Starting phenix.real_space_refine
on Thu Jul 24 01:55:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xmf_38475/07_2025/8xmf_38475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xmf_38475/07_2025/8xmf_38475.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xmf_38475/07_2025/8xmf_38475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xmf_38475/07_2025/8xmf_38475.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xmf_38475/07_2025/8xmf_38475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xmf_38475/07_2025/8xmf_38475.cif"
  }
  resolution = 3.64
  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=  -0.002 sd=   0.060
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      8      6.06       5
     S      52      5.16       5
     C    3245      2.51       5
     N     780      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4929
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2365
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2357
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 71
    Chain: "B"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 121
          Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 10
    Chain: "A"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 86
          Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 10

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2274  SG  CYS B 433      47.132  34.125  96.780  1.00159.45           S
  ATOM   2359  SG  CYS B 446      45.358  32.849  87.669  1.00120.18           S
  ATOM   2365  SG  CYS B 447      45.777  37.314  87.705  1.00125.67           S
  ATOM   4652  SG  CYS A 437      23.534  28.522  91.663  1.00150.23           S
  ATOM   2298  SG  CYS B 437      53.483  28.164  92.832  1.00147.75           S
  ATOM   4628  SG  CYS A 433      29.856  22.059  96.573  1.00150.75           S
  ATOM   4716  SG  CYS A 446      31.375  22.860  86.211  1.00121.94           S
  ATOM   4722  SG  CYS A 447      30.698  18.796  88.022  1.00131.94           S

  Time building chain proxies: 4.45, per 1000 atoms: 0.90
  Number of scatterers: 4929
  At special positions: 0
  Unit cell: (77.376, 56.576, 121.472, 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      8     29.99
     S      52     16.00
     O     844      8.00
     N     780      7.00
     C    3245      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=2.04

  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 786.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 408 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 413 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS B 437 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A 387 "
        pdb="ZN    ZN A 602 " - pdb=" NE2 HIS A 370 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A 433 "
      pdb="  ZN A 603 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS A 373 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 447 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 446 "
      pdb="  ZN A 604 "
        pdb="ZN    ZN A 604 " - pdb=" NE2 HIS A  43 "
        pdb="ZN    ZN A 604 " - pdb=" NE2 HIS A 251 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 433 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS B 370 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B 387 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" NE2 HIS B 373 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 447 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 446 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B 251 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B  43 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS A 437 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 408 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 413 "


  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1208

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 3 sheets defined
      63.7% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'B' and resid 11 through 33
      removed outlier: 4.145A  pdb=" N   LEU B  17 " --> pdb=" O   CYS B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 62
    Processing helix  chain 'B' and resid 76 through 106
    Processing helix  chain 'B' and resid 112 through 133
      removed outlier: 3.507A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 112 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   CYS B 132 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 273
    Processing helix  chain 'B' and resid 291 through 298
