Starting phenix.real_space_refine
on Sat May 10 03:17:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xma_38469/05_2025/8xma_38469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xma_38469/05_2025/8xma_38469.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xma_38469/05_2025/8xma_38469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xma_38469/05_2025/8xma_38469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xma_38469/05_2025/8xma_38469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xma_38469/05_2025/8xma_38469.cif"
  }
  resolution = 2.65
  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=  -0.003 sd=   0.082
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      44      5.16       5
     C    3196      2.51       5
     N     785      2.21       5
     O     825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4858
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2297
          Classifications: {'peptide': 300}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 9, 'TRANS': 290}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "A"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2297
          Classifications: {'peptide': 301}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 291}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 35
    Chain: "B"
      Number of atoms: 167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 167
          Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 3}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 97
          Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 5

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2193  SG  CYS B 433      28.140  24.694  47.545  1.00105.86           S
  ATOM   4518  SG  CYS A 437      29.976  26.843  21.278  1.00103.74           S
  ATOM   2291  SG  CYS B 446      28.119  34.000  44.671  1.00 90.42           S
  ATOM   2297  SG  CYS B 447      23.736  34.233  45.401  1.00 86.30           S
  ATOM   4490  SG  CYS A 433      37.829  23.700  29.217  1.00103.95           S
  ATOM   2221  SG  CYS B 437      34.991  30.521  54.029  1.00107.45           S
  ATOM   4588  SG  CYS A 446      35.783  33.297  30.016  1.00 85.99           S
  ATOM   4594  SG  CYS A 447      39.783  34.078  29.191  1.00 81.80           S

  Time building chain proxies: 3.75, per 1000 atoms: 0.77
  Number of scatterers: 4858
  At special positions: 0
  Unit cell: (59.648, 108.112, 68.968, 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      44     16.00
     O     825      8.00
     N     785      7.00
     C    3196      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 534.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 387 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 370 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 433 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A 413 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A 408 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS B 437 "
      pdb="  ZN A 603 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS A 373 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 446 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 447 "
      pdb="  ZN A 604 "
        pdb="ZN    ZN A 604 " - pdb=" NE2 HIS A 251 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B 387 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS B 370 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 433 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" ND1 HIS B 413 "
        pdb="ZN    ZN B 602 " - pdb=" ND1 HIS B 408 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS A 437 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B 373 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 446 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 447 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" NE2 HIS B 251 "


  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1138

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      69.6% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 33
    Processing helix  chain 'B' and resid 34 through 42
      removed outlier: 3.546A  pdb=" N   PHE B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 61
    Processing helix  chain 'B' and resid 76 through 106
    Processing helix  chain 'B' and resid 112 through 135
    Processing helix  chain 'B' and resid 241 through 272
    Processing helix  chain 'B' and resid 310 through 314
      removed outlier: 3.983A  pdb=" N   LEU B 314 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 314'
    Processing helix  chain 'B' and resid 315 through 344
      removed outlier: 3.629A  pdb=" N   THR B 319 " --> pdb=" O   TYR B 315 " (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 392 through 394
      No H-bonds generated for 'chain 'B' and resid 392 through 394'
    Processing helix  chain 'B' and resid 395 through 410
      removed outlier: 3.660A  pdb=" N   THR B 402 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   HIS B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 33
    Processing helix  chain 'A' and resid 34 through 44
      removed outlier: 3.851A  pdb=" N   LEU A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 61
