Starting phenix.real_space_refine
on Thu Mar  6 04:14:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xma_38469/03_2025/8xma_38469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xma_38469/03_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_38469/03_2025/8xma_38469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xma_38469/03_2025/8xma_38469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xma_38469/03_2025/8xma_38469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xma_38469/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.05, per 1000 atoms: 0.83
  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: 1.43
  Conformation dependent library (CDL) restraints added in 549.2 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: 0.73
  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: 1.33

  Time building geometry restraints manager: 1.64 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:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.080
  Find NCS groups from input model:        0.180
  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:13.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.170
-------------------------------------------------------------------------------
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      :  0.004   0.061   4955  Z= 0.291
  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 

*********************** 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  : 0.543 
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: 1.3557
  time to fit residues: 190.3560
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  : 0.492 
-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.152619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.112615 restraints weight = 4500.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.23
r_work: 0.3218 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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   4955  Z= 0.251
  Angle     :  0.596   8.221   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 

*********************** 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  : 0.579 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8300 (pm20) cc_final: 0.8031 (pp20)
REVERT: B  401 LYS cc_start: 0.7560 (mttm) cc_final: 0.7356 (mptm)
REVERT: B  434 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7581 (mm-30)
REVERT: B  445 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6293 (tm-30)
REVERT: A   37 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7534 (ttm)
REVERT: A   65 HIS cc_start: 0.7777 (m90) cc_final: 0.6785 (p-80)
REVERT: A   78 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7659 (mt-10)
REVERT: A  108 HIS cc_start: 0.7004 (m90) cc_final: 0.6626 (m-70)
REVERT: A  112 GLN cc_start: 0.7479 (mt0) cc_final: 0.7191 (pt0)
REVERT: A  129 LEU cc_start: 0.7733 (tt) cc_final: 0.7485 (mp)
REVERT: A  368 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8281 (pp20)
REVERT: A  397 MET cc_start: 0.8056 (tpt) cc_final: 0.7843 (mmt)
  outliers start: 21
  outliers final: 5
  residues processed: 103
  average time/residue: 1.2147
  time to fit residues: 130.0459
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  : 0.556 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0170
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.8220

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.153063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113084 restraints weight = 4465.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.25
r_work: 0.3204 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4955  Z= 0.209
  Angle     :  0.517   5.778   6763  Z= 0.250
  Chirality :  0.039   0.259    857
  Planarity :  0.003   0.046    790
  Dihedral  : 11.926 137.574   1113
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.68 %
    Favored  : 81.06 %
  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:  3.58 (0.35), residues: 585
  helix:  3.17 (0.25), residues: 392
  sheet:  1.00 (0.90), residues: 47
  loop :  0.59 (0.56), residues: 146

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   0.007   0.001   PHE A 249 
 TYR   0.018   0.002   TYR B 396 
 ARG   0.004   0.000   ARG B  63 

*********************** 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
  103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.505 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8301 (pm20) cc_final: 0.8051 (pp20)
REVERT: B   99 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6916 (mm-30)
REVERT: B  368 GLU cc_start: 0.8108 (pp20) cc_final: 0.7641 (pp20)
REVERT: B  434 GLU cc_start: 0.8020 (mp0) cc_final: 0.7734 (mm-30)
REVERT: A   37 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7421 (ttm)
REVERT: A   65 HIS cc_start: 0.7749 (m90) cc_final: 0.6744 (p-80)
REVERT: A  108 HIS cc_start: 0.7011 (m90) cc_final: 0.6787 (m-70)
REVERT: A  112 GLN cc_start: 0.7528 (mt0) cc_final: 0.7272 (pt0)
REVERT: A  129 LEU cc_start: 0.7670 (tt) cc_final: 0.7428 (mp)
  outliers start: 16
  outliers final: 7
  residues processed: 91
  average time/residue: 1.0666
  time to fit residues: 101.3754
Evaluate side-chains
  91 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
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 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:    0.9980
   chunk 50 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7578

