Starting phenix.real_space_refine
on Tue Mar 11 20:18:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cn0_30412/03_2025/7cn0_30412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cn0_30412/03_2025/7cn0_30412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2025/7cn0_30412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2025/7cn0_30412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2025/7cn0_30412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2025/7cn0_30412.cif"
  }
  resolution = 3.9
  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=  -0.000 sd=   1.000
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
     K       2      8.98       5
     S      24      5.16       5
     C    4412      2.51       5
     N    1076      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6602
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1650
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 8, 'TRANS': 212}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 101
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 4.05, per 1000 atoms: 0.61
  Number of scatterers: 6602
  At special positions: 0
  Unit cell: (106.964, 106.964, 77.792, 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)
     K       2     19.00
     S      24     16.00
     O    1088      8.00
     N    1076      7.00
     C    4412      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: 1.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1656

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      77.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 404 through 431
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 456 through 473
      removed outlier: 3.874A  pdb=" N   MET A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE A 464 " --> pdb=" O   ASP A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 497
      removed outlier: 4.407A  pdb=" N   VAL A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   HIS A 492 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 505
    Processing helix  chain 'A' and resid 522 through 532
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.796A  pdb=" N   ARG A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS A 538 " --> pdb=" O   ARG A 534 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 533 through 538'
    Processing helix  chain 'A' and resid 548 through 575
    Processing helix  chain 'A' and resid 585 through 593
      removed outlier: 3.795A  pdb=" N   ASP A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 624
      removed outlier: 4.002A  pdb=" N   ALA A 614 " --> pdb=" O   LYS A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 666
      removed outlier: 4.058A  pdb=" N   ALA A 653 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE A 656 " --> pdb=" O   TYR A 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 431
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 456 through 473
      removed outlier: 3.874A  pdb=" N   MET B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE B 464 " --> pdb=" O   ASP B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 497
      removed outlier: 4.407A  pdb=" N   VAL B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   HIS B 492 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 505
    Processing helix  chain 'B' and resid 522 through 532
    Processing helix  chain 'B' and resid 533 through 538
      removed outlier: 3.796A  pdb=" N   ARG B 537 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS B 538 " --> pdb=" O   ARG B 534 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 533 through 538'
    Processing helix  chain 'B' and resid 548 through 575
    Processing helix  chain 'B' and resid 585 through 593
      removed outlier: 3.795A  pdb=" N   ASP B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 624
      removed outlier: 4.002A  pdb=" N   ALA B 614 " --> pdb=" O   LYS B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 666
      removed outlier: 4.058A  pdb=" N   ALA B 653 " --> pdb=" O   SER B 649 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE B 656 " --> pdb=" O   TYR B 652 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 431
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 456 through 473
      removed outlier: 3.874A  pdb=" N   MET C 462 " --> pdb=" O   ILE C 458 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE C 464 " --> pdb=" O   ASP C 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 497
      removed outlier: 4.407A  pdb=" N   VAL C 491 " --> pdb=" O   GLY C 487 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   HIS C 492 " --> pdb=" O   ARG C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 498 through 505
    Processing helix  chain 'C' and resid 522 through 532
    Processing helix  chain 'C' and resid 533 through 538
      removed outlier: 3.796A  pdb=" N   ARG C 537 " --> pdb=" O   VAL C 533 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS C 538 " --> pdb=" O   ARG C 534 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 533 through 538'
    Processing helix  chain 'C' and resid 548 through 575
    Processing helix  chain 'C' and resid 585 through 593