      removed outlier: 4.161A  pdb=" N   VAL B 295 " --> pdb=" O   CYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 344
      removed outlier: 4.095A  pdb=" N   VAL B 323 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      Proline residue:  B 334  - end of helix
    Processing helix  chain 'B' and resid 352 through 362
    Processing helix  chain 'B' and resid 399 through 410
      removed outlier: 3.658A  pdb=" N   HIS B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 33
      removed outlier: 3.842A  pdb=" N   LEU A  17 " --> pdb=" O   CYS A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 63
      removed outlier: 4.131A  pdb=" N   ARG A  63 " --> pdb=" O   ARG A  59 " (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 133
    Processing helix  chain 'A' and resid 245 through 273
    Processing helix  chain 'A' and resid 291 through 298
    Processing helix  chain 'A' and resid 315 through 344
      Proline residue:  A 334  - end of helix
    Processing helix  chain 'A' and resid 352 through 362
    Processing helix  chain 'A' and resid 392 through 394
      No H-bonds generated for 'chain 'A' and resid 392 through 394'
    Processing helix  chain 'A' and resid 395 through 410
      removed outlier: 3.666A  pdb=" N   VAL A 399 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   HIS A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 444
    Processing sheet with id=AA1, first strand: chain 'B' and resid 370 through 378
      removed outlier: 5.483A  pdb=" N   GLU B 371 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   HIS B 387 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ARG B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   GLN B 418 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ALA B 386 " --> pdb=" O   GLN B 418 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 376
      removed outlier: 6.518A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 414 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 376
      removed outlier: 6.518A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   GLN A 418 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA A 386 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE A 388 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    954 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: 1.30

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 833
        1.33 -     1.45: 1184
        1.45 -     1.57: 2937
        1.57 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 5026
  Sorted by residual:
  bond pdb=" CA  GLU A 420 "
       pdb=" C   GLU A 420 "
    ideal  model  delta    sigma   weight residual
    1.525  1.475  0.050 1.29e-02 6.01e+03 1.52e+01
  bond pdb=" CA  GLU A 420 "
       pdb=" CB  GLU A 420 "
    ideal  model  delta    sigma   weight residual
    1.525  1.481  0.044 1.29e-02 6.01e+03 1.19e+01
  bond pdb=" CAX Y01 A 606 "
       pdb=" OAF Y01 A 606 "
    ideal  model  delta    sigma   weight residual
    1.247  1.308 -0.061 2.00e-02 2.50e+03 9.39e+00
  bond pdb=" CAX Y01 B 606 "
       pdb=" OAH Y01 B 606 "
    ideal  model  delta    sigma   weight residual
    1.248  1.309 -0.061 2.00e-02 2.50e+03 9.18e+00
  bond pdb=" CAX Y01 B 607 "
       pdb=" OAH Y01 B 607 "
    ideal  model  delta    sigma   weight residual
    1.248  1.308 -0.060 2.00e-02 2.50e+03 9.10e+00
  ... (remaining 5021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 6589
        1.53 -     3.06: 219
        3.06 -     4.58: 50
        4.58 -     6.11: 11
        6.11 -     7.64: 4
  Bond angle restraints: 6873
  Sorted by residual:
  angle pdb=" N   LYS A 444 "
        pdb=" CA  LYS A 444 "
        pdb=" C   LYS A 444 "
      ideal   model   delta    sigma   weight residual
     111.07  107.17    3.90 1.07e+00 8.73e-01 1.33e+01
  angle pdb=" N   GLU B 420 "
        pdb=" CA  GLU B 420 "
        pdb=" C   GLU B 420 "
      ideal   model   delta    sigma   weight residual
     107.69  100.85    6.84 2.01e+00 2.48e-01 1.16e+01
  angle pdb=" CA  PRO A 290 "
        pdb=" C   PRO A 290 "
        pdb=" O   PRO A 290 "
      ideal   model   delta    sigma   weight residual
     121.34  118.15    3.19 1.14e+00 7.69e-01 7.84e+00
  angle pdb=" N   GLN B 440 "
        pdb=" CA  GLN B 440 "
        pdb=" C   GLN B 440 "
      ideal   model   delta    sigma   weight residual
     108.76  113.41   -4.65 1.69e+00 3.50e-01 7.56e+00
  angle pdb=" C   PHE A 287 "
        pdb=" CA  PHE A 287 "
        pdb=" CB  PHE A 287 "
      ideal   model   delta    sigma   weight residual
     108.76  112.27   -3.51 1.37e+00 5.33e-01 6.55e+00
