Starting phenix.real_space_refine
on Thu Jun  5 04:20:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xm6_38465/06_2025/8xm6_38465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xm6_38465/06_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_38465/06_2025/8xm6_38465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xm6_38465/06_2025/8xm6_38465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xm6_38465/06_2025/8xm6_38465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xm6_38465/06_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-5710/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: 4.41, per 1000 atoms: 0.85
  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: 1.60
  Conformation dependent library (CDL) restraints added in 866.6 milliseconds
  
  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: 0.48
  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: 1.32

  Time building geometry restraints manager: 1.84 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:             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:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     18.750
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.170
-------------------------------------------------------------------------------
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      :  0.015   0.502   5339  Z= 0.524
  Angle     :  0.681   7.753   7276  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12957 (  328)
  hydrogen bonds       : angle       4.09099 (  969)
  metal coordination   : bond        0.24471 (   18)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.61137 (    4)
  covalent geometry    : bond        0.00449 ( 5319)
  covalent geometry    : angle       0.68110 ( 7272)

*********************** 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  : 0.550 
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: 0.1610
  time to fit residues: 25.3992
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  : 0.551 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.192307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157208 restraints weight = 5257.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.13
r_work: 0.3600 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5339  Z= 0.133
  Angle     :  0.636   8.643   7276  Z= 0.280
  Chirality :  0.045   0.352    916
  Planarity :  0.004   0.034    853
  Dihedral  : 13.806 121.989   1282
  Min Nonbonded Distance : 1.519

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.71 %
    Favored  : 84.75 %
  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 (0.36), residues: 629
  helix:  3.00 (0.25), residues: 394
  sheet: -0.48 (0.90), residues: 45
  loop : -0.16 (0.51), residues: 190

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   0.005   0.001   TYR B 396 
 ARG   0.003   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  328)
  hydrogen bonds       : angle       3.31466 (  969)
  metal coordination   : bond        0.00967 (   18)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.36657 (    4)
  covalent geometry    : bond        0.00295 ( 5319)
  covalent geometry    : angle       0.63585 ( 7272)

*********************** 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
  120 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.499 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7539 (ttm)
REVERT: B  106 GLU cc_start: 0.7262 (mp0) cc_final: 0.6360 (pt0)
REVERT: B  135 HIS cc_start: 0.7127 (p90) cc_final: 0.6913 (p90)
REVERT: B  245 MET cc_start: 0.7074 (ttm) cc_final: 0.6517 (tpp)
REVERT: B  359 GLU cc_start: 0.7802 (mt-10) cc_final: 0.6967 (mp0)
REVERT: A  125 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (mm)
REVERT: A  245 MET cc_start: 0.5979 (tmm) cc_final: 0.5710 (tmm)
REVERT: A  409 ASN cc_start: 0.8030 (m-40) cc_final: 0.7740 (m-40)
  outliers start: 8
  outliers final: 2
  residues processed: 116
  average time/residue: 0.1527
  time to fit residues: 23.3600
Evaluate side-chains
  112 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:   30.0000
   chunk 2 optimal weight:    0.5980
   chunk 25 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 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 410 HIS
A 127 ASN
A 345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.191949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.155921 restraints weight = 5314.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.15
r_work: 0.3571 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5339  Z= 0.117
  Angle     :  0.561   6.229   7276  Z= 0.256
  Chirality :  0.041   0.222    916
  Planarity :  0.004   0.033    853
  Dihedral  : 12.685 145.983   1282
  Min Nonbonded Distance : 1.636

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.06 %
    Favored  : 81.27 %
  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:  3.00 (0.25), residues: 392
  sheet: -0.38 (0.90), residues: 45
  loop : -0.19 (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   0.006   0.001   TYR B 396 
 ARG   0.002   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  328)
  hydrogen bonds       : angle       3.20148 (  969)
  metal coordination   : bond        0.00249 (   18)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.32647 (    4)
  covalent geometry    : bond        0.00272 ( 5319)
  covalent geometry    : angle       0.56102 ( 7272)