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.152112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.112032 restraints weight = 4347.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.09
r_work: 0.3158 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4955  Z= 0.193
  Angle     :  0.478   4.985   6763  Z= 0.237
  Chirality :  0.038   0.190    857
  Planarity :  0.003   0.041    790
  Dihedral  : 11.588 139.460   1113
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.50 %
    Favored  : 79.84 %
  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:  3.23 (0.24), residues: 392
  sheet:  1.04 (0.89), residues: 48
  loop :  0.57 (0.56), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 312 
 HIS   0.004   0.001   HIS B 135 
 PHE   0.012   0.001   PHE B  88 
 TYR   0.017   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B  63 

*********************** 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: 18
    poor density    : 83
  time to evaluate  : 0.532 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8021 (pp20)
REVERT: B  368 GLU cc_start: 0.8179 (pp20) cc_final: 0.7612 (pp20)
REVERT: B  434 GLU cc_start: 0.8017 (mp0) cc_final: 0.7720 (mm-30)
REVERT: B  445 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6392 (tm-30)
REVERT: A   37 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7492 (ttm)
REVERT: A   65 HIS cc_start: 0.7754 (m90) cc_final: 0.6929 (p-80)
REVERT: A  108 HIS cc_start: 0.7373 (m90) cc_final: 0.7064 (m-70)
REVERT: A  112 GLN cc_start: 0.7631 (mt0) cc_final: 0.7358 (pt0)
REVERT: A  129 LEU cc_start: 0.7820 (tt) cc_final: 0.7603 (mp)
  outliers start: 18
  outliers final: 8
  residues processed: 89
  average time/residue: 1.3421
  time to fit residues: 124.3359
Evaluate side-chains
  91 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
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  129 LEU
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:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.151139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110971 restraints weight = 4370.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.09
r_work: 0.3137 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4955  Z= 0.203
  Angle     :  0.476   5.013   6763  Z= 0.237
  Chirality :  0.038   0.133    857
  Planarity :  0.003   0.039    790
  Dihedral  : 11.340 141.019   1113
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.13 %
    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:  3.64 (0.35), residues: 585
  helix:  3.25 (0.24), residues: 392
  sheet:  0.69 (0.88), residues: 49
  loop :  0.60 (0.55), residues: 144

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  21 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.002   0.000   ARG B  63 

*********************** 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
  95 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.593 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (pp20)
REVERT: B  368 GLU cc_start: 0.8157 (pp20) cc_final: 0.7812 (pp20)
REVERT: B  401 LYS cc_start: 0.7520 (mptm) cc_final: 0.7257 (mptm)
REVERT: B  434 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7681 (mp0)
REVERT: A   37 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7514 (ttm)
REVERT: A   65 HIS cc_start: 0.7945 (m90) cc_final: 0.6932 (p-80)
REVERT: A  108 HIS cc_start: 0.7380 (m90) cc_final: 0.7058 (m-70)
REVERT: A  112 GLN cc_start: 0.7659 (mt0) cc_final: 0.7374 (pt0)
REVERT: A  129 LEU cc_start: 0.7861 (tt) cc_final: 0.7650 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 85
  average time/residue: 2.0394
  time to fit residues: 179.4960
Evaluate side-chains
  89 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0970
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.152210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112393 restraints weight = 4323.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.07
r_work: 0.3160 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4955  Z= 0.169
  Angle     :  0.446   4.950   6763  Z= 0.224
  Chirality :  0.037   0.142    857
  Planarity :  0.003   0.037    790
  Dihedral  : 11.220 141.633   1113
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.72 %
    Favored  : 78.00 %
  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:  3.76 (0.35), residues: 585
  helix:  3.36 (0.24), residues: 392
  sheet:  0.58 (0.87), residues: 50
  loop :  0.63 (0.56), residues: 143

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  88 
 TYR   0.016   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  63 

