Starting phenix.real_space_refine
on Tue Jan 14 01:05:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xma_38469/01_2025/8xma_38469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xma_38469/01_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_38469/01_2025/8xma_38469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xma_38469/01_2025/8xma_38469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xma_38469/01_2025/8xma_38469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xma_38469/01_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-5571/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: 3.66, per 1000 atoms: 0.75
  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: 1.44
  Conformation dependent library (CDL) restraints added in 599.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 387 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 370 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 433 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" 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: 0.44
  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: 1.20

  Time building geometry restraints manager: 1.63 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:             1.530
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.640
  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:12.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.030
-------------------------------------------------------------------------------
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  : 0.497 
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: 1.4183
  time to fit residues: 199.1328
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  : 0.530 
-------------------------------------------------------------------------------
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   4955  Z= 0.251
  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 

*********************** 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  : 0.476 
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: 1.2394
  time to fit residues: 132.5963
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  : 0.562 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 6 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.152908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.112894 restraints weight = 4469.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.23
r_work: 0.3212 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4955  Z= 0.196
  Angle     :  0.519   5.627   6763  Z= 0.249
  Chirality :  0.038   0.226    857
  Planarity :  0.003   0.044    790
  Dihedral  : 11.907 138.620   1113
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  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:  3.63 (0.35), residues: 585
  helix:  3.20 (0.25), residues: 392
  sheet:  1.23 (0.90), residues: 46
  loop :  0.53 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 312 
 HIS   0.006   0.001   HIS B 135 
 PHE   0.007   0.001   PHE B 104 
 TYR   0.018   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B 361 

*********************** 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
  101 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.542 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8228 (pm20) cc_final: 0.7999 (pp20)
REVERT: B  368 GLU cc_start: 0.8098 (pp20) cc_final: 0.7677 (pp20)
REVERT: B  401 LYS cc_start: 0.7564 (mttm) cc_final: 0.7362 (mptm)
REVERT: B  434 GLU cc_start: 0.8006 (mp0) cc_final: 0.7747 (mm-30)
REVERT: A   37 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7433 (ttm)
REVERT: A   65 HIS cc_start: 0.7767 (m90) cc_final: 0.6770 (p-80)
REVERT: A  108 HIS cc_start: 0.7028 (m90) cc_final: 0.6814 (m-70)
REVERT: A  112 GLN cc_start: 0.7522 (mt0) cc_final: 0.7286 (pt0)
REVERT: A  129 LEU cc_start: 0.7711 (tt) cc_final: 0.7473 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 89
  average time/residue: 1.1194
  time to fit residues: 103.9962
Evaluate side-chains
  90 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0970
   chunk 32 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 16 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 = 0.3796 r_free = 0.3796 target = 0.151388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111530 restraints weight = 4347.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.07
r_work: 0.3148 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4955  Z= 0.200
  Angle     :  0.483   5.003   6763  Z= 0.239
  Chirality :  0.038   0.191    857
  Planarity :  0.003   0.041    790
  Dihedral  : 11.579 139.172   1113
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 16.29 %
    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:  3.65 (0.35), residues: 585
  helix:  3.23 (0.24), residues: 392
  sheet:  1.02 (0.89), residues: 48
  loop :  0.57 (0.56), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 312 
 HIS   0.004   0.001   HIS B 135 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.018   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
  103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.541 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8031 (pp20)
REVERT: B  368 GLU cc_start: 0.8182 (pp20) cc_final: 0.7598 (pp20)
REVERT: B  434 GLU cc_start: 0.7997 (mp0) cc_final: 0.7705 (mm-30)
REVERT: B  445 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6397 (tm-30)
REVERT: A   37 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7491 (ttm)
REVERT: A   65 HIS cc_start: 0.7757 (m90) cc_final: 0.6932 (p-80)
REVERT: A   78 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7662 (mt-10)
REVERT: A  108 HIS cc_start: 0.7390 (m90) cc_final: 0.7070 (m-70)
REVERT: A  112 GLN cc_start: 0.7634 (mt0) cc_final: 0.7354 (pt0)
REVERT: A  129 LEU cc_start: 0.7855 (tt) cc_final: 0.7638 (mp)
  outliers start: 19
  outliers final: 8
  residues processed: 91
  average time/residue: 1.2094
  time to fit residues: 114.7549
Evaluate side-chains
  92 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 23 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0070
   chunk 58 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0980
   overall best weight:    0.4598