      removed outlier: 3.747A  pdb=" N   VAL A  48 " --> pdb=" O   MET A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 106
    Processing helix  chain 'A' and resid 112 through 134
      removed outlier: 3.508A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 272
      removed outlier: 3.572A  pdb=" N   ASN A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 314
    Processing helix  chain 'A' and resid 315 through 344
      removed outlier: 3.596A  pdb=" N   THR A 319 " --> pdb=" O   TYR A 315 " (cutoff:3.500A)
      Proline residue:  A 334  - end of helix
    Processing helix  chain 'A' and resid 352 through 363
      removed outlier: 3.907A  pdb=" N   VAL A 363 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 410
      removed outlier: 4.090A  pdb=" N   VAL A 399 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 4.143A  pdb=" N   GLN A 445 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 368 through 378
      removed outlier: 6.643A  pdb=" N   VAL B 369 " --> pdb=" O   LYS B 389 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   LYS B 389 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   GLU B 371 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   HIS B 387 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ARG B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE B 382 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   THR B 416 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ALA B 384 " --> pdb=" O   THR B 416 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   GLN B 418 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ALA B 386 " --> pdb=" O   GLN B 418 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLU B 420 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE B 388 " --> pdb=" O   GLU B 420 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 378
      removed outlier: 6.744A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ARG A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ILE A 382 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   THR A 416 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA A 384 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   GLN A 418 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ALA A 386 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    963 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: 1.22

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 806
        1.32 -     1.45: 1175
        1.45 -     1.57: 2910
        1.57 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 4955
  Sorted by residual:
  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 9.27e+00
  bond pdb=" CAX Y01 B 607 "
       pdb=" OAH Y01 B 607 "
    ideal  model  delta    sigma   weight residual
    1.248  1.309 -0.061 2.00e-02 2.50e+03 9.22e+00
  bond pdb=" CAX Y01 B 606 "
       pdb=" OAF Y01 B 606 "
    ideal  model  delta    sigma   weight residual
    1.247  1.307 -0.060 2.00e-02 2.50e+03 8.98e+00
  bond pdb=" CAX Y01 B 608 "
       pdb=" OAF Y01 B 608 "
    ideal  model  delta    sigma   weight residual
    1.247  1.307 -0.060 2.00e-02 2.50e+03 8.88e+00
  bond pdb=" C   GLU B 106 "
       pdb=" N   PRO B 107 "
    ideal  model  delta    sigma   weight residual
    1.331  1.366 -0.035 1.31e-02 5.83e+03 7.30e+00
  ... (remaining 4950 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 6573
        1.63 -     3.25: 159
        3.25 -     4.88: 19
        4.88 -     6.50: 7
        6.50 -     8.13: 5
  Bond angle restraints: 6763
  Sorted by residual:
  angle pdb=" C   GLU B 106 "
        pdb=" N   PRO B 107 "
        pdb=" CA  PRO B 107 "
      ideal   model   delta    sigma   weight residual
     119.85  116.67    3.18 1.01e+00 9.80e-01 9.88e+00
  angle pdb=" N   PRO B 107 "
        pdb=" CA  PRO B 107 "
        pdb=" C   PRO B 107 "
      ideal   model   delta    sigma   weight residual
     111.38  116.25   -4.87 1.59e+00 3.96e-01 9.37e+00
  angle pdb=" CCM AV0 A 605 "
        pdb=" CBS AV0 A 605 "
        pdb=" O1  AV0 A 605 "
      ideal   model   delta    sigma   weight residual
     109.17  117.30   -8.13 3.00e+00 1.11e-01 7.34e+00
  angle pdb=" CA  PRO B 107 "
        pdb=" C   PRO B 107 "
        pdb=" O   PRO B 107 "
      ideal   model   delta    sigma   weight residual
     121.67  118.44    3.23 1.22e+00 6.72e-01 7.03e+00
  angle pdb=" CAL Y01 A 606 "
        pdb=" CAX Y01 A 606 "
        pdb=" OAH Y01 A 606 "
      ideal   model   delta    sigma   weight residual
     115.62  123.18   -7.56 3.00e+00 1.11e-01 6.36e+00
  ... (remaining 6758 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.91: 3003
       26.91 -    53.82: 140
       53.82 -    80.74: 45
       80.74 -   107.65: 29
      107.65 -   134.56: 28
  Dihedral angle restraints: 3245
    sinusoidal: 1504
      harmonic: 1741
  Sorted by residual:
  dihedral pdb=" CBQ AV0 A 605 "
           pdb=" CBS AV0 A 605 "
           pdb=" CCM AV0 A 605 "
           pdb=" O1  AV0 A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.26 -155.18 -134.56     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" CCD AV0 A 605 "
           pdb=" CCS AV0 A 605 "
           pdb=" OBZ AV0 A 605 "