  ... (remaining 6868 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.86: 2995
       26.86 -    53.71: 160
       53.71 -    80.57: 15
       80.57 -   107.43: 19
      107.43 -   134.28: 15
  Dihedral angle restraints: 3204
    sinusoidal: 1357
      harmonic: 1847
  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
      93.00   37.81   55.19     1      1.00e+01 1.00e-02 4.12e+01
  dihedral pdb=" CB  CYS A 276 "
           pdb=" SG  CYS A 276 "
           pdb=" SG  CYS A 282 "
           pdb=" CB  CYS A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.38   45.62     1      1.00e+01 1.00e-02 2.89e+01
  dihedral pdb=" OAJ AV0 B 605 "
           pdb=" CBN AV0 B 605 "
           pdb=" CCD AV0 B 605 "
           pdb=" OBZ AV0 B 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.90  -69.38  134.28     1      3.00e+01 1.11e-03 1.81e+01
  ... (remaining 3201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 731
       0.052 -    0.104: 126
       0.104 -    0.156: 15
       0.156 -    0.208: 2
       0.208 -    0.260: 3
  Chirality restraints: 877
  Sorted by residual:
  chirality pdb=" CA  GLU B 371 "
            pdb=" N   GLU B 371 "
            pdb=" C   GLU B 371 "
            pdb=" CB  GLU B 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  CYS A 291 "
            pdb=" N   CYS A 291 "
            pdb=" C   CYS A 291 "
            pdb=" CB  CYS A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CCV AV0 A 605 "
            pdb=" CCR AV0 A 605 "
            pdb=" CCT AV0 A 605 "
            pdb=" OAU AV0 A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.50    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 874 not shown)

  Planarity restraints: 814
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 284 "   -0.047 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO A 285 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  43 "   -0.020 2.00e-02 2.50e+03   1.79e-02 4.81e+00
        pdb=" CG  HIS B  43 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  43 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  43 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  43 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  43 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 289 "    0.034 5.00e-02 4.00e+02   5.23e-02 4.37e+00
        pdb=" N   PRO A 290 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "    0.029 5.00e-02 4.00e+02
  ... (remaining 811 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 47
        2.57 -     3.15: 4237
        3.15 -     3.73: 7826
        3.73 -     4.32: 9483
        4.32 -     4.90: 15716
  Nonbonded interactions: 37309
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  47 "
            pdb="ZN    ZN B 603 "
     model   vdw
     1.982 2.230
  nonbonded pdb=" OD1 ASP B 255 "
            pdb="ZN    ZN B 603 "
     model   vdw
     1.986 2.230
  nonbonded pdb=" OD2 ASP A  47 "
            pdb="ZN    ZN A 604 "
     model   vdw
     1.987 2.230
  nonbonded pdb=" OE2 GLU A 371 "
            pdb="ZN    ZN A 603 "
     model   vdw
     1.992 2.230
  nonbonded pdb=" OD2 ASP A 255 "
            pdb="ZN    ZN A 604 "
     model   vdw
     1.992 2.230
  ... (remaining 37304 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 11 through 280 or (resid 281 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 282 through 442 or (resid 443 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 444 through 447 or resid 60 \ 
1 through 606))
  selection = (chain 'B' and (resid 11 through 305 or (resid 306 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 307 through 349 or (resid 350 through 352 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 353 through 360 \ 
 or (resid 361 and (name N or name CA or name C or name O or name CB )) or resid \ 
 362 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 group one per residue
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:             1.230
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.660
  Find NCS groups from input model:        0.190
  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:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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   0.283   5050  Z= 0.546
  Angle     :  0.693   7.640   6877  Z= 0.365
  Chirality :  0.042   0.260    877
  Planarity :  0.005   0.072    814
  Dihedral  : 19.980 134.282   1990
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.35), residues: 620
  helix:  2.05 (0.26), residues: 378
  sheet:  0.32 (0.89), residues: 42
  loop : -1.29 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 312 