*********************** 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  : 0.534 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7528 (ttm)
REVERT: B  359 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7074 (mp0)
REVERT: B  371 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7221 (mm-30)
REVERT: B  409 ASN cc_start: 0.7930 (m-40) cc_final: 0.7629 (t0)
REVERT: B  434 GLU cc_start: 0.7565 (pt0) cc_final: 0.7298 (pt0)
REVERT: A  104 PHE cc_start: 0.7624 (m-10) cc_final: 0.7414 (m-80)
REVERT: A  112 GLN cc_start: 0.8000 (pt0) cc_final: 0.7110 (tp40)
REVERT: A  125 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8154 (mm)
REVERT: A  245 MET cc_start: 0.6122 (tmm) cc_final: 0.5671 (tmm)
REVERT: A  409 ASN cc_start: 0.8154 (m-40) cc_final: 0.7846 (m-40)
  outliers start: 19
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1428
  time to fit residues: 24.3550
Evaluate side-chains
  129 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  338 GLU
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:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.187592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.151083 restraints weight = 5404.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.15
r_work: 0.3540 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5339  Z= 0.155
  Angle     :  0.594   6.542   7276  Z= 0.277
  Chirality :  0.041   0.197    916
  Planarity :  0.004   0.036    853
  Dihedral  : 12.033 131.185   1282
  Min Nonbonded Distance : 1.657

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.15 %
    Favored  : 77.80 %
  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:  2.45 (0.35), residues: 629
  helix:  2.77 (0.25), residues: 391
  sheet: -0.70 (0.90), residues: 44
  loop : -0.22 (0.50), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.010   0.001   PHE A  21 
 TYR   0.006   0.001   TYR A 396 
 ARG   0.002   0.000   ARG B 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03749 (  328)
  hydrogen bonds       : angle       3.30067 (  969)
  metal coordination   : bond        0.00247 (   18)
  SS BOND              : bond        0.00203 (    2)
  SS BOND              : angle       0.43211 (    4)
  covalent geometry    : bond        0.00373 ( 5319)
  covalent geometry    : angle       0.59442 ( 7272)

*********************** 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
  139 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.543 
Fit side-chains
REVERT: B   19 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8215 (t80)
REVERT: B   44 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7648 (ttm)
REVERT: B  245 MET cc_start: 0.7155 (ttm) cc_final: 0.6925 (tpp)
REVERT: B  359 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6993 (mp0)
REVERT: B  409 ASN cc_start: 0.8063 (m-40) cc_final: 0.7737 (t0)
REVERT: A  125 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8222 (mm)
REVERT: A  245 MET cc_start: 0.6188 (tmm) cc_final: 0.5733 (tmm)
REVERT: A  409 ASN cc_start: 0.8301 (m-40) cc_final: 0.7954 (m-40)
  outliers start: 21
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1640
  time to fit residues: 27.2205
Evaluate side-chains
  130 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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  104 PHE
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  338 GLU
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  263 VAL
Chi-restraints excluded: chain A residue  311 CYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0770
   chunk 53 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.6340

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.192051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155921 restraints weight = 5334.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.17
r_work: 0.3582 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5339  Z= 0.110
  Angle     :  0.539   6.321   7276  Z= 0.250
  Chirality :  0.039   0.192    916
  Planarity :  0.003   0.034    853
  Dihedral  : 11.400 120.598   1282
  Min Nonbonded Distance : 1.653

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.04 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.63 (0.35), residues: 629
  helix:  2.93 (0.25), residues: 392
  sheet: -0.51 (0.92), residues: 44
  loop : -0.24 (0.50), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.012   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 333 
 ARG   0.002   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03289 (  328)
  hydrogen bonds       : angle       3.16419 (  969)
  metal coordination   : bond        0.00146 (   18)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.34358 (    4)
  covalent geometry    : bond        0.00258 ( 5319)
  covalent geometry    : angle       0.53930 ( 7272)