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.153667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.113743 restraints weight = 4350.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.09
r_work: 0.3179 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4955  Z= 0.146
  Angle     :  0.440   4.911   6763  Z= 0.219
  Chirality :  0.037   0.136    857
  Planarity :  0.003   0.037    790
  Dihedral  : 11.229 141.661   1113
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.53 %
    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:  3.43 (0.24), residues: 392
  sheet:  0.90 (0.90), residues: 49
  loop :  0.64 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.006   0.001   PHE B 104 
 TYR   0.015   0.001   TYR B 396 
 ARG   0.003   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
  100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.574 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7944 (pp20)
REVERT: B  368 GLU cc_start: 0.8122 (pp20) cc_final: 0.7691 (pp20)
REVERT: B  401 LYS cc_start: 0.7457 (mptm) cc_final: 0.7214 (mptm)
REVERT: B  434 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7694 (mm-30)
REVERT: A   37 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7471 (ttm)
REVERT: A   65 HIS cc_start: 0.7696 (m90) cc_final: 0.6815 (p-80)
REVERT: A   78 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7698 (mt-10)
REVERT: A  108 HIS cc_start: 0.7275 (m90) cc_final: 0.6895 (m-70)
REVERT: A  112 GLN cc_start: 0.7587 (mt0) cc_final: 0.7296 (pt0)
REVERT: A  129 LEU cc_start: 0.7834 (tt) cc_final: 0.7623 (mp)
REVERT: A  246 ARG cc_start: 0.7699 (tpt170) cc_final: 0.6363 (ttp80)
  outliers start: 16
  outliers final: 8
  residues processed: 91
  average time/residue: 1.2137
  time to fit residues: 114.9204
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  : 0.510 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 32 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.153096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.112914 restraints weight = 4323.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.09
r_work: 0.3167 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4955  Z= 0.162
  Angle     :  0.440   4.892   6763  Z= 0.221
  Chirality :  0.037   0.138    857
  Planarity :  0.003   0.036    790
  Dihedral  : 11.110 141.911   1113
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 18.33 %
    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:  3.90 (0.35), residues: 585
  helix:  3.44 (0.24), residues: 392
  sheet:  0.96 (0.90), residues: 48
  loop :  0.66 (0.55), residues: 145

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   0.012   0.001   PHE B  88 
 TYR   0.015   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
  100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.487 
Fit side-chains
REVERT: B   78 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7945 (pp20)
REVERT: B  368 GLU cc_start: 0.8025 (pp20) cc_final: 0.7710 (pp20)
REVERT: B  434 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7648 (mm-30)
REVERT: A   37 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7514 (ttm)
REVERT: A   65 HIS cc_start: 0.7710 (m90) cc_final: 0.6766 (p-80)
REVERT: A  108 HIS cc_start: 0.7260 (m90) cc_final: 0.6934 (m-70)
REVERT: A  112 GLN cc_start: 0.7598 (mt0) cc_final: 0.7263 (pt0)
REVERT: A  129 LEU cc_start: 0.7876 (tt) cc_final: 0.7667 (mp)
  outliers start: 19
  outliers final: 9
  residues processed: 91
  average time/residue: 1.1164
  time to fit residues: 105.9040
Evaluate side-chains
  91 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
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  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  324 MET
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:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.151570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.111693 restraints weight = 4229.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.06
r_work: 0.3146 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4955  Z= 0.203
  Angle     :  0.473   5.964   6763  Z= 0.235
  Chirality :  0.038   0.130    857
  Planarity :  0.003   0.035    790
  Dihedral  : 11.174 141.373   1113
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  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:  3.75 (0.35), residues: 585
  helix:  3.32 (0.24), residues: 392
  sheet:  0.82 (0.90), residues: 48
  loop :  0.63 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 312 
 HIS   0.003   0.000   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 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
  100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.668 
Fit side-chains
REVERT: B   10 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7601 (mtt180)
REVERT: B   78 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7995 (pp20)
REVERT: B  368 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7726 (pp20)
REVERT: B  401 LYS cc_start: 0.7448 (mptm) cc_final: 0.7196 (mptp)
REVERT: B  434 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7755 (mp0)
REVERT: A   37 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7491 (ttm)
REVERT: A   65 HIS cc_start: 0.7770 (m90) cc_final: 0.6902 (p-80)
REVERT: A  112 GLN cc_start: 0.7682 (mt0) cc_final: 0.7307 (pt0)
REVERT: A  129 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7652 (mp)
REVERT: A  368 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8263 (pp20)
  outliers start: 21
  outliers final: 9
  residues processed: 88
  average time/residue: 1.3297
  time to fit residues: 121.8129
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  : 0.519 
-------------------------------------------------------------------------------
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  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:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.151494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.111646 restraints weight = 4268.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.06
r_work: 0.3144 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4955  Z= 0.195
  Angle     :  0.462   5.386   6763  Z= 0.231
  Chirality :  0.038   0.136    857
  Planarity :  0.003   0.034    790
  Dihedral  : 11.023 141.056   1113
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.33 %
    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:  3.71 (0.35), residues: 585
  helix:  3.32 (0.24), residues: 392
  sheet:  0.54 (0.87), residues: 50
  loop :  0.67 (0.55), 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   0.007   0.001   PHE B  88 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.002   0.000   ARG A  76 