      removed outlier: 3.795A  pdb=" N   ASP C 591 " --> pdb=" O   HIS C 587 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 606 through 624
      removed outlier: 4.002A  pdb=" N   ALA C 614 " --> pdb=" O   LYS C 610 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 634 through 666
      removed outlier: 4.058A  pdb=" N   ALA C 653 " --> pdb=" O   SER C 649 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE C 656 " --> pdb=" O   TYR C 652 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 431
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 456 through 473
      removed outlier: 3.874A  pdb=" N   MET D 462 " --> pdb=" O   ILE D 458 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ILE D 464 " --> pdb=" O   ASP D 460 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 497
      removed outlier: 4.407A  pdb=" N   VAL D 491 " --> pdb=" O   GLY D 487 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   HIS D 492 " --> pdb=" O   ARG D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 505
    Processing helix  chain 'D' and resid 522 through 532
    Processing helix  chain 'D' and resid 533 through 538
      removed outlier: 3.796A  pdb=" N   ARG D 537 " --> pdb=" O   VAL D 533 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS D 538 " --> pdb=" O   ARG D 534 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 533 through 538'
    Processing helix  chain 'D' and resid 548 through 575
    Processing helix  chain 'D' and resid 585 through 593
      removed outlier: 3.795A  pdb=" N   ASP D 591 " --> pdb=" O   HIS D 587 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 606 through 624
      removed outlier: 4.002A  pdb=" N   ALA D 614 " --> pdb=" O   LYS D 610 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 634 through 666
      removed outlier: 4.058A  pdb=" N   ALA D 653 " --> pdb=" O   SER D 649 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE D 656 " --> pdb=" O   TYR D 652 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1332 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: 1.82

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1964
        1.34 -     1.46: 1484
        1.46 -     1.57: 3272
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 6756
  Sorted by residual:
  bond pdb=" C   THR D 425 "
       pdb=" N   PRO D 426 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.20e-02 6.94e+03 3.37e+00
  bond pdb=" C   THR C 425 "
       pdb=" N   PRO C 426 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.20e-02 6.94e+03 3.37e+00
  bond pdb=" C   THR B 425 "
       pdb=" N   PRO B 426 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.20e-02 6.94e+03 3.37e+00
  bond pdb=" C   THR A 425 "
       pdb=" N   PRO A 426 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.20e-02 6.94e+03 3.37e+00
  bond pdb=" CA  ILE A 521 "
       pdb=" CB  ILE A 521 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.010 1.05e-02 9.07e+03 8.77e-01
  ... (remaining 6751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 8660
        1.16 -     2.32: 436
        2.32 -     3.49: 100
        3.49 -     4.65: 20
        4.65 -     5.81: 8
  Bond angle restraints: 9224
  Sorted by residual:
  angle pdb=" N   PHE A 498 "
        pdb=" CA  PHE A 498 "
        pdb=" C   PHE A 498 "
      ideal   model   delta    sigma   weight residual
     114.62  111.11    3.51 1.14e+00 7.69e-01 9.47e+00
  angle pdb=" N   PHE B 498 "
        pdb=" CA  PHE B 498 "
        pdb=" C   PHE B 498 "
      ideal   model   delta    sigma   weight residual
     114.62  111.11    3.51 1.14e+00 7.69e-01 9.47e+00
  angle pdb=" N   PHE C 498 "
        pdb=" CA  PHE C 498 "
        pdb=" C   PHE C 498 "
      ideal   model   delta    sigma   weight residual
     114.62  111.11    3.51 1.14e+00 7.69e-01 9.47e+00
  angle pdb=" N   PHE D 498 "
        pdb=" CA  PHE D 498 "
        pdb=" C   PHE D 498 "
      ideal   model   delta    sigma   weight residual
     114.62  111.11    3.51 1.14e+00 7.69e-01 9.47e+00
  angle pdb=" CA  PHE C 498 "
        pdb=" C   PHE C 498 "
        pdb=" N   LEU C 499 "
      ideal   model   delta    sigma   weight residual
     119.71  116.85    2.86 1.17e+00 7.31e-01 5.97e+00
  ... (remaining 9219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    10.01: 3108
       10.01 -    20.02: 452
       20.02 -    30.02: 184
       30.02 -    40.03: 68
       40.03 -    50.03: 32
  Dihedral angle restraints: 3844
    sinusoidal: 1292
      harmonic: 2552
  Sorted by residual:
  dihedral pdb=" CA  PHE C 656 "
           pdb=" C   PHE C 656 "
           pdb=" N   GLY C 657 "
           pdb=" CA  GLY C 657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  PHE D 656 "
           pdb=" C   PHE D 656 "
           pdb=" N   GLY D 657 "
           pdb=" CA  GLY D 657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  PHE A 656 "
           pdb=" C   PHE A 656 "
           pdb=" N   GLY A 657 "
           pdb=" CA  GLY A 657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 3841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 744
       0.036 -    0.071: 312
       0.071 -    0.107: 56
       0.107 -    0.142: 20
       0.142 -    0.178: 4
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CA  THR C 425 "
