Starting phenix.real_space_refine
on Tue Mar  3 15:28:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cn0_30412/03_2026/7cn0_30412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cn0_30412/03_2026/7cn0_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2026/7cn0_30412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2026/7cn0_30412.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2026/7cn0_30412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cn0_30412/03_2026/7cn0_30412.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6602
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      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: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "C"
      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: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "D"
      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: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          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}
  Time building chain proxies: 1.56, per 1000 atoms: 0.24
  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: 0.62
  Conformation dependent library (CDL) restraints added in 253.0 milliseconds
  

  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: 0.14
  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: 0.81

  Time building geometry restraints manager: 0.79 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:             3.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.140
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
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= 0.170
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG D 488 
 TYR   0.018   0.002   TYR C 616 
 PHE   0.011   0.001   PHE B 640 
 TRP   0.009   0.002   TRP D 585 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6756)
  covalent geometry    : angle       0.62326 ( 9224)
  hydrogen bonds       : bond        0.06344 (  476)
  hydrogen bonds       : angle       3.93856 ( 1332)

*********************** 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  : 0.239 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7588 (ttmt)
REVERT: A  652 TYR cc_start: 0.8355 (t80) cc_final: 0.8067 (t80)
REVERT: B  610 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7595 (ttmt)
REVERT: B  652 TYR cc_start: 0.8359 (t80) cc_final: 0.8068 (t80)
REVERT: C  610 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7591 (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: 0.7585 (ttmt)
REVERT: D  652 TYR cc_start: 0.8355 (t80) cc_final: 0.8064 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0719
  time to fit residues: 15.4735
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  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.2784

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

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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.181349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.142481 restraints weight = 11662.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.142297 restraints weight = 8021.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.144168 restraints weight = 6640.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.144717 restraints weight = 5301.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.144676 restraints weight = 4781.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6756  Z= 0.143
  Angle     :  0.594   6.390   9224  Z= 0.299
  Chirality :  0.041   0.154   1136
  Planarity :  0.003   0.019   1100
  Dihedral  :  4.765  17.722    920
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 20.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.28), residues: 836
  helix: -0.48 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.18 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 541 
 TYR   0.014   0.002   TYR A 616 
 PHE   0.014   0.002   PHE C 617 
 TRP   0.006   0.001   TRP B 585 
 HIS   0.001   0.001   HIS D 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6756)
  covalent geometry    : angle       0.59357 ( 9224)
  hydrogen bonds       : bond        0.03465 (  476)
  hydrogen bonds       : angle       4.23109 ( 1332)

*********************** 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
  175 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7584 (ttmt)
REVERT: B  610 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7420 (ttmt)
REVERT: C  610 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7596 (ttmt)
REVERT: D  610 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7590 (ttmt)
  outliers start: 16
  outliers final: 8
  residues processed: 163
  average time/residue: 0.0708
  time to fit residues: 15.6980
Evaluate side-chains
  152 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 54 optimal weight:    0.0040
   overall best weight:    1.4596

-------------------------------------------------------------------------------
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 = 0.4199 r_free = 0.4199 target = 0.180170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.145239 restraints weight = 11521.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.141500 restraints weight = 9903.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.143265 restraints weight = 8494.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.143997 restraints weight = 5866.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.144350 restraints weight = 5076.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6756  Z= 0.154
  Angle     :  0.585   6.319   9224  Z= 0.298
  Chirality :  0.041   0.153   1136
  Planarity :  0.003   0.018   1100
  Dihedral  :  4.619  16.857    920
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.93 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.29), residues: 836
  helix: -0.15 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.99 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 531 
 TYR   0.012   0.002   TYR B 616 
 PHE   0.012   0.001   PHE D 640 
 TRP   0.005   0.001   TRP B 568 
 HIS   0.001   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6756)
  covalent geometry    : angle       0.58465 ( 9224)
  hydrogen bonds       : bond        0.03523 (  476)
  hydrogen bonds       : angle       4.17272 ( 1332)