*********************** 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
  102 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.576 
Fit side-chains
REVERT: B   10 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7597 (mtt180)
REVERT: B   78 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7981 (pp20)
REVERT: B  368 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (pp20)
REVERT: B  401 LYS cc_start: 0.7475 (mptm) cc_final: 0.7036 (mmmt)
REVERT: B  405 ASP cc_start: 0.8079 (m-30) cc_final: 0.7612 (p0)
REVERT: B  434 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7759 (mp0)
REVERT: A   37 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7511 (ttm)
REVERT: A   65 HIS cc_start: 0.7958 (m90) cc_final: 0.6856 (p-80)
REVERT: A  112 GLN cc_start: 0.7681 (mt0) cc_final: 0.7319 (pt0)
REVERT: A  129 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7664 (mp)
  outliers start: 20
  outliers final: 10
  residues processed: 90
  average time/residue: 1.2693
  time to fit residues: 119.3871
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  : 0.598 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.151080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.111389 restraints weight = 4239.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.06
r_work: 0.3140 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3324

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= 0.198
  Angle     :  0.469   5.550   6763  Z= 0.235
  Chirality :  0.038   0.140    857
  Planarity :  0.003   0.033    790
  Dihedral  : 10.954 140.552   1113
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.53 %
    Favored  : 77.39 %
  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:  3.30 (0.24), residues: 392
  sheet:  0.52 (0.87), residues: 50
  loop :  0.63 (0.55), 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   0.017   0.002   TYR B 396 
 ARG   0.003   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
  103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.543 
Fit side-chains
REVERT: B   10 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7590 (mtt180)
REVERT: B   78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7989 (pp20)
REVERT: B  368 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7755 (pp20)
REVERT: B  401 LYS cc_start: 0.7488 (mptm) cc_final: 0.7037 (mmmt)
REVERT: B  434 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7757 (mp0)
REVERT: A   37 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7514 (ttm)
REVERT: A   65 HIS cc_start: 0.8001 (m90) cc_final: 0.6954 (p-80)
REVERT: A  112 GLN cc_start: 0.7690 (mt0) cc_final: 0.7329 (pt0)
REVERT: A  129 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7665 (mp)
REVERT: A  366 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7875 (p)
REVERT: A  368 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8316 (pp20)
  outliers start: 20
  outliers final: 11
  residues processed: 91
  average time/residue: 1.3284
  time to fit residues: 125.3802
Evaluate side-chains
  102 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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   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  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  106 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0570
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.151606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111989 restraints weight = 4300.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.06
r_work: 0.3151 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3364

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= 0.183
  Angle     :  0.457   5.476   6763  Z= 0.229
  Chirality :  0.037   0.141    857
  Planarity :  0.003   0.033    790
  Dihedral  : 10.839 140.233   1113
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.74 %
    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:  3.74 (0.35), residues: 585
  helix:  3.35 (0.24), residues: 392
  sheet:  0.55 (0.87), residues: 50
  loop :  0.63 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 312 
 HIS   0.003   0.000   HIS B 135 
 PHE   0.007   0.001   PHE B  88 
 TYR   0.016   0.001   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
  100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.679 
Fit side-chains
REVERT: B   10 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7563 (mtt180)
REVERT: B   78 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7980 (pp20)
REVERT: B  368 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7728 (pp20)
REVERT: B  401 LYS cc_start: 0.7473 (mptm) cc_final: 0.7040 (mmmt)
REVERT: B  405 ASP cc_start: 0.8089 (m-30) cc_final: 0.7646 (p0)
REVERT: B  434 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7738 (mp0)
REVERT: A   37 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7488 (ttm)
REVERT: A   65 HIS cc_start: 0.8001 (m90) cc_final: 0.6960 (p-80)
REVERT: A  112 GLN cc_start: 0.7674 (mt0) cc_final: 0.7314 (pt0)
REVERT: A  129 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7666 (mp)
REVERT: A  366 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (p)
REVERT: A  368 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8316 (pp20)
  outliers start: 18
  outliers final: 9
  residues processed: 88
  average time/residue: 1.4441
  time to fit residues: 131.8601
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  : 0.507 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0570
   chunk 55 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.153575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.114180 restraints weight = 4283.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.07
r_work: 0.3183 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4955  Z= 0.147
  Angle     :  0.434   5.502   6763  Z= 0.218
  Chirality :  0.037   0.142    857
  Planarity :  0.003   0.032    790
  Dihedral  : 10.668 140.070   1113
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.53 %
    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:  3.90 (0.35), residues: 585
  helix:  3.48 (0.24), residues: 392
  sheet:  0.68 (0.87), residues: 50
  loop :  0.63 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 312 
 HIS   0.002   0.000   HIS B 135 
 PHE   0.008   0.001   PHE B  88 
 TYR   0.014   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4490.55 seconds
wall clock time: 80 minutes 28.94 seconds (4828.94 seconds total)