            pdb=" N   THR C 425 "
            pdb=" C   THR C 425 "
            pdb=" CB  THR C 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CA  THR D 425 "
            pdb=" N   THR D 425 "
            pdb=" C   THR D 425 "
            pdb=" CB  THR D 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CA  THR B 425 "
            pdb=" N   THR B 425 "
            pdb=" C   THR B 425 "
            pdb=" CB  THR B 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 7.89e-01
  ... (remaining 1133 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 616 "    0.010 2.00e-02 2.50e+03   7.61e-03 1.16e+00
        pdb=" CG  TYR C 616 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 616 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 616 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 616 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 616 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 616 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 616 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 616 "   -0.010 2.00e-02 2.50e+03   7.61e-03 1.16e+00
        pdb=" CG  TYR B 616 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 616 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 616 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 616 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 616 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 616 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 616 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 616 "   -0.010 2.00e-02 2.50e+03   7.61e-03 1.16e+00
        pdb=" CG  TYR A 616 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 616 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 616 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 616 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 616 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 616 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 616 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.50: 32
        2.50 -     3.16: 5920
        3.16 -     3.82: 12816
        3.82 -     4.48: 15316
        4.48 -     5.14: 25262
  Nonbonded interactions: 59346
  Sorted by model distance:
  nonbonded pdb=" CG  LEU A 646 "
            pdb=" CE  MET D 554 "
     model   vdw
     1.843 3.890
  nonbonded pdb=" CE  MET A 554 "
            pdb=" CG  LEU B 646 "
     model   vdw
     1.843 3.890
  nonbonded pdb=" CE  MET B 554 "
            pdb=" CG  LEU C 646 "
     model   vdw
     1.843 3.890
  nonbonded pdb=" CE  MET C 554 "
            pdb=" CG  LEU D 646 "
     model   vdw
     1.844 3.890
  nonbonded pdb=" CD2 LEU A 646 "
            pdb=" CE  MET D 554 "
     model   vdw
     1.867 3.880
  ... (remaining 59341 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 402 through 666)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.110
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
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   0.023   6756  Z= 0.227
  Angle     :  0.623   5.810   9224  Z= 0.347
  Chirality :  0.041   0.178   1136
  Planarity :  0.003   0.016   1100
  Dihedral  : 13.322  50.033   2188
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.25), residues: 836
  helix: -1.49 (0.17), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.85 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 585 
 HIS   0.002   0.001   HIS A 492 
 PHE   0.011   0.001   PHE B 640 
 TYR   0.018   0.002   TYR C 616 
 ARG   0.001   0.000   ARG D 488 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7584 (ttmt)
REVERT: A  652 TYR cc_start: 0.8354 (t80) cc_final: 0.8068 (t80)
REVERT: B  610 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7590 (ttmt)
REVERT: B  652 TYR cc_start: 0.8359 (t80) cc_final: 0.8067 (t80)
REVERT: C  610 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7587 (ttmt)
REVERT: C  652 TYR cc_start: 0.8356 (t80) cc_final: 0.8067 (t80)
REVERT: D  610 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7579 (ttmt)
REVERT: D  652 TYR cc_start: 0.8355 (t80) cc_final: 0.8063 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1937
  time to fit residues: 40.7831
Evaluate side-chains
  125 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN
A 562 HIS
A 576 GLN
A 587 HIS
A 588 ASN
B 470 ASN
B 562 HIS
B 576 GLN
B 587 HIS
B 588 ASN
C 562 HIS
C 576 GLN
C 587 HIS
C 588 ASN
D 470 ASN
D 562 HIS
D 576 GLN
D 587 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.177930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140701 restraints weight = 11546.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.138262 restraints weight = 9369.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.140346 restraints weight = 6829.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6756  Z= 0.294
  Angle     :  0.649   6.629   9224  Z= 0.331
  Chirality :  0.043   0.153   1136
  Planarity :  0.003   0.018   1100
  Dihedral  :  5.019  18.619    920
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.37 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.28), residues: 836
  helix: -0.67 (0.19), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.31 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 568 
 HIS   0.002   0.001   HIS B 587 