           pdb=" CCW AV0 A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.29  -71.44  130.73     1      3.00e+01 1.11e-03 1.76e+01
  dihedral pdb=" CCD AV0 A 605 "
           pdb=" CCS AV0 A 605 "
           pdb=" OBZ AV0 A 605 "
           pdb=" OCB AV0 A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.59  168.89  129.70     1      3.00e+01 1.11e-03 1.75e+01
  ... (remaining 3242 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 645
       0.045 -    0.090: 173
       0.090 -    0.135: 34
       0.135 -    0.181: 2
       0.181 -    0.226: 3
  Chirality restraints: 857
  Sorted by residual:
  chirality pdb=" CA  PRO B 107 "
            pdb=" N   PRO B 107 "
            pdb=" C   PRO B 107 "
            pdb=" CB  PRO B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CCW AV0 A 605 "
            pdb=" CCS AV0 A 605 "
            pdb=" CCU AV0 A 605 "
            pdb=" OAV AV0 A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.50    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CCV AV0 B 605 "
            pdb=" CCR AV0 B 605 "
            pdb=" CCT AV0 B 605 "
            pdb=" OAU AV0 B 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.50    0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 854 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 112 "   -0.035 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO A 113 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 113 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 113 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 269 "   -0.011 2.00e-02 2.50e+03   1.15e-02 2.32e+00
        pdb=" CG  PHE A 269 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 269 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 269 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 269 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 269 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 269 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 106 "   -0.019 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO B 107 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 45
        2.55 -     3.13: 3742
        3.13 -     3.72: 7700
        3.72 -     4.31: 9972
        4.31 -     4.90: 17135
  Nonbonded interactions: 38594
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  47 "
            pdb="ZN    ZN B 604 "
     model   vdw
     1.957 2.230
  nonbonded pdb=" OE2 GLU A 420 "
            pdb="ZN    ZN A 601 "
     model   vdw
     1.981 2.230
  nonbonded pdb=" OE2 GLU B 420 "
            pdb="ZN    ZN B 601 "
     model   vdw
     1.983 2.230
  nonbonded pdb=" OE2 GLU B 371 "
            pdb="ZN    ZN B 603 "
     model   vdw
     1.983 2.230
  nonbonded pdb=" OD2 ASP A 255 "
            pdb="ZN    ZN A 604 "
     model   vdw
     1.987 2.230
  ... (remaining 38589 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 136 or resid 240 through 447 or resid 601 throug \ 
h 606))
  selection = (chain 'B' and (resid 6 through 136 or resid 240 through 353 or (resid 354 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 355 through 404 or  \ 
(resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ 
 through 447 or resid 601 through 606))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  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:          0.180
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.570
  Find NCS groups from input model:        0.200
  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:11.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
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   0.407   4975  Z= 0.509
  Angle     :  0.627   8.127   6763  Z= 0.302
  Chirality :  0.042   0.226    857
  Planarity :  0.004   0.054    790
  Dihedral  : 23.456 134.561   2107
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.44 (0.35), residues: 585
  helix:  3.18 (0.25), residues: 387
  sheet:  1.28 (0.88), residues: 46
  loop :  0.12 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 312 
 HIS   0.003   0.001   HIS B 135 
 PHE   0.026   0.001   PHE A 269 
 TYR   0.006   0.001   TYR B 270 
 ARG   0.006   0.000   ARG B 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11187 (  323)
  hydrogen bonds       : angle       4.08726 (  963)
  metal coordination   : bond        0.21927 (   20)
  covalent geometry    : bond        0.00422 ( 4955)
  covalent geometry    : angle       0.62665 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.532 
Fit side-chains
REVERT: B  381 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7598 (mtp85)
REVERT: A   63 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8064 (mtt180)
REVERT: A   65 HIS cc_start: 0.7182 (m90) cc_final: 0.6942 (p-80)
REVERT: A   78 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7143 (mt-10)
REVERT: A  108 HIS cc_start: 0.7109 (m-70) cc_final: 0.6523 (m90)
REVERT: A  129 LEU cc_start: 0.7822 (tt) cc_final: 0.7498 (mp)
REVERT: A  246 ARG cc_start: 0.7504 (tpt170) cc_final: 0.6364 (ttp80)
REVERT: A  380 SER cc_start: 0.8366 (t) cc_final: 0.8136 (p)
REVERT: A  434 GLU cc_start: 0.7275 (mp0) cc_final: 0.6949 (mp0)
  outliers start: 0
  outliers final: 1
  residues processed: 136
  average time/residue: 1.3029
  time to fit residues: 183.2553