*********************** 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
  133 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8156 (t80)
REVERT: B   44 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7504 (ttm)
REVERT: B  245 MET cc_start: 0.6981 (ttm) cc_final: 0.6739 (tpp)
REVERT: B  359 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7009 (mp0)
REVERT: B  409 ASN cc_start: 0.8117 (m-40) cc_final: 0.7788 (t0)
REVERT: A  112 GLN cc_start: 0.7851 (pt0) cc_final: 0.6978 (tp40)
REVERT: A  125 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8171 (mm)
REVERT: A  245 MET cc_start: 0.6104 (tmm) cc_final: 0.5763 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 122
  average time/residue: 0.1945
  time to fit residues: 30.9545
Evaluate side-chains
  125 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   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 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 = 0.4128 r_free = 0.4128 target = 0.189309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.152903 restraints weight = 5355.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.15
r_work: 0.3558 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5339  Z= 0.140
  Angle     :  0.585   7.859   7276  Z= 0.270
  Chirality :  0.040   0.196    916
  Planarity :  0.004   0.035    853
  Dihedral  : 11.239 110.458   1282
  Min Nonbonded Distance : 1.699

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 20.66 %
    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:  2.54 (0.35), residues: 629
  helix:  2.85 (0.25), residues: 390
  sheet: -0.69 (0.91), residues: 44
  loop : -0.17 (0.50), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B 135 
 PHE   0.011   0.001   PHE B  21 
 TYR   0.005   0.001   TYR A 333 
 ARG   0.004   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  328)
  hydrogen bonds       : angle       3.25582 (  969)
  metal coordination   : bond        0.00201 (   18)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.36902 (    4)
  covalent geometry    : bond        0.00338 ( 5319)
  covalent geometry    : angle       0.58461 ( 7272)

*********************** 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
  133 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8185 (t80)
REVERT: B   25 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7558 (tm-30)
REVERT: B   44 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7583 (ttm)
REVERT: B  245 MET cc_start: 0.6993 (ttm) cc_final: 0.6757 (tpp)
REVERT: B  359 GLU cc_start: 0.7770 (mt-10) cc_final: 0.6973 (mp0)
REVERT: B  397 MET cc_start: 0.6848 (tpp) cc_final: 0.5814 (ptp)
REVERT: B  409 ASN cc_start: 0.8230 (m-40) cc_final: 0.7843 (t0)
REVERT: A  112 GLN cc_start: 0.7829 (pt0) cc_final: 0.6928 (tp40)
REVERT: A  125 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8173 (mm)
REVERT: A  245 MET cc_start: 0.6156 (tmm) cc_final: 0.5789 (tmm)
  outliers start: 24
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1952
  time to fit residues: 30.5928
Evaluate side-chains
  127 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   25 GLU
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  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  314 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  399 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 31 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.191161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.154544 restraints weight = 5365.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.16
r_work: 0.3581 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5339  Z= 0.115
  Angle     :  0.556   6.949   7276  Z= 0.255
  Chirality :  0.039   0.194    916
  Planarity :  0.003   0.034    853
  Dihedral  : 10.686 104.666   1282
  Min Nonbonded Distance : 1.680

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.24 %
    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:  2.70 (0.36), residues: 629
  helix:  2.98 (0.25), residues: 387
  sheet: -0.65 (0.91), residues: 44
  loop : -0.06 (0.50), residues: 198

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   0.011   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 333 
 ARG   0.003   0.000   ARG B 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  328)
  hydrogen bonds       : angle       3.18274 (  969)
  metal coordination   : bond        0.00157 (   18)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.34455 (    4)
  covalent geometry    : bond        0.00276 ( 5319)
  covalent geometry    : angle       0.55582 ( 7272)