*********************** 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
  103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.557 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (pp20)
REVERT: B  368 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7672 (pp20)
REVERT: B  434 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7700 (mp0)
REVERT: A   37 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7529 (ttm)
REVERT: A   65 HIS cc_start: 0.7932 (m90) cc_final: 0.6900 (p-80)
REVERT: A  108 HIS cc_start: 0.7417 (m90) cc_final: 0.7057 (m-70)
REVERT: A  112 GLN cc_start: 0.7653 (mt0) cc_final: 0.7317 (pt0)
REVERT: A  129 LEU cc_start: 0.7869 (tt) cc_final: 0.7669 (mp)
  outliers start: 21
  outliers final: 9
  residues processed: 92
  average time/residue: 1.1451
  time to fit residues: 109.8522
Evaluate side-chains
  90 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
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   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  135 HIS
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0030
   chunk 52 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.7392

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.151737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.111949 restraints weight = 4252.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.06
r_work: 0.3148 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4955  Z= 0.186
  Angle     :  0.465   5.795   6763  Z= 0.230
  Chirality :  0.037   0.133    857
  Planarity :  0.003   0.037    790
  Dihedral  : 11.213 141.520   1113
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.13 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.72 (0.35), residues: 585
  helix:  3.35 (0.24), residues: 392
  sheet:  0.49 (0.87), residues: 50
  loop :  0.60 (0.56), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.016   0.001   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

*********************** 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
  101 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.517 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7961 (pp20)
REVERT: B  368 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7761 (pp20)
REVERT: B  401 LYS cc_start: 0.7456 (mptm) cc_final: 0.7188 (mptp)
REVERT: B  434 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7765 (mp0)
REVERT: A   37 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7477 (ttm)
REVERT: A   65 HIS cc_start: 0.7950 (m90) cc_final: 0.6920 (p-80)
REVERT: A  108 HIS cc_start: 0.7427 (m90) cc_final: 0.7191 (m170)
REVERT: A  112 GLN cc_start: 0.7630 (mt0) cc_final: 0.7295 (pt0)
REVERT: A  129 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7668 (mp)
REVERT: A  368 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8251 (pp20)
  outliers start: 20
  outliers final: 10
  residues processed: 89
  average time/residue: 1.1483
  time to fit residues: 106.7211
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  : 0.482 
-------------------------------------------------------------------------------
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   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:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:   50.0000
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.152461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.112902 restraints weight = 4267.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.06
r_work: 0.3162 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4955  Z= 0.164
  Angle     :  0.446   5.310   6763  Z= 0.222
  Chirality :  0.037   0.139    857
  Planarity :  0.003   0.035    790
  Dihedral  : 11.009 141.719   1113
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 18.13 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.82 (0.35), residues: 585
  helix:  3.41 (0.24), residues: 392
  sheet:  0.56 (0.87), residues: 50
  loop :  0.66 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.010   0.001   PHE B  88 
 TYR   0.015   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  63 

*********************** 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
  100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.573 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7943 (pp20)
REVERT: B  368 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7760 (pp20)
REVERT: B  401 LYS cc_start: 0.7440 (mptm) cc_final: 0.7018 (mmmt)
REVERT: B  405 ASP cc_start: 0.8109 (m-30) cc_final: 0.7641 (p0)
REVERT: B  434 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7772 (mp0)
REVERT: A   37 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7479 (ttm)
REVERT: A   65 HIS cc_start: 0.7951 (m90) cc_final: 0.6926 (p-80)
REVERT: A  108 HIS cc_start: 0.7420 (m90) cc_final: 0.7180 (m170)
REVERT: A  112 GLN cc_start: 0.7611 (mt0) cc_final: 0.7298 (pt0)
REVERT: A  129 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7675 (mp)
REVERT: A  246 ARG cc_start: 0.7657 (tpt170) cc_final: 0.6357 (ttp80)
REVERT: A  368 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8303 (pp20)
  outliers start: 21
  outliers final: 10
  residues processed: 89
  average time/residue: 1.2148
  time to fit residues: 112.6022
Evaluate side-chains
  95 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0570
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.152554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113193 restraints weight = 4237.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.05
r_work: 0.3166 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4955  Z= 0.162
  Angle     :  0.451   5.658   6763  Z= 0.224
  Chirality :  0.037   0.143    857
  Planarity :  0.003   0.035    790
  Dihedral  : 10.907 141.475   1113
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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:  3.87 (0.35), residues: 585
  helix:  3.45 (0.24), residues: 392
  sheet:  0.56 (0.87), residues: 50
  loop :  0.68 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.009   0.001   PHE B  88 
 TYR   0.015   0.001   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