*********************** 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
  174 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7357 (ttmt)
REVERT: A  652 TYR cc_start: 0.7938 (t80) cc_final: 0.7599 (t80)
REVERT: B  610 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7361 (ttmt)
REVERT: B  652 TYR cc_start: 0.7935 (t80) cc_final: 0.7598 (t80)
REVERT: C  610 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7359 (ttmt)
REVERT: C  652 TYR cc_start: 0.7944 (t80) cc_final: 0.7598 (t80)
REVERT: D  610 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7543 (ttmt)
REVERT: D  652 TYR cc_start: 0.7938 (t80) cc_final: 0.7583 (t80)
  outliers start: 24
  outliers final: 8
  residues processed: 162
  average time/residue: 0.0713
  time to fit residues: 15.5957
Evaluate side-chains
  150 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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 58 optimal weight:    0.1980
   chunk 11 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0040
   chunk 71 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   overall best weight:    2.0196

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.175404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.141781 restraints weight = 11813.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.139377 restraints weight = 11711.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.141036 restraints weight = 10957.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.141619 restraints weight = 7510.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.142003 restraints weight = 7306.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1805

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= 0.190
  Angle     :  0.621   6.414   9224  Z= 0.317
  Chirality :  0.043   0.149   1136
  Planarity :  0.003   0.017   1100
  Dihedral  :  4.687  16.825    920
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 25.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.29), residues: 836
  helix: -0.09 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.01 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 531 
 TYR   0.014   0.002   TYR B 616 
 PHE   0.014   0.002   PHE B 640 
 TRP   0.025   0.002   TRP D 585 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 6756)
  covalent geometry    : angle       0.62115 ( 9224)
  hydrogen bonds       : bond        0.03716 (  476)
  hydrogen bonds       : angle       4.31516 ( 1332)

*********************** 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
  200 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 156
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  610 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7405 (ttmt)
REVERT: A  652 TYR cc_start: 0.8223 (t80) cc_final: 0.7832 (t80)
REVERT: B  610 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7419 (ttmt)
REVERT: B  652 TYR cc_start: 0.8222 (t80) cc_final: 0.7837 (t80)
REVERT: C  610 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7416 (ttmt)
REVERT: C  652 TYR cc_start: 0.8229 (t80) cc_final: 0.7838 (t80)
REVERT: D  610 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7553 (ttmt)
REVERT: D  652 TYR cc_start: 0.8239 (t80) cc_final: 0.7842 (t80)
  outliers start: 44
  outliers final: 24
  residues processed: 188
  average time/residue: 0.0671
  time to fit residues: 17.3936
Evaluate side-chains
  172 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  417 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  650 LEU
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain B residue  417 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  650 LEU
Chi-restraints excluded: chain B residue  659 VAL
Chi-restraints excluded: chain C residue  417 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  650 LEU
Chi-restraints excluded: chain C residue  659 VAL
Chi-restraints excluded: chain D residue  417 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  650 LEU
Chi-restraints excluded: chain D residue  659 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.181164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.140680 restraints weight = 11757.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.143210 restraints weight = 7652.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.144881 restraints weight = 5800.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.145767 restraints weight = 4866.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.146480 restraints weight = 4398.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6756  Z= 0.115
  Angle     :  0.567   6.270   9224  Z= 0.286
  Chirality :  0.041   0.168   1136
  Planarity :  0.003   0.020   1100
  Dihedral  :  4.329  15.358    920
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 30.86 %
    Favored  : 66.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.30), residues: 836
  helix:  0.25 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.68 (0.52), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 531 
 TYR   0.011   0.001   TYR D 542 
 PHE   0.017   0.001   PHE D 617 
 TRP   0.025   0.002   TRP B 585 
 HIS   0.001   0.000   HIS B 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6756)
  covalent geometry    : angle       0.56697 ( 9224)
  hydrogen bonds       : bond        0.03208 (  476)
  hydrogen bonds       : angle       3.99985 ( 1332)