 PHE   0.013   0.002   PHE A 640 
 TYR   0.018   0.002   TYR C 616 
 ARG   0.004   0.001   ARG A 531 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7400 (ttmt)
REVERT: B  610 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7406 (ttmt)
REVERT: C  610 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7588 (ttmt)
REVERT: D  610 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7592 (ttmt)
  outliers start: 20
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1734
  time to fit residues: 36.0774
Evaluate side-chains
  148 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  618 THR
Chi-restraints excluded: chain C residue  650 LEU
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  618 THR
Chi-restraints excluded: chain D residue  650 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 39 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
D 588 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.178467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.142793 restraints weight = 11570.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.140629 restraints weight = 7885.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.142195 restraints weight = 7032.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6756  Z= 0.259
  Angle     :  0.620   6.347   9224  Z= 0.317
  Chirality :  0.042   0.154   1136
  Planarity :  0.003   0.019   1100
  Dihedral  :  4.812  17.592    920
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.77 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.29), residues: 836
  helix: -0.31 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.98 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 568 
 HIS   0.001   0.001   HIS D 587 
 PHE   0.011   0.001   PHE A 463 
 TYR   0.013   0.002   TYR D 616 
 ARG   0.008   0.001   ARG D 531 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7338 (ttmt)
REVERT: A  652 TYR cc_start: 0.8037 (t80) cc_final: 0.7652 (t80)
REVERT: B  610 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7347 (ttmt)
REVERT: B  652 TYR cc_start: 0.8030 (t80) cc_final: 0.7642 (t80)
REVERT: C  610 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7350 (ttmt)
REVERT: C  652 TYR cc_start: 0.8047 (t80) cc_final: 0.7646 (t80)
REVERT: D  610 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7548 (ttmt)
REVERT: D  652 TYR cc_start: 0.8038 (t80) cc_final: 0.7645 (t80)
  outliers start: 24
  outliers final: 8
  residues processed: 164
  average time/residue: 0.1768
  time to fit residues: 38.5211
Evaluate side-chains
  148 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  618 THR
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  618 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0070
   chunk 57 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0670
   chunk 30 optimal weight:    0.3980
   chunk 55 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
A 592 GLN
B 592 GLN
C 592 GLN
D 592 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.183094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.144912 restraints weight = 11781.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.145006 restraints weight = 8378.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.146742 restraints weight = 6116.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6756  Z= 0.139
  Angle     :  0.552   6.383   9224  Z= 0.275
  Chirality :  0.039   0.144   1136
  Planarity :  0.004   0.042   1100
  Dihedral  :  4.235  15.540    920
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 26.70 %
    Favored  : 68.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.30), residues: 836
  helix:  0.20 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.69 (0.52), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 585 
 HIS   0.001   0.000   HIS C 587 
 PHE   0.007   0.001   PHE D 617 
 TYR   0.010   0.001   TYR C 542 
 ARG   0.009   0.001   ARG B 531 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  415 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5936 (tt)
REVERT: A  528 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8284 (mtp180)
REVERT: A  610 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7553 (ttmt)
REVERT: A  652 TYR cc_start: 0.8133 (t80) cc_final: 0.7667 (t80)
REVERT: B  415 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5921 (tt)
REVERT: B  528 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.8279 (mtp180)
REVERT: B  610 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7363 (ttmt)
REVERT: B  652 TYR cc_start: 0.8131 (t80) cc_final: 0.7663 (t80)
REVERT: C  415 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5934 (tt)
REVERT: C  528 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8287 (mtp180)
REVERT: C  610 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7549 (ttmt)
REVERT: C  652 TYR cc_start: 0.8137 (t80) cc_final: 0.7664 (t80)
REVERT: D  415 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5935 (tt)
REVERT: D  528 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.8288 (mtp180)
REVERT: D  610 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7539 (ttmt)
REVERT: D  652 TYR cc_start: 0.8141 (t80) cc_final: 0.7671 (t80)
  outliers start: 32
  outliers final: 8
  residues processed: 180