Evaluate side-chains
  89 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN
B 135 HIS
A 108 HIS
A 127 ASN
A 440 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.152459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.112462 restraints weight = 4467.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.22
r_work: 0.3218 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4975  Z= 0.166
  Angle     :  0.596   8.222   6763  Z= 0.281
  Chirality :  0.042   0.266    857
  Planarity :  0.004   0.051    790
  Dihedral  : 14.735 131.335   1115
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 12.63 %
    Favored  : 83.10 %
  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:  3.56 (0.35), residues: 585
  helix:  3.11 (0.25), residues: 393
  sheet:  1.40 (0.88), residues: 45
  loop :  0.51 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 312 
 HIS   0.005   0.001   HIS B 135 
 PHE   0.011   0.001   PHE B  21 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.005   0.001   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  323)
  hydrogen bonds       : angle       3.25361 (  963)
  metal coordination   : bond        0.01330 (   20)
  covalent geometry    : bond        0.00385 ( 4955)
  covalent geometry    : angle       0.59574 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8294 (pm20) cc_final: 0.8023 (pp20)
REVERT: B  401 LYS cc_start: 0.7542 (mttm) cc_final: 0.7337 (mptm)
REVERT: B  434 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7571 (mm-30)
REVERT: B  445 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.6272 (tm-30)
REVERT: A   37 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7520 (ttm)
REVERT: A   65 HIS cc_start: 0.7766 (m90) cc_final: 0.6767 (p-80)
REVERT: A   78 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: A  108 HIS cc_start: 0.6996 (m90) cc_final: 0.6617 (m-70)
REVERT: A  112 GLN cc_start: 0.7469 (mt0) cc_final: 0.7176 (pt0)
REVERT: A  129 LEU cc_start: 0.7710 (tt) cc_final: 0.7463 (mp)
REVERT: A  368 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8266 (pp20)
REVERT: A  397 MET cc_start: 0.8032 (tpt) cc_final: 0.7820 (mmt)
  outliers start: 21
  outliers final: 5
  residues processed: 103
  average time/residue: 1.2825
  time to fit residues: 137.2171
Evaluate side-chains
  94 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  368 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.151557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.111497 restraints weight = 4484.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.23
r_work: 0.3190 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4975  Z= 0.147
  Angle     :  0.533   5.635   6763  Z= 0.257
  Chirality :  0.039   0.244    857
  Planarity :  0.003   0.045    790
  Dihedral  : 11.977 138.283   1113
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.27 %
    Favored  : 81.26 %
  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:  3.48 (0.35), residues: 585
  helix:  3.12 (0.25), residues: 390
  sheet:  1.05 (0.89), residues: 48
  loop :  0.46 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 312 
 HIS   0.006   0.001   HIS B 135 
 PHE   0.008   0.001   PHE A 249 
 TYR   0.019   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03810 (  323)
  hydrogen bonds       : angle       3.18959 (  963)
  metal coordination   : bond        0.00507 (   20)
  covalent geometry    : bond        0.00347 ( 4955)
  covalent geometry    : angle       0.53287 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.502 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8277 (pm20) cc_final: 0.7961 (pp20)
REVERT: B   99 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6934 (mm-30)
REVERT: B  368 GLU cc_start: 0.8141 (pp20) cc_final: 0.7609 (pp20)
REVERT: B  401 LYS cc_start: 0.7463 (mttm) cc_final: 0.7262 (mptm)
REVERT: B  434 GLU cc_start: 0.8019 (mp0) cc_final: 0.7710 (mm-30)
REVERT: A   37 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7437 (ttm)
REVERT: A   65 HIS cc_start: 0.7772 (m90) cc_final: 0.6736 (p-80)
REVERT: A   78 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7933 (mt-10)
REVERT: A  108 HIS cc_start: 0.7288 (m90) cc_final: 0.7027 (m-70)
REVERT: A  112 GLN cc_start: 0.7556 (mt0) cc_final: 0.7286 (pt0)
REVERT: A  129 LEU cc_start: 0.7700 (tt) cc_final: 0.7464 (mp)
REVERT: A  397 MET cc_start: 0.8037 (tpt) cc_final: 0.7835 (mmt)
  outliers start: 17
  outliers final: 9
  residues processed: 94
  average time/residue: 1.0355
  time to fit residues: 101.7250
Evaluate side-chains
  96 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   30 ARG
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.152132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.112225 restraints weight = 4348.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.08
r_work: 0.3157 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4975  Z= 0.120
  Angle     :  0.473   4.986   6763  Z= 0.234
  Chirality :  0.038   0.184    857
  Planarity :  0.003   0.041    790
  Dihedral  : 11.552 139.693   1113
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 17.31 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.67 (0.35), residues: 585
  helix:  3.24 (0.24), residues: 393