*********************** 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
  180 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8159 (mtp180)
REVERT: A  610 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7526 (ttmt)
REVERT: A  652 TYR cc_start: 0.8200 (t80) cc_final: 0.7851 (t80)
REVERT: B  528 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8160 (mtp180)
REVERT: B  610 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7529 (ttmt)
REVERT: B  652 TYR cc_start: 0.8192 (t80) cc_final: 0.7846 (t80)
REVERT: C  528 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8161 (mtp180)
REVERT: C  610 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7526 (ttmt)
REVERT: C  652 TYR cc_start: 0.8199 (t80) cc_final: 0.7849 (t80)
REVERT: D  528 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8164 (mtp180)
REVERT: D  610 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7527 (ttmt)
REVERT: D  652 TYR cc_start: 0.8210 (t80) cc_final: 0.7868 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 176
  average time/residue: 0.0747
  time to fit residues: 17.7102
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  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain B residue  417 LEU
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain C residue  417 LEU
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  550 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0040
   chunk 63 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7594

-------------------------------------------------------------------------------
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 = 0.180630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.142092 restraints weight = 11849.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.141635 restraints weight = 8667.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.143362 restraints weight = 6964.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.143769 restraints weight = 5159.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.144001 restraints weight = 4950.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2606

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= 0.119
  Angle     :  0.563   6.282   9224  Z= 0.288
  Chirality :  0.041   0.144   1136
  Planarity :  0.003   0.023   1100
  Dihedral  :  4.276  14.978    920
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 32.25 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.30), residues: 836
  helix:  0.27 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.33 (0.51), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 531 
 TYR   0.011   0.001   TYR B 542 
 PHE   0.015   0.001   PHE A 617 
 TRP   0.019   0.001   TRP A 585 
 HIS   0.001   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6756)
  covalent geometry    : angle       0.56343 ( 9224)
  hydrogen bonds       : bond        0.03242 (  476)
  hydrogen bonds       : angle       4.01108 ( 1332)

*********************** 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
  152 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8234 (mtp180)
REVERT: A  610 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7523 (ttmt)
REVERT: A  652 TYR cc_start: 0.8199 (t80) cc_final: 0.7861 (t80)
REVERT: B  528 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.8233 (mtp180)
REVERT: B  610 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7347 (ttmt)
REVERT: B  652 TYR cc_start: 0.8205 (t80) cc_final: 0.7869 (t80)
REVERT: C  528 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.8238 (mtp180)
REVERT: C  610 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7517 (ttmt)
REVERT: C  652 TYR cc_start: 0.8206 (t80) cc_final: 0.7867 (t80)
REVERT: D  528 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8242 (mtp180)
REVERT: D  610 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7518 (ttmt)
REVERT: D  652 TYR cc_start: 0.8211 (t80) cc_final: 0.7856 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 148
  average time/residue: 0.0657
  time to fit residues: 13.5112
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  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  471 PHE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  550 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 D residue  471 PHE
Chi-restraints excluded: chain D residue  532 LEU
Chi-restraints excluded: chain D residue  550 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0050
   chunk 79 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 77 optimal weight:    0.1980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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 = 0.4225 r_free = 0.4225 target = 0.181997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.141430 restraints weight = 11622.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144058 restraints weight = 7310.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145796 restraints weight = 5446.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.146730 restraints weight = 4522.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.147366 restraints weight = 4069.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6756  Z= 0.110
  Angle     :  0.585   9.774   9224  Z= 0.284
  Chirality :  0.040   0.145   1136
  Planarity :  0.003   0.022   1100
  Dihedral  :  4.170  14.927    920
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 30.40 %
    Favored  : 66.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.30), residues: 836
  helix:  0.43 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.93 (0.52), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 531 
 TYR   0.009   0.001   TYR D 542 
 PHE   0.013   0.001   PHE B 617 
 TRP   0.016   0.001   TRP D 585 
 HIS   0.000   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6756)
  covalent geometry    : angle       0.58475 ( 9224)
  hydrogen bonds       : bond        0.03120 (  476)
  hydrogen bonds       : angle       3.92203 ( 1332)