 HIS   0.015   0.001   HIS B  43 
 PHE   0.026   0.001   PHE B 294 
 TYR   0.009   0.001   TYR B 396 
 ARG   0.001   0.000   ARG A  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08781 (  316)
  hydrogen bonds       : angle       4.22056 (  954)
  metal coordination   : bond        0.21669 (   22)
  SS BOND              : bond        0.00619 (    2)
  SS BOND              : angle       1.12772 (    4)
  covalent geometry    : bond        0.00469 ( 5026)
  covalent geometry    : angle       0.69236 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.542 
Fit side-chains
REVERT: B   99 GLU cc_start: 0.8673 (tp30) cc_final: 0.8400 (tp30)
REVERT: B  103 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8783 (ttm110)
REVERT: B  355 ASN cc_start: 0.8121 (t0) cc_final: 0.7864 (t0)
REVERT: B  360 LEU cc_start: 0.9467 (mm) cc_final: 0.9245 (mm)
REVERT: B  408 HIS cc_start: 0.9138 (t70) cc_final: 0.8489 (t70)
REVERT: A   41 SER cc_start: 0.9339 (p) cc_final: 0.8660 (p)
REVERT: A   59 ARG cc_start: 0.8428 (ttm170) cc_final: 0.7961 (tpm170)
REVERT: A   99 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7773 (mm-30)
REVERT: A  294 PHE cc_start: 0.8003 (t80) cc_final: 0.7623 (t80)
REVERT: A  380 SER cc_start: 0.9221 (t) cc_final: 0.8934 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1494
  time to fit residues: 37.5198
Evaluate side-chains
  168 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0570
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 GLN
B 413 HIS
** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 HIS
A 127 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.180820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.131833 restraints weight = 7255.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.137356 restraints weight = 3952.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.140892 restraints weight = 2795.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.028   1.964   5050  Z= 0.931
  Angle     :  0.646   8.245   6877  Z= 0.310
  Chirality :  0.043   0.355    877
  Planarity :  0.004   0.047    814
  Dihedral  : 13.342 102.761   1019
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.72 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.35), residues: 620
  helix:  2.14 (0.26), residues: 378
  sheet: -0.25 (0.82), residues: 48
  loop : -1.17 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 273 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.016   0.001   PHE A  19 
 TYR   0.014   0.001   TYR A 270 
 ARG   0.002   0.000   ARG B 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  316)
  hydrogen bonds       : angle       3.71715 (  954)
  metal coordination   : bond        0.41871 (   22)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       0.33894 (    4)
  covalent geometry    : bond        0.00296 ( 5026)
  covalent geometry    : angle       0.64617 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 187
  time to evaluate  : 0.539 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.6691 (mmm160) cc_final: 0.6379 (mmm160)
REVERT: B  320 LEU cc_start: 0.9077 (tp) cc_final: 0.8809 (tp)
REVERT: B  355 ASN cc_start: 0.8183 (t0) cc_final: 0.7917 (t0)
REVERT: A   59 ARG cc_start: 0.8475 (ttm170) cc_final: 0.7967 (tpm170)
REVERT: A   99 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8214 (tp30)
REVERT: A  294 PHE cc_start: 0.8093 (t80) cc_final: 0.7408 (t80)
REVERT: A  345 GLN cc_start: 0.8668 (mm110) cc_final: 0.8391 (mm-40)
REVERT: A  380 SER cc_start: 0.9239 (t) cc_final: 0.8969 (t)
  outliers start: 16
  outliers final: 13
  residues processed: 188
  average time/residue: 0.1651
  time to fit residues: 39.5159
Evaluate side-chains
  188 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    0.0040
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 27 optimal weight:    0.2980
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 HIS
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 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 = 0.4361 r_free = 0.4361 target = 0.182597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.133582 restraints weight = 7146.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.139103 restraints weight = 3982.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.142627 restraints weight = 2847.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5050  Z= 0.125
  Angle     :  0.608   8.541   6877  Z= 0.297
  Chirality :  0.040   0.233    877
  Planarity :  0.004   0.032    814
  Dihedral  : 10.049  92.312   1019
  Min Nonbonded Distance : 1.689