  sheet:  1.01 (0.89), residues: 48
  loop :  0.58 (0.56), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 312 
 HIS   0.004   0.000   HIS B 135 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.018   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03522 (  323)
  hydrogen bonds       : angle       3.10827 (  963)
  metal coordination   : bond        0.00329 (   20)
  covalent geometry    : bond        0.00279 ( 4955)
  covalent geometry    : angle       0.47299 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.572 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8006 (pp20)
REVERT: B  368 GLU cc_start: 0.8184 (pp20) cc_final: 0.7618 (pp20)
REVERT: B  434 GLU cc_start: 0.8008 (mp0) cc_final: 0.7681 (mm-30)
REVERT: B  445 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6390 (tm-30)
REVERT: A   22 MET cc_start: 0.8550 (ttm) cc_final: 0.8318 (mtp)
REVERT: A   37 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7479 (ttm)
REVERT: A   65 HIS cc_start: 0.7765 (m90) cc_final: 0.6934 (p-80)
REVERT: A   78 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8011 (mt-10)
REVERT: A  108 HIS cc_start: 0.7385 (m90) cc_final: 0.7080 (m-70)
REVERT: A  112 GLN cc_start: 0.7639 (mt0) cc_final: 0.7368 (pt0)
REVERT: A  129 LEU cc_start: 0.7870 (tt) cc_final: 0.7618 (mp)
  outliers start: 17
  outliers final: 7
  residues processed: 90
  average time/residue: 1.1378
  time to fit residues: 106.7200
Evaluate side-chains
  91 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.151241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.111158 restraints weight = 4365.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.09
r_work: 0.3141 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4975  Z= 0.127
  Angle     :  0.472   4.995   6763  Z= 0.235
  Chirality :  0.038   0.133    857
  Planarity :  0.003   0.039    790
  Dihedral  : 11.312 140.874   1113
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.13 %
    Favored  : 78.21 %
  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:  3.64 (0.35), residues: 585
  helix:  3.27 (0.24), residues: 393
  sheet:  0.46 (0.86), residues: 51
  loop :  0.62 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 312 
 HIS   0.004   0.001   HIS B 135 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  323)
  hydrogen bonds       : angle       3.09243 (  963)
  metal coordination   : bond        0.00357 (   20)
  covalent geometry    : bond        0.00301 ( 4955)
  covalent geometry    : angle       0.47198 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.671 
Fit side-chains
REVERT: B   10 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7569 (mtt90)
REVERT: B   78 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8055 (pp20)
REVERT: B  368 GLU cc_start: 0.8075 (pp20) cc_final: 0.7692 (pp20)
REVERT: B  401 LYS cc_start: 0.7497 (mptm) cc_final: 0.7238 (mptm)
REVERT: B  434 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7702 (mp0)
REVERT: A   37 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7530 (ttm)
REVERT: A   65 HIS cc_start: 0.7916 (m90) cc_final: 0.6913 (p-80)
REVERT: A   78 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: A  108 HIS cc_start: 0.7511 (m90) cc_final: 0.7149 (m-70)
REVERT: A  112 GLN cc_start: 0.7672 (mt0) cc_final: 0.7380 (pt0)
REVERT: A  129 LEU cc_start: 0.7849 (tt) cc_final: 0.7642 (mp)
  outliers start: 18
  outliers final: 8
  residues processed: 87
  average time/residue: 1.2285
  time to fit residues: 111.1248
Evaluate side-chains
  92 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.150580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.110718 restraints weight = 4336.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.08
r_work: 0.3131 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4975  Z= 0.133
  Angle     :  0.469   4.991   6763  Z= 0.236
  Chirality :  0.038   0.141    857
  Planarity :  0.003   0.037    790
  Dihedral  : 11.233 140.966   1113
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 16.90 %
    Favored  : 78.41 %
  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:  3.66 (0.35), residues: 585
  helix:  3.27 (0.24), residues: 393
  sheet:  0.55 (0.87), residues: 50
  loop :  0.65 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 312 
 HIS   0.004   0.001   HIS B 135 
 PHE   0.007   0.001   PHE B  21 
 TYR   0.017   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  323)
  hydrogen bonds       : angle       3.13159 (  963)
  metal coordination   : bond        0.00337 (   20)
  covalent geometry    : bond        0.00316 ( 4955)
  covalent geometry    : angle       0.46923 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 0.573 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7993 (pp20)
REVERT: B  368 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7643 (pp20)
REVERT: B  434 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7764 (mp0)
REVERT: B  445 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6393 (tm-30)
REVERT: A   37 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7520 (ttm)
REVERT: A   65 HIS cc_start: 0.7943 (m90) cc_final: 0.6879 (p-80)
REVERT: A   78 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7719 (mt-10)