*********************** 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
  172 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8211 (mtp180)
REVERT: A  610 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7429 (ttmt)
REVERT: A  652 TYR cc_start: 0.8214 (t80) cc_final: 0.7950 (t80)
REVERT: B  528 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.8211 (mtp180)
REVERT: B  610 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7428 (ttmt)
REVERT: B  652 TYR cc_start: 0.8227 (t80) cc_final: 0.7956 (t80)
REVERT: C  528 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8213 (mtp180)
REVERT: C  610 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7426 (ttmt)
REVERT: C  652 TYR cc_start: 0.8232 (t80) cc_final: 0.7956 (t80)
REVERT: D  528 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8215 (mtp180)
REVERT: D  610 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7488 (ttmt)
REVERT: D  652 TYR cc_start: 0.8231 (t80) cc_final: 0.7961 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 160
  average time/residue: 0.0674
  time to fit residues: 14.9320
Evaluate side-chains
  164 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain B residue  471 PHE
Chi-restraints excluded: chain B residue  542 TYR
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  542 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  618 THR
Chi-restraints excluded: chain D residue  471 PHE
Chi-restraints excluded: chain D residue  542 TYR
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  618 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.4075 r_free = 0.4075 target = 0.169844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.129431 restraints weight = 12442.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.129764 restraints weight = 8760.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130963 restraints weight = 5884.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.131715 restraints weight = 5036.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.131698 restraints weight = 4374.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6756  Z= 0.111
  Angle     :  0.575   8.295   9224  Z= 0.281
  Chirality :  0.040   0.144   1136
  Planarity :  0.003   0.018   1100
  Dihedral  :  4.133  15.690    920
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 30.71 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.30), residues: 836
  helix:  0.46 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.12 (0.51), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 531 
 TYR   0.008   0.001   TYR D 542 
 PHE   0.012   0.001   PHE A 617 
 TRP   0.015   0.001   TRP D 585 
 HIS   0.001   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6756)
  covalent geometry    : angle       0.57510 ( 9224)
  hydrogen bonds       : bond        0.03093 (  476)
  hydrogen bonds       : angle       3.87619 ( 1332)

*********************** 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
  176 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8173 (mtp180)
REVERT: A  610 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7235 (ttmt)
REVERT: A  652 TYR cc_start: 0.8340 (t80) cc_final: 0.7980 (t80)
REVERT: B  528 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8174 (mtp180)
REVERT: B  610 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7235 (ttmt)
REVERT: B  652 TYR cc_start: 0.8350 (t80) cc_final: 0.8007 (t80)
REVERT: C  528 ARG cc_start: 0.8603 (mtt-85) cc_final: 0.8178 (mtp180)
REVERT: C  610 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7426 (ttmt)
REVERT: C  652 TYR cc_start: 0.8354 (t80) cc_final: 0.8009 (t80)
REVERT: D  528 ARG cc_start: 0.8612 (mtt-85) cc_final: 0.8187 (mtp180)
REVERT: D  610 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7457 (ttmt)
REVERT: D  652 TYR cc_start: 0.8358 (t80) cc_final: 0.8000 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 164
  average time/residue: 0.0663
  time to fit residues: 15.2268
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  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain B residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain C residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain D residue  542 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0000
   chunk 80 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 84 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.5544

-------------------------------------------------------------------------------
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 = 0.4080 r_free = 0.4080 target = 0.170716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.127956 restraints weight = 12416.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.130607 restraints weight = 7116.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132264 restraints weight = 5137.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.133288 restraints weight = 4243.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.133741 restraints weight = 3805.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6756  Z= 0.109
  Angle     :  0.586   8.129   9224  Z= 0.286
  Chirality :  0.041   0.167   1136
  Planarity :  0.003   0.021   1100
  Dihedral  :  4.135  19.929    920
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 31.33 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.30), residues: 836
  helix:  0.55 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.00 (0.51), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 531 
 TYR   0.007   0.001   TYR D 542 
 PHE   0.011   0.001   PHE B 617 
 TRP   0.014   0.001   TRP D 585 
 HIS   0.000   0.000   HIS C 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6756)
  covalent geometry    : angle       0.58573 ( 9224)
  hydrogen bonds       : bond        0.03179 (  476)
  hydrogen bonds       : angle       3.84961 ( 1332)