  average time/residue: 0.1516
  time to fit residues: 37.7480
Evaluate side-chains
  156 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  542 TYR
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain C residue  542 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  542 TYR
Chi-restraints excluded: chain D residue  550 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.180555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.139375 restraints weight = 11484.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142083 restraints weight = 7215.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.143927 restraints weight = 5335.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6756  Z= 0.168
  Angle     :  0.571   6.562   9224  Z= 0.285
  Chirality :  0.041   0.162   1136
  Planarity :  0.003   0.018   1100
  Dihedral  :  4.239  14.964    920
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 29.17 %
    Favored  : 67.28 %
  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: -0.31 (0.29), residues: 836
  helix:  0.22 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.48 (0.52), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 585 
 HIS   0.001   0.000   HIS A 492 
 PHE   0.011   0.001   PHE A 640 
 TYR   0.008   0.001   TYR D 542 
 ARG   0.007   0.001   ARG A 531 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  415 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5841 (tt)
REVERT: A  528 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8172 (mtp180)
REVERT: A  610 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7483 (ttmt)
REVERT: A  652 TYR cc_start: 0.8193 (t80) cc_final: 0.7803 (t80)
REVERT: B  415 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5840 (tt)
REVERT: B  528 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8171 (mtp180)
REVERT: B  610 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7483 (ttmt)
REVERT: B  652 TYR cc_start: 0.8189 (t80) cc_final: 0.7803 (t80)
REVERT: C  415 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5839 (tt)
REVERT: C  528 ARG cc_start: 0.8577 (mtt-85) cc_final: 0.8172 (mtp180)
REVERT: C  610 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7481 (ttmt)
REVERT: C  652 TYR cc_start: 0.8198 (t80) cc_final: 0.7803 (t80)
REVERT: D  415 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5843 (tt)
REVERT: D  528 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.8171 (mtp180)
REVERT: D  610 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7480 (ttmt)
REVERT: D  652 TYR cc_start: 0.8196 (t80) cc_final: 0.7804 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 164
  average time/residue: 0.1569
  time to fit residues: 35.4649
Evaluate side-chains
  166 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain C residue  650 LEU
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  532 LEU
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  623 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 76 optimal weight:    8.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.171251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.127830 restraints weight = 11943.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130595 restraints weight = 7116.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.132273 restraints weight = 5210.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6756  Z= 0.153
  Angle     :  0.538   6.271   9224  Z= 0.268
  Chirality :  0.040   0.148   1136
  Planarity :  0.002   0.018   1100
  Dihedral  :  4.128  14.708    920
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 27.78 %
    Favored  : 67.90 %
  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: -0.02 (0.30), residues: 836
  helix:  0.43 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.36 (0.52), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 585 
 HIS   0.001   0.000   HIS C 492 
 PHE   0.008   0.001   PHE C 640 
 TYR   0.009   0.001   TYR C 542 
 ARG   0.006   0.001   ARG C 531 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  415 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5732 (tt)
REVERT: A  528 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8098 (mtp180)
REVERT: A  610 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7445 (ttmt)
REVERT: A  652 TYR cc_start: 0.8209 (t80) cc_final: 0.7843 (t80)
REVERT: B  415 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5733 (tt)
REVERT: B  528 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8099 (mtp180)
REVERT: B  610 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7443 (ttmt)
REVERT: B  652 TYR cc_start: 0.8203 (t80) cc_final: 0.7841 (t80)
REVERT: C  415 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5727 (tt)
REVERT: C  528 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8099 (mtp180)
REVERT: C  610 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7439 (ttmt)
REVERT: C  652 TYR cc_start: 0.8214 (t80) cc_final: 0.7841 (t80)
REVERT: D  415 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5733 (tt)
REVERT: D  528 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8097 (mtp180)
REVERT: D  610 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7440 (ttmt)
REVERT: D  652 TYR cc_start: 0.8208 (t80) cc_final: 0.7845 (t80)