REVERT: A  112 GLN cc_start: 0.7630 (mt0) cc_final: 0.7297 (pt0)
REVERT: A  129 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7688 (mp)
REVERT: A  368 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8369 (pp20)
  outliers start: 23
  outliers final: 9
  residues processed: 93
  average time/residue: 1.0573
  time to fit residues: 102.7818
Evaluate side-chains
  97 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  368 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0970
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.151342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.111899 restraints weight = 4233.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.05
r_work: 0.3146 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4975  Z= 0.118
  Angle     :  0.457   4.986   6763  Z= 0.229
  Chirality :  0.037   0.139    857
  Planarity :  0.003   0.036    790
  Dihedral  : 11.144 141.228   1113
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.11 %
    Favored  : 78.62 %
  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:  3.68 (0.35), residues: 585
  helix:  3.31 (0.24), residues: 393
  sheet:  0.56 (0.87), residues: 50
  loop :  0.56 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.006   0.001   PHE B  21 
 TYR   0.016   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  323)
  hydrogen bonds       : angle       3.07335 (  963)
  metal coordination   : bond        0.00289 (   20)
  covalent geometry    : bond        0.00276 ( 4955)
  covalent geometry    : angle       0.45720 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.520 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7986 (pp20)
REVERT: B  368 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7766 (pp20)
REVERT: B  434 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (mp0)
REVERT: A   37 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7515 (ttm)
REVERT: A   65 HIS cc_start: 0.7918 (m90) cc_final: 0.6839 (p-80)
REVERT: A   69 LYS cc_start: 0.8303 (tptp) cc_final: 0.8090 (tptm)
REVERT: A   78 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: A  112 GLN cc_start: 0.7622 (mt0) cc_final: 0.7303 (pt0)
REVERT: A  129 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7650 (mp)
REVERT: A  368 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8345 (pp20)
  outliers start: 21
  outliers final: 11
  residues processed: 90
  average time/residue: 1.1003
  time to fit residues: 103.6151
Evaluate side-chains
  97 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  368 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:   50.0000
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   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 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.151025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111236 restraints weight = 4276.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.07
r_work: 0.3139 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4975  Z= 0.122
  Angle     :  0.461   4.967   6763  Z= 0.232
  Chirality :  0.037   0.135    857
  Planarity :  0.003   0.035    790
  Dihedral  : 11.089 140.864   1113
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 15.48 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.66 (0.35), residues: 585
  helix:  3.29 (0.24), residues: 393
  sheet:  0.48 (0.87), residues: 50
  loop :  0.61 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  323)
  hydrogen bonds       : angle       3.07964 (  963)
  metal coordination   : bond        0.00311 (   20)
  covalent geometry    : bond        0.00287 ( 4955)
  covalent geometry    : angle       0.46071 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.532 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7974 (pp20)
REVERT: B  368 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7777 (pp20)
REVERT: B  401 LYS cc_start: 0.7510 (mptm) cc_final: 0.7286 (mptm)
REVERT: B  405 ASP cc_start: 0.8080 (m-30) cc_final: 0.7625 (p0)
REVERT: B  434 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7759 (mp0)
REVERT: A   37 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7523 (ttm)
REVERT: A   65 HIS cc_start: 0.7931 (m90) cc_final: 0.6806 (p-80)
REVERT: A   69 LYS cc_start: 0.8268 (tptp) cc_final: 0.8050 (tptm)
REVERT: A   78 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7998 (mt-10)
REVERT: A  112 GLN cc_start: 0.7618 (mt0) cc_final: 0.7278 (pt0)
REVERT: A  129 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7661 (mp)
REVERT: A  366 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7899 (p)
REVERT: A  368 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8291 (pp20)
  outliers start: 27
  outliers final: 11
  residues processed: 95
  average time/residue: 1.1120
  time to fit residues: 110.3770
Evaluate side-chains
  101 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  368 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0370
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.151027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.111791 restraints weight = 4247.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.04
r_work: 0.3149 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4975  Z= 0.115