*********************** 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
  169 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8187 (mtp180)
REVERT: A  610 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7431 (ttmt)
REVERT: A  652 TYR cc_start: 0.8316 (t80) cc_final: 0.8020 (t80)
REVERT: B  528 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8188 (mtp180)
REVERT: B  610 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7430 (ttmt)
REVERT: B  652 TYR cc_start: 0.8336 (t80) cc_final: 0.8035 (t80)
REVERT: C  528 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8189 (mtp180)
REVERT: C  610 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7427 (ttmt)
REVERT: C  652 TYR cc_start: 0.8338 (t80) cc_final: 0.8036 (t80)
REVERT: D  528 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8203 (mtp180)
REVERT: D  610 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7479 (ttmt)
REVERT: D  652 TYR cc_start: 0.8331 (t80) cc_final: 0.8041 (t80)
  outliers start: 20
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0627
  time to fit residues: 13.7059
Evaluate side-chains
  165 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain B residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain C residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain D residue  542 TYR
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 81 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 30 optimal weight:    0.4980
   chunk 78 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   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 = 0.4068 r_free = 0.4068 target = 0.169249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126609 restraints weight = 12291.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.129352 restraints weight = 7007.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131018 restraints weight = 4997.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.131861 restraints weight = 4121.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.132488 restraints weight = 3726.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6756  Z= 0.119
  Angle     :  0.605   8.023   9224  Z= 0.295
  Chirality :  0.042   0.166   1136
  Planarity :  0.003   0.023   1100
  Dihedral  :  4.177  21.353    920
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 31.48 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.30), residues: 836
  helix:  0.63 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.73 (0.51), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 531 
 TYR   0.014   0.002   TYR D 420 
 PHE   0.011   0.001   PHE D 617 
 TRP   0.014   0.001   TRP A 585 
 HIS   0.001   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6756)
  covalent geometry    : angle       0.60500 ( 9224)
  hydrogen bonds       : bond        0.03298 (  476)
  hydrogen bonds       : angle       3.85019 ( 1332)

********************** 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
  160 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  528 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8152 (mtp180)
REVERT: A  610 LYS cc_start: 0.7892 (mtmt) cc_final: 0.7449 (ttmt)
REVERT: A  652 TYR cc_start: 0.8337 (t80) cc_final: 0.8102 (t80)
REVERT: B  528 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8153 (mtp180)
REVERT: B  610 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7450 (ttmt)
REVERT: B  652 TYR cc_start: 0.8351 (t80) cc_final: 0.8056 (t80)
REVERT: C  528 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8153 (mtp180)
REVERT: C  610 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7446 (ttmt)
REVERT: C  652 TYR cc_start: 0.8353 (t80) cc_final: 0.8057 (t80)
REVERT: D  528 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8166 (mtp180)
REVERT: D  610 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7434 (ttmt)
REVERT: D  652 TYR cc_start: 0.8353 (t80) cc_final: 0.8105 (t80)
  outliers start: 20
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0656
  time to fit residues: 13.4609
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  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain B residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain C residue  542 TYR
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  471 PHE
Chi-restraints excluded: chain D residue  542 TYR
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 73 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4082 r_free = 0.4082 target = 0.171968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.129815 restraints weight = 12150.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.132439 restraints weight = 7047.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.134059 restraints weight = 5090.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.134919 restraints weight = 4205.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135576 restraints weight = 3804.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6756  Z= 0.122
  Angle     :  0.590   7.894   9224  Z= 0.292
  Chirality :  0.042   0.163   1136
  Planarity :  0.003   0.018   1100
  Dihedral  :  4.186  22.031    920
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 31.79 %
    Favored  : 65.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.30), residues: 836
  helix:  0.71 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.68 (0.51), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 531 
 TYR   0.007   0.001   TYR A 652 
 PHE   0.025   0.001   PHE D 617 
 TRP   0.014   0.001   TRP D 585 
 HIS   0.001   0.000   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6756)
  covalent geometry    : angle       0.59018 ( 9224)
  hydrogen bonds       : bond        0.03279 (  476)
  hydrogen bonds       : angle       3.84717 ( 1332)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1138.52 seconds
wall clock time: 20 minutes 20.13 seconds (1220.13 seconds total)