  outliers start: 28
  outliers final: 20
  residues processed: 176
  average time/residue: 0.1739
  time to fit residues: 40.7278
Evaluate side-chains
  176 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  542 TYR
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  542 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  532 LEU
Chi-restraints excluded: chain D residue  542 TYR
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  623 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0050
   chunk 4 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    0.6794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.170689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.127117 restraints weight = 12073.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.129976 restraints weight = 7055.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.131779 restraints weight = 5069.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6756  Z= 0.156
  Angle     :  0.548   6.197   9224  Z= 0.273
  Chirality :  0.041   0.166   1136
  Planarity :  0.003   0.023   1100
  Dihedral  :  4.120  14.365    920
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 30.40 %
    Favored  : 64.66 %
  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:  0.10 (0.30), residues: 836
  helix:  0.51 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.27 (0.52), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.001   0.000   HIS D 562 
 PHE   0.012   0.001   PHE C 463 
 TYR   0.007   0.001   TYR C 542 
 ARG   0.001   0.000   ARG B 488 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  415 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5729 (tt)
REVERT: A  528 ARG cc_start: 0.8653 (mtt-85) cc_final: 0.8321 (mtp180)
REVERT: A  610 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7404 (ttmt)
REVERT: A  652 TYR cc_start: 0.8255 (t80) cc_final: 0.7904 (t80)
REVERT: B  415 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5727 (tt)
REVERT: B  528 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8319 (mtp180)
REVERT: B  610 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7400 (ttmt)
REVERT: B  652 TYR cc_start: 0.8251 (t80) cc_final: 0.7902 (t80)
REVERT: C  415 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5726 (tt)
REVERT: C  528 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.8320 (mtp180)
REVERT: C  610 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7398 (ttmt)
REVERT: C  652 TYR cc_start: 0.8256 (t80) cc_final: 0.7902 (t80)
REVERT: D  415 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5752 (tt)
REVERT: D  528 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8329 (mtp180)
REVERT: D  610 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7400 (ttmt)
REVERT: D  652 TYR cc_start: 0.8254 (t80) cc_final: 0.7908 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 172
  average time/residue: 0.1478
  time to fit residues: 35.0817
Evaluate side-chains
  168 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  542 TYR
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  542 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  532 LEU
Chi-restraints excluded: chain D residue  542 TYR
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  623 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.180786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144688 restraints weight = 11598.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144911 restraints weight = 8570.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.146124 restraints weight = 6460.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6756  Z= 0.200
  Angle     :  0.600   9.312   9224  Z= 0.292
  Chirality :  0.042   0.158   1136
  Planarity :  0.003   0.030   1100
  Dihedral  :  4.285  16.672    920
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 32.72 %
    Favored  : 64.20 %
  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:  0.07 (0.30), residues: 836
  helix:  0.47 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.27 (0.54), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 585 
 HIS   0.001   0.000   HIS A 492 
 PHE   0.012   0.001   PHE D 463 
 TYR   0.009   0.002   TYR A 616 
 ARG   0.001   0.000   ARG C 488 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A  415 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5901 (tt)
REVERT: A  610 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7311 (ttmt)
REVERT: A  652 TYR cc_start: 0.8235 (t80) cc_final: 0.8033 (t80)
REVERT: B  415 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5901 (tt)
REVERT: B  610 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7314 (ttmt)
REVERT: B  652 TYR cc_start: 0.8230 (t80) cc_final: 0.8000 (t80)
REVERT: C  415 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5909 (tt)
REVERT: C  610 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7491 (ttmt)
REVERT: C  652 TYR cc_start: 0.8233 (t80) cc_final: 0.8006 (t80)
REVERT: D  415 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5904 (tt)
REVERT: D  610 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7492 (ttmt)
REVERT: D  652 TYR cc_start: 0.8230 (t80) cc_final: 0.8014 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 160