  Angle     :  0.465   5.596   6763  Z= 0.230
  Chirality :  0.037   0.141    857
  Planarity :  0.003   0.035    790
  Dihedral  : 10.960 140.649   1113
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 17.72 %
    Favored  : 78.82 %
  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:  3.69 (0.35), residues: 585
  helix:  3.32 (0.24), residues: 393
  sheet:  0.52 (0.87), residues: 50
  loop :  0.58 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.011   0.001   PHE B  88 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  323)
  hydrogen bonds       : angle       3.06565 (  963)
  metal coordination   : bond        0.00280 (   20)
  covalent geometry    : bond        0.00270 ( 4955)
  covalent geometry    : angle       0.46471 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.565 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7985 (pp20)
REVERT: B  368 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7775 (pp20)
REVERT: B  401 LYS cc_start: 0.7538 (mptm) cc_final: 0.7303 (mptm)
REVERT: B  434 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7752 (mp0)
REVERT: A   37 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7512 (ttm)
REVERT: A   65 HIS cc_start: 0.7952 (m90) cc_final: 0.6936 (p-80)
REVERT: A   78 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7993 (mt-10)
REVERT: A  112 GLN cc_start: 0.7610 (mt0) cc_final: 0.7263 (pt0)
REVERT: A  129 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7662 (mp)
REVERT: A  366 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7918 (p)
  outliers start: 17
  outliers final: 10
  residues processed: 89
  average time/residue: 1.1558
  time to fit residues: 107.2354
Evaluate side-chains
  96 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.150256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110629 restraints weight = 4317.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.07
r_work: 0.3125 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4975  Z= 0.128
  Angle     :  0.474   4.986   6763  Z= 0.237
  Chirality :  0.038   0.131    857
  Planarity :  0.003   0.035    790
  Dihedral  : 10.922 139.553   1113
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.72 %
    Favored  : 78.62 %
  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:  3.62 (0.35), residues: 585
  helix:  3.26 (0.24), residues: 393
  sheet:  0.44 (0.86), residues: 50
  loop :  0.60 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 312 
 HIS   0.003   0.001   HIS B 135 
 PHE   0.010   0.001   PHE B  88 
 TYR   0.018   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  323)
  hydrogen bonds       : angle       3.10511 (  963)
  metal coordination   : bond        0.00344 (   20)
  covalent geometry    : bond        0.00305 ( 4955)
  covalent geometry    : angle       0.47386 ( 6763)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.528 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (pp20)
REVERT: B  368 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7752 (pp20)
REVERT: B  401 LYS cc_start: 0.7527 (mptm) cc_final: 0.7267 (mptm)
REVERT: B  405 ASP cc_start: 0.8109 (m-30) cc_final: 0.7685 (p0)
REVERT: B  434 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7717 (mp0)
REVERT: A   37 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7488 (ttm)
REVERT: A   65 HIS cc_start: 0.7998 (m90) cc_final: 0.6932 (p-80)
REVERT: A   78 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7960 (mt-10)
REVERT: A  112 GLN cc_start: 0.7662 (mt0) cc_final: 0.7279 (pt0)
REVERT: A  129 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7694 (mp)
REVERT: A  366 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7892 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 88
  average time/residue: 1.1465
  time to fit residues: 105.0851
Evaluate side-chains
  98 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0060
   chunk 55 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0370
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.4074

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.152647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113309 restraints weight = 4304.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.07
r_work: 0.3172 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4975  Z= 0.097
  Angle     :  0.443   5.015   6763  Z= 0.222
  Chirality :  0.037   0.146    857
  Planarity :  0.003   0.034    790
  Dihedral  : 10.718 139.863   1113
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.94 %
    Favored  : 78.21 %
  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:  3.85 (0.35), residues: 585
  helix:  3.44 (0.24), residues: 393
  sheet:  0.65 (0.87), residues: 50
  loop :  0.62 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 312 
 HIS   0.002   0.000   HIS B 135 
 PHE   0.011   0.001   PHE B  88 
 TYR   0.015   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  323)
  hydrogen bonds       : angle       3.03133 (  963)
  metal coordination   : bond        0.00187 (   20)
  covalent geometry    : bond        0.00221 ( 4955)
  covalent geometry    : angle       0.44306 ( 6763)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4309.58 seconds
wall clock time: 75 minutes 4.57 seconds (4504.57 seconds total)