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 25.75 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.35), residues: 620
  helix:  2.12 (0.26), residues: 378
  sheet: -0.07 (0.90), residues: 42
  loop : -1.06 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 273 
 HIS   0.010   0.001   HIS B 413 
 PHE   0.021   0.001   PHE B 287 
 TYR   0.006   0.001   TYR B 396 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  316)
  hydrogen bonds       : angle       3.55435 (  954)
  metal coordination   : bond        0.00870 (   22)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       0.28103 (    4)
  covalent geometry    : bond        0.00276 ( 5026)
  covalent geometry    : angle       0.60846 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.558 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.7763 (tpt170) cc_final: 0.7154 (tpt170)
REVERT: B  246 ARG cc_start: 0.6716 (mmm160) cc_final: 0.6472 (mmm160)
REVERT: B  320 LEU cc_start: 0.9034 (tp) cc_final: 0.8786 (tp)
REVERT: B  355 ASN cc_start: 0.8160 (t0) cc_final: 0.7747 (t0)
REVERT: A   59 ARG cc_start: 0.8464 (ttm170) cc_final: 0.7963 (tpm170)
REVERT: A   99 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8224 (tp30)
REVERT: A  294 PHE cc_start: 0.8013 (t80) cc_final: 0.7272 (t80)
  outliers start: 19
  outliers final: 18
  residues processed: 186
  average time/residue: 0.1604
  time to fit residues: 38.2295
Evaluate side-chains
  187 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 ASN
A 345 GLN
** A 408 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 = 0.4344 r_free = 0.4344 target = 0.181413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.131130 restraints weight = 7227.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.136573 restraints weight = 4060.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.140013 restraints weight = 2927.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5050  Z= 0.133
  Angle     :  0.610   8.050   6877  Z= 0.304
  Chirality :  0.040   0.153    877
  Planarity :  0.003   0.033    814
  Dihedral  :  9.166  87.929   1019
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 26.56 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.35), residues: 620
  helix:  2.17 (0.26), residues: 378
  sheet: -0.27 (0.89), residues: 42
  loop : -1.05 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 273 
 HIS   0.004   0.001   HIS B 413 
 PHE   0.017   0.001   PHE A  19 
 TYR   0.006   0.001   TYR A 396 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  316)
  hydrogen bonds       : angle       3.54366 (  954)
  metal coordination   : bond        0.00570 (   22)
  SS BOND              : bond        0.00420 (    2)
  SS BOND              : angle       2.75691 (    4)
  covalent geometry    : bond        0.00304 ( 5026)
  covalent geometry    : angle       0.60618 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 0.500 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7547 (tpt90)
REVERT: B  246 ARG cc_start: 0.6761 (mmm160) cc_final: 0.6516 (mmm160)
REVERT: B  320 LEU cc_start: 0.9058 (tp) cc_final: 0.8809 (tp)
REVERT: B  355 ASN cc_start: 0.8026 (t0) cc_final: 0.7768 (t0)
REVERT: A   59 ARG cc_start: 0.8508 (ttm170) cc_final: 0.7957 (tpm170)
REVERT: A   99 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8277 (tp30)
REVERT: A  294 PHE cc_start: 0.8022 (t80) cc_final: 0.7246 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 179
  average time/residue: 0.1489
  time to fit residues: 34.3804
Evaluate side-chains
  186 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 HIS
A 284 ASN
** A 408 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 = 0.4327 r_free = 0.4327 target = 0.180446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.129575 restraints weight = 7314.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.134923 restraints weight = 4141.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.138310 restraints weight = 3003.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5050  Z= 0.143
  Angle     :  0.595   6.050   6877  Z= 0.300
  Chirality :  0.040   0.215    877
  Planarity :  0.003   0.034    814
  Dihedral  :  8.954  86.458   1019
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 27.77 %
    Favored  : 66.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.35), residues: 620
  helix:  2.13 (0.26), residues: 378
  sheet: -0.29 (0.89), residues: 42
  loop : -1.00 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 273 
 HIS   0.004   0.001   HIS B 413 
 PHE   0.014   0.001   PHE B 287 
 TYR   0.013   0.001   TYR A 396 