  average time/residue: 0.1616
  time to fit residues: 36.0059
Evaluate side-chains
  160 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  623 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.2586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.180466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.144237 restraints weight = 11689.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.144815 restraints weight = 8179.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.145767 restraints weight = 6060.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6756  Z= 0.208
  Angle     :  0.624   8.848   9224  Z= 0.301
  Chirality :  0.042   0.153   1136
  Planarity :  0.003   0.020   1100
  Dihedral  :  4.350  18.079    920
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 32.72 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.30), residues: 836
  helix:  0.53 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.02 (0.54), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 585 
 HIS   0.001   0.000   HIS C 492 
 PHE   0.023   0.002   PHE A 617 
 TYR   0.011   0.002   TYR B 616 
 ARG   0.001   0.000   ARG D 541 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A  415 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5835 (tt)
REVERT: A  610 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7373 (ttmt)
REVERT: A  652 TYR cc_start: 0.8292 (t80) cc_final: 0.8037 (t80)
REVERT: B  415 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5830 (tt)
REVERT: B  610 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7376 (ttmt)
REVERT: B  652 TYR cc_start: 0.8280 (t80) cc_final: 0.8031 (t80)
REVERT: C  415 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5836 (tt)
REVERT: C  610 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7548 (ttmt)
REVERT: C  652 TYR cc_start: 0.8283 (t80) cc_final: 0.8034 (t80)
REVERT: D  415 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5837 (tt)
REVERT: D  610 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7545 (ttmt)
REVERT: D  652 TYR cc_start: 0.8287 (t80) cc_final: 0.8045 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 156
  average time/residue: 0.1651
  time to fit residues: 35.0940
Evaluate side-chains
  160 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  618 THR
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  618 THR
Chi-restraints excluded: chain D residue  623 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0970
   chunk 49 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.3696

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.172442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.130474 restraints weight = 11895.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.133176 restraints weight = 6869.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.134918 restraints weight = 4943.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6756  Z= 0.141
  Angle     :  0.582   8.630   9224  Z= 0.277
  Chirality :  0.040   0.147   1136
  Planarity :  0.002   0.018   1100
  Dihedral  :  4.093  18.363    920
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 33.95 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.31), residues: 836
  helix:  0.74 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.81 (0.55), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 585 
 HIS   0.001   0.000   HIS A 402 
 PHE   0.023   0.001   PHE A 617 
 TYR   0.009   0.001   TYR C 542 
 ARG   0.001   0.000   ARG A 531 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7493 (ttmt)
REVERT: B  610 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7487 (ttmt)
REVERT: C  610 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7485 (ttmt)
REVERT: D  610 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7490 (ttmt)
  outliers start: 16
  outliers final: 12
  residues processed: 172
  average time/residue: 0.1544
  time to fit residues: 36.4553
Evaluate side-chains
  160 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  623 THR
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  623 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0980
   chunk 35 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.172885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.129535 restraints weight = 12038.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132180 restraints weight = 7108.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133846 restraints weight = 5189.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6756  Z= 0.149
  Angle     :  0.607   8.558   9224  Z= 0.289
  Chirality :  0.041   0.172   1136
  Planarity :  0.003   0.018   1100
  Dihedral  :  4.162  18.339    920
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 34.41 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.30), residues: 836
  helix:  0.81 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.02 (0.54), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 585 
 HIS   0.001   0.000   HIS A 492 
 PHE   0.023   0.001   PHE A 617 
 TYR   0.014   0.002   TYR B 420 
 ARG   0.001   0.000   ARG B 531 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2186.39 seconds
wall clock time: 38 minutes 41.29 seconds (2321.29 seconds total)