*********************** 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
  133 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8172 (t80)
REVERT: B   25 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7512 (pp20)
REVERT: B   44 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7481 (ttm)
REVERT: B  245 MET cc_start: 0.6993 (ttm) cc_final: 0.6750 (tpp)
REVERT: B  359 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7005 (mp0)
REVERT: B  397 MET cc_start: 0.6623 (tpp) cc_final: 0.5677 (mtp)
REVERT: B  409 ASN cc_start: 0.8251 (m-40) cc_final: 0.7808 (t0)
REVERT: A  112 GLN cc_start: 0.7749 (pt0) cc_final: 0.6969 (tp40)
REVERT: A  125 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8165 (mm)
REVERT: A  245 MET cc_start: 0.6092 (tmm) cc_final: 0.5330 (tmm)
  outliers start: 21
  outliers final: 13
  residues processed: 119
  average time/residue: 0.1521
  time to fit residues: 23.7837
Evaluate side-chains
  125 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   25 GLU
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  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  314 LEU
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:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 265 ASN ** 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 = 0.4131 r_free = 0.4131 target = 0.189665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153238 restraints weight = 5407.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.21
r_work: 0.3562 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5339  Z= 0.129
  Angle     :  0.577   6.811   7276  Z= 0.266
  Chirality :  0.040   0.197    916
  Planarity :  0.004   0.035    853
  Dihedral  : 10.387 104.184   1282
  Min Nonbonded Distance : 1.714

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 22.01 %
    Favored  : 73.94 %
  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:  2.63 (0.35), residues: 629
  helix:  2.87 (0.25), residues: 389
  sheet: -0.72 (0.91), residues: 44
  loop : -0.00 (0.50), residues: 196

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   0.011   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 333 
 ARG   0.004   0.000   ARG A 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  328)
  hydrogen bonds       : angle       3.24671 (  969)
  metal coordination   : bond        0.00167 (   18)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.34659 (    4)
  covalent geometry    : bond        0.00310 ( 5319)
  covalent geometry    : angle       0.57754 ( 7272)

*********************** 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: 21
    poor density    : 106
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8186 (t80)
REVERT: B   44 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7503 (ttm)
REVERT: B  135 HIS cc_start: 0.6913 (p90) cc_final: 0.6651 (p90)
REVERT: B  245 MET cc_start: 0.7039 (ttm) cc_final: 0.6803 (tpp)
REVERT: B  359 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7081 (mp0)
REVERT: B  397 MET cc_start: 0.6608 (tpp) cc_final: 0.5594 (mtp)
REVERT: B  409 ASN cc_start: 0.8278 (m-40) cc_final: 0.7816 (t0)
REVERT: A  112 GLN cc_start: 0.7799 (pt0) cc_final: 0.6920 (tp40)
REVERT: A  125 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8180 (mm)
REVERT: A  245 MET cc_start: 0.5942 (tmm) cc_final: 0.5230 (tmm)
  outliers start: 21
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1473
  time to fit residues: 22.5934
Evaluate side-chains
  124 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   24 LEU
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  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  314 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 265 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.190822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154674 restraints weight = 5320.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.17
r_work: 0.3565 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5339  Z= 0.126
  Angle     :  0.566   6.370   7276  Z= 0.262
  Chirality :  0.040   0.196    916
  Planarity :  0.004   0.035    853
  Dihedral  :  9.808 104.123   1282
  Min Nonbonded Distance : 1.704

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 22.39 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.61 (0.35), residues: 629
  helix:  2.89 (0.25), residues: 388
  sheet: -0.76 (0.91), residues: 44
  loop : -0.06 (0.50), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 375 
 HIS   0.009   0.001   HIS B 135 
 PHE   0.011   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 333 
 ARG   0.005   0.000   ARG A 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  328)
  hydrogen bonds       : angle       3.24650 (  969)
  metal coordination   : bond        0.00181 (   18)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.37221 (    4)
  covalent geometry    : bond        0.00302 ( 5319)
  covalent geometry    : angle       0.56640 ( 7272)