 ARG   0.003   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  316)
  hydrogen bonds       : angle       3.54767 (  954)
  metal coordination   : bond        0.00402 (   22)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.54062 (    4)
  covalent geometry    : bond        0.00333 ( 5026)
  covalent geometry    : angle       0.59489 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.511 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8029 (tpt170) cc_final: 0.7562 (tpt90)
REVERT: B  246 ARG cc_start: 0.6764 (mmm160) cc_final: 0.6534 (mmm160)
REVERT: B  320 LEU cc_start: 0.9060 (tp) cc_final: 0.8792 (tp)
REVERT: B  355 ASN cc_start: 0.8041 (t0) cc_final: 0.7825 (t0)
REVERT: B  362 ASN cc_start: 0.8137 (t0) cc_final: 0.7916 (t0)
REVERT: A   59 ARG cc_start: 0.8513 (ttm170) cc_final: 0.7963 (tpm170)
REVERT: A   99 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8184 (tp30)
REVERT: A  103 ARG cc_start: 0.9005 (ttm170) cc_final: 0.8764 (ttm110)
  outliers start: 29
  outliers final: 25
  residues processed: 183
  average time/residue: 0.1518
  time to fit residues: 35.8934
Evaluate side-chains
  191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 HIS
A 362 ASN
** A 408 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 = 0.4320 r_free = 0.4320 target = 0.180139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.130270 restraints weight = 7314.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.135471 restraints weight = 4187.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.138805 restraints weight = 3042.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5050  Z= 0.131
  Angle     :  0.589   6.276   6877  Z= 0.297
  Chirality :  0.040   0.177    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.674  83.563   1019
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 29.38 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.35), residues: 620
  helix:  2.11 (0.26), residues: 378
  sheet: -0.34 (0.88), residues: 42
  loop : -1.04 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 273 
 HIS   0.003   0.001   HIS B 413 
 PHE   0.019   0.001   PHE A  19 
 TYR   0.012   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  316)
  hydrogen bonds       : angle       3.52153 (  954)
  metal coordination   : bond        0.00343 (   22)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.47979 (    4)
  covalent geometry    : bond        0.00304 ( 5026)
  covalent geometry    : angle       0.58942 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 0.460 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7512 (tpt90)
REVERT: B  246 ARG cc_start: 0.6752 (mmm160) cc_final: 0.6486 (mmm160)
REVERT: B  320 LEU cc_start: 0.9040 (tp) cc_final: 0.8757 (tp)
REVERT: B  355 ASN cc_start: 0.8085 (t0) cc_final: 0.7808 (t0)
REVERT: B  404 LYS cc_start: 0.8853 (tptp) cc_final: 0.8318 (tptt)
REVERT: A   59 ARG cc_start: 0.8506 (ttm170) cc_final: 0.7960 (tpm170)
REVERT: A   99 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8083 (tp30)
REVERT: A  103 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8752 (ttm110)
  outliers start: 28
  outliers final: 25
  residues processed: 178
  average time/residue: 0.1569
  time to fit residues: 35.6643
Evaluate side-chains
  187 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0050
   chunk 35 optimal weight:    6.9990
   chunk 28 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
B 345 GLN
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 HIS
A 362 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.180394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.131188 restraints weight = 7242.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.136363 restraints weight = 4130.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.139677 restraints weight = 3011.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5050  Z= 0.126
  Angle     :  0.589   6.720   6877  Z= 0.299
  Chirality :  0.040   0.150    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.512  81.868   1019
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 30.58 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.34), residues: 620
  helix:  2.11 (0.26), residues: 378
  sheet: -0.47 (0.87), residues: 42
  loop : -1.09 (0.43), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 273 
 HIS   0.003   0.001   HIS A 413 
 PHE   0.015   0.001   PHE B 287 
 TYR   0.011   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  316)
  hydrogen bonds       : angle       3.50994 (  954)
