B 104 
 TYR   0.004   0.000   TYR B 396 
 ARG   0.006   0.000   ARG B 361 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.672 
Fit side-chains
REVERT: B   19 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8070 (t80)
REVERT: B   44 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7263 (ttm)
REVERT: B  106 GLU cc_start: 0.7080 (mp0) cc_final: 0.6677 (tp30)
REVERT: B  245 MET cc_start: 0.6946 (ttm) cc_final: 0.6644 (ttm)
REVERT: B  359 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7193 (mp0)
REVERT: B  397 MET cc_start: 0.6079 (mmm) cc_final: 0.5546 (mtp)
REVERT: B  409 ASN cc_start: 0.8266 (m-40) cc_final: 0.7871 (t0)
REVERT: A  112 GLN cc_start: 0.7542 (pt0) cc_final: 0.6623 (tp40)
REVERT: A  125 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8108 (mm)
REVERT: A  245 MET cc_start: 0.5918 (tmm) cc_final: 0.5257 (tmm)
  outliers start: 16
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1474
  time to fit residues: 22.5469
Evaluate side-chains
  117 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.189744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.153186 restraints weight = 5439.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.19
r_work: 0.3512 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5319  Z= 0.246
  Angle     :  0.602   7.187   7272  Z= 0.281
  Chirality :  0.041   0.199    916
  Planarity :  0.004   0.035    853
  Dihedral  :  9.748 102.413   1282
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.01 %
    Favored  : 74.90 %
  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:  2.64 (0.35), residues: 629
  helix:  2.85 (0.25), residues: 388
  sheet: -0.57 (0.87), residues: 47
  loop :  0.06 (0.50), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 375 
 HIS   0.009   0.002   HIS B 135 
 PHE   0.013   0.001   PHE B  21 
 TYR   0.008   0.001   TYR B 396 
 ARG   0.007   0.001   ARG B 361 

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8117 (t80)
REVERT: B   44 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7461 (ttm)
REVERT: B   63 ARG cc_start: 0.7891 (ptp-170) cc_final: 0.7690 (ptp-170)
REVERT: B  106 GLU cc_start: 0.7175 (mp0) cc_final: 0.6654 (tp30)
REVERT: B  245 MET cc_start: 0.7135 (ttm) cc_final: 0.6899 (tpp)
REVERT: B  359 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7123 (mp0)
REVERT: B  397 MET cc_start: 0.6288 (mmm) cc_final: 0.5489 (mtp)
REVERT: B  409 ASN cc_start: 0.8361 (m-40) cc_final: 0.8010 (m110)
REVERT: A  125 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8148 (mm)
  outliers start: 16
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1692
  time to fit residues: 25.5320
Evaluate side-chains
  120 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0770
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.191991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.155778 restraints weight = 5472.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.21
r_work: 0.3587 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5319  Z= 0.181
  Angle     :  0.555   6.976   7272  Z= 0.260
  Chirality :  0.040   0.194    916
  Planarity :  0.003   0.034    853
  Dihedral  :  9.466 102.873   1282
  Min Nonbonded Distance : 1.738

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.81 %
    Favored  : 74.90 %
  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:  2.70 (0.36), residues: 629
  helix:  2.96 (0.25), residues: 389
  sheet: -0.49 (0.90), residues: 45
  loop : -0.10 (0.50), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 375 
 HIS   0.009   0.001   HIS B 135 
 PHE   0.009   0.001   PHE B 104 
 TYR   0.006   0.001   TYR B 396 
 ARG   0.006   0.000   ARG B 361 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2573.74 seconds
wall clock time: 48 minutes 9.51 seconds (2889.51 seconds total)