*********************** 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
  128 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.584 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7377 (ttm)
REVERT: B  135 HIS cc_start: 0.6921 (p90) cc_final: 0.6640 (p90)
REVERT: B  245 MET cc_start: 0.7017 (ttm) cc_final: 0.6766 (tpp)
REVERT: B  359 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7014 (mp0)
REVERT: B  397 MET cc_start: 0.6597 (tpp) cc_final: 0.5678 (mtp)
REVERT: B  409 ASN cc_start: 0.8295 (m-40) cc_final: 0.7915 (m110)
REVERT: A  125 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8172 (mm)
  outliers start: 21
  outliers final: 16
  residues processed: 116
  average time/residue: 0.2110
  time to fit residues: 32.3568
Evaluate side-chains
  125 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  104 PHE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  338 GLU
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  314 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 31 optimal weight:    0.0980
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
B 370 HIS
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.191497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154937 restraints weight = 5446.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.20
r_work: 0.3584 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.386   5339  Z= 0.211
  Angle     :  0.566   9.050   7276  Z= 0.261
  Chirality :  0.040   0.195    916
  Planarity :  0.003   0.034    853
  Dihedral  :  9.665 103.991   1282
  Min Nonbonded Distance : 1.705

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 22.97 %
    Favored  : 73.36 %
  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:  2.67 (0.35), residues: 629
  helix:  2.95 (0.25), residues: 390
  sheet: -0.70 (0.91), residues: 44
  loop : -0.11 (0.50), residues: 195

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   0.010   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 333 
 ARG   0.003   0.000   ARG A 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  328)
  hydrogen bonds       : angle       3.24198 (  969)
  metal coordination   : bond        0.09098 (   18)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.31048 (    4)
  covalent geometry    : bond        0.00277 ( 5319)
  covalent geometry    : angle       0.56597 ( 7272)

********************** 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
  130 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.559 
Fit side-chains
REVERT: B   44 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7323 (ttm)
REVERT: B  135 HIS cc_start: 0.6870 (p90) cc_final: 0.6583 (p90)
REVERT: B  245 MET cc_start: 0.6997 (ttm) cc_final: 0.6748 (tpp)
REVERT: B  359 GLU cc_start: 0.7796 (mt-10) cc_final: 0.6999 (mp0)
REVERT: B  397 MET cc_start: 0.6528 (tpp) cc_final: 0.5739 (mtp)
REVERT: B  409 ASN cc_start: 0.8327 (m-40) cc_final: 0.7925 (m110)
REVERT: A  125 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8154 (mm)
  outliers start: 19
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1773
  time to fit residues: 27.5107
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  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  314 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:    7.9990
   chunk 56 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.190979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.154028 restraints weight = 5527.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.19
r_work: 0.3575 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5339  Z= 0.115
  Angle     :  0.566   8.727   7276  Z= 0.262
  Chirality :  0.040   0.195    916
  Planarity :  0.003   0.034    853
  Dihedral  :  9.565 103.868   1282
  Min Nonbonded Distance : 1.710

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.97 %
    Favored  : 73.94 %
  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:  2.69 (0.35), residues: 629
  helix:  2.95 (0.25), residues: 389
  sheet: -0.67 (0.91), residues: 44
  loop : -0.06 (0.50), residues: 196

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   0.010   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 333 
 ARG   0.004   0.000   ARG A 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03322 (  328)
  hydrogen bonds       : angle       3.23543 (  969)
  metal coordination   : bond        0.00156 (   18)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       0.30674 (    4)
  covalent geometry    : bond        0.00274 ( 5319)
  covalent geometry    : angle       0.56580 ( 7272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2933.76 seconds
wall clock time: 52 minutes 53.99 seconds (3173.99 seconds total)