  metal coordination   : bond        0.00288 (   22)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       0.44487 (    4)
  covalent geometry    : bond        0.00290 ( 5026)
  covalent geometry    : angle       0.58873 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.494 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7677 (tpt90)
REVERT: B  246 ARG cc_start: 0.6748 (mmm160) cc_final: 0.6495 (mmm160)
REVERT: B  320 LEU cc_start: 0.9015 (tp) cc_final: 0.8738 (tp)
REVERT: B  355 ASN cc_start: 0.8083 (t0) cc_final: 0.7809 (t0)
REVERT: B  404 LYS cc_start: 0.8848 (tptp) cc_final: 0.8296 (tptt)
REVERT: A   59 ARG cc_start: 0.8517 (ttm170) cc_final: 0.7948 (tpm170)
REVERT: A   99 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8182 (tp30)
  outliers start: 29
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1471
  time to fit residues: 34.4048
Evaluate side-chains
  191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0670
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0670
   chunk 11 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0170
   overall best weight:    1.0298

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
A  85 ASN
A 362 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.179241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.128982 restraints weight = 7247.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.134161 restraints weight = 4166.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.137475 restraints weight = 3037.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5050  Z= 0.148
  Angle     :  0.611   7.077   6877  Z= 0.310
  Chirality :  0.040   0.134    877
  Planarity :  0.003   0.034    814
  Dihedral  :  8.406  82.485   1019
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 30.18 %
    Favored  : 63.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.34), residues: 620
  helix:  2.05 (0.26), residues: 378
  sheet: -0.12 (0.87), residues: 40
  loop : -1.12 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 273 
 HIS   0.004   0.001   HIS B 108 
 PHE   0.007   0.001   PHE A  42 
 TYR   0.013   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  316)
  hydrogen bonds       : angle       3.58762 (  954)
  metal coordination   : bond        0.00334 (   22)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.57094 (    4)
  covalent geometry    : bond        0.00348 ( 5026)
  covalent geometry    : angle       0.61080 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 0.594 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7651 (tpt90)
REVERT: B   68 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8629 (tp40)
REVERT: B  246 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6515 (mmm160)
REVERT: B  320 LEU cc_start: 0.9045 (tp) cc_final: 0.8770 (tp)
REVERT: B  355 ASN cc_start: 0.8109 (t0) cc_final: 0.7821 (t0)
REVERT: B  404 LYS cc_start: 0.8857 (tptp) cc_final: 0.8244 (tppt)
REVERT: A   59 ARG cc_start: 0.8531 (ttm170) cc_final: 0.7953 (tpm170)
REVERT: A   99 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8077 (tp30)
  outliers start: 33
  outliers final: 30
  residues processed: 176
  average time/residue: 0.1675
  time to fit residues: 38.0858
Evaluate side-chains
  193 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.1980
   chunk 13 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
A 362 ASN
** A 408 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 = 0.4313 r_free = 0.4313 target = 0.179493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.129699 restraints weight = 7282.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.134936 restraints weight = 4132.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138339 restraints weight = 2992.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5050  Z= 0.134
  Angle     :  0.602   7.006   6877  Z= 0.309
  Chirality :  0.040   0.136    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.270  81.446   1019
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 31.79 %
    Favored  : 62.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.34), residues: 620
  helix:  2.13 (0.27), residues: 378
  sheet: -0.07 (0.85), residues: 40
  loop : -1.17 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 273 
 HIS   0.004   0.001   HIS B 108 
 PHE   0.021   0.001   PHE A  19 
 TYR   0.017   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  316)
  hydrogen bonds       : angle       3.60194 (  954)
  metal coordination   : bond        0.00273 (   22)
  SS BOND              : bond        0.00200 (    2)
  SS BOND              : angle       0.45734 (    4)