*********************** 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
  98 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.566 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7959 (pp20)
REVERT: B  368 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7758 (pp20)
REVERT: B  401 LYS cc_start: 0.7412 (mptm) cc_final: 0.6996 (mmmt)
REVERT: B  405 ASP cc_start: 0.8080 (m-30) cc_final: 0.7576 (p0)
REVERT: B  434 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7749 (mp0)
REVERT: A   37 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7472 (ttm)
REVERT: A   65 HIS cc_start: 0.7981 (m90) cc_final: 0.6924 (p-80)
REVERT: A   69 LYS cc_start: 0.8323 (tptp) cc_final: 0.8107 (tptm)
REVERT: A  112 GLN cc_start: 0.7661 (mt0) cc_final: 0.7320 (pt0)
REVERT: A  129 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7678 (mp)
REVERT: A  246 ARG cc_start: 0.7631 (tpt170) cc_final: 0.6336 (ttp80)
REVERT: A  368 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8291 (pp20)
  outliers start: 18
  outliers final: 10
  residues processed: 88
  average time/residue: 1.5132
  time to fit residues: 138.5883
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  : 0.582 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0970
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.150820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111190 restraints weight = 4321.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.07
r_work: 0.3142 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
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      :  0.003   0.026   4955  Z= 0.202
  Angle     :  0.474   5.119   6763  Z= 0.236
  Chirality :  0.038   0.131    857
  Planarity :  0.003   0.035    790
  Dihedral  : 10.913 140.442   1113
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.53 %
    Favored  : 78.00 %
  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:  3.74 (0.35), residues: 585
  helix:  3.35 (0.24), residues: 392
  sheet:  0.43 (0.86), residues: 50
  loop :  0.67 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 312 
 HIS   0.003   0.001   HIS B 135 
 PHE   0.008   0.001   PHE B  88 
 TYR   0.017   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

********************** 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
  95 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.507 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8010 (pp20)
REVERT: B  368 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7767 (pp20)
REVERT: B  401 LYS cc_start: 0.7491 (mptm) cc_final: 0.7040 (mmmt)
REVERT: B  434 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7747 (mp0)
REVERT: A   37 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7505 (ttm)
REVERT: A   65 HIS cc_start: 0.8008 (m90) cc_final: 0.6912 (p-80)
REVERT: A  112 GLN cc_start: 0.7680 (mt0) cc_final: 0.7287 (pt0)
REVERT: A  129 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7681 (mp)
REVERT: A  366 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7876 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 86
  average time/residue: 1.2296
  time to fit residues: 110.1392
Evaluate side-chains
  92 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
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  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
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:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   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 ** 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 = 0.3790 r_free = 0.3790 target = 0.151120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111476 restraints weight = 4333.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.07
r_work: 0.3144 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4955  Z= 0.189
  Angle     :  0.459   5.153   6763  Z= 0.230
  Chirality :  0.037   0.134    857
  Planarity :  0.003   0.034    790
  Dihedral  : 10.835 139.838   1113
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.14 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.75 (0.35), residues: 585
  helix:  3.37 (0.24), residues: 392
  sheet:  0.47 (0.87), residues: 50
  loop :  0.66 (0.54), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.008   0.001   PHE B  88 
 TYR   0.017   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5059.97 seconds
wall clock time: 90 minutes 32.58 seconds (5432.58 seconds total)