  covalent geometry    : bond        0.00313 ( 5026)
  covalent geometry    : angle       0.60246 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 0.824 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7894 (tpt90)
REVERT: B   68 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8629 (tp40)
REVERT: B  246 ARG cc_start: 0.6760 (mmm160) cc_final: 0.6508 (mmm160)
REVERT: B  320 LEU cc_start: 0.9020 (tp) cc_final: 0.8736 (tp)
REVERT: B  355 ASN cc_start: 0.8097 (t0) cc_final: 0.7809 (t0)
REVERT: B  404 LYS cc_start: 0.8852 (tptp) cc_final: 0.8234 (tppt)
REVERT: A   59 ARG cc_start: 0.8528 (ttm170) cc_final: 0.7954 (tpm170)
REVERT: A   99 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8183 (tp30)
  outliers start: 28
  outliers final: 28
  residues processed: 173
  average time/residue: 0.2008
  time to fit residues: 45.4156
Evaluate side-chains
  191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
A  85 ASN
A 362 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.180484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.130155 restraints weight = 7214.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.135377 restraints weight = 4104.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138760 restraints weight = 2980.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5050  Z= 0.137
  Angle     :  0.607   7.197   6877  Z= 0.312
  Chirality :  0.040   0.150    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.224  81.019   1019
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 30.78 %
    Favored  : 62.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.34), residues: 620
  helix:  2.12 (0.26), residues: 376
  sheet:  0.03 (0.85), residues: 40
  loop : -1.22 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 273 
 HIS   0.004   0.001   HIS B 108 
 PHE   0.007   0.001   PHE A  42 
 TYR   0.017   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  316)
  hydrogen bonds       : angle       3.62093 (  954)
  metal coordination   : bond        0.00261 (   22)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       0.48747 (    4)
  covalent geometry    : bond        0.00319 ( 5026)
  covalent geometry    : angle       0.60701 ( 6873)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 0.730 
Fit side-chains
REVERT: B   25 GLU cc_start: 0.8783 (tp30) cc_final: 0.8497 (tp30)
REVERT: B   30 ARG cc_start: 0.8139 (tpt170) cc_final: 0.7793 (mmm-85)
REVERT: B   68 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8622 (tp40)
REVERT: B  246 ARG cc_start: 0.6709 (mmm160) cc_final: 0.6477 (mmm160)
REVERT: B  320 LEU cc_start: 0.9020 (tp) cc_final: 0.8735 (tp)
REVERT: B  355 ASN cc_start: 0.8081 (t0) cc_final: 0.7806 (t0)
REVERT: B  404 LYS cc_start: 0.8845 (tptp) cc_final: 0.8232 (tppt)
REVERT: A   59 ARG cc_start: 0.8534 (ttm170) cc_final: 0.7956 (tpm170)
REVERT: A   99 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7981 (tp30)
  outliers start: 32
  outliers final: 31
  residues processed: 174
  average time/residue: 0.2334
  time to fit residues: 53.1127
Evaluate side-chains
  191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  362 ASN
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
A 345 GLN
A 362 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.179964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.130429 restraints weight = 7266.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.135694 restraints weight = 4122.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.138972 restraints weight = 2973.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5050  Z= 0.134
  Angle     :  0.613   7.218   6877  Z= 0.313
  Chirality :  0.040   0.152    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.190  80.672   1019
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 31.59 %
    Favored  : 61.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.34), residues: 620
  helix:  2.10 (0.26), residues: 376
  sheet:  0.13 (0.86), residues: 40
  loop : -1.22 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 273 
 HIS   0.004   0.001   HIS B 108 
 PHE   0.005   0.001   PHE B  88 
 TYR   0.019   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  316)
  hydrogen bonds       : angle       3.62518 (  954)
  metal coordination   : bond        0.00251 (   22)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.44338 (    4)
  covalent geometry    : bond        0.00313 ( 5026)
  covalent geometry    : angle       0.61329 ( 6873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2228.69 seconds
wall clock time: 41 minutes 12.77 seconds (2472.77 seconds total)