Starting phenix.real_space_refine
on Thu Feb 13 18:35:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ty8_26169/02_2025/7ty8_26169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty8_26169/02_2025/7ty8_26169.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ty8_26169/02_2025/7ty8_26169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty8_26169/02_2025/7ty8_26169.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty8_26169/02_2025/7ty8_26169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty8_26169/02_2025/7ty8_26169.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.029
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      36      5.16       5
     C    5800      2.51       5
     N    1314      2.21       5
     O    1433      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8591
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 4067
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 4067
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 186
          Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 186
          Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
  Time building chain proxies: 4.79, per 1000 atoms: 0.56
  Number of scatterers: 8591
  At special positions: 0
  Unit cell: (125.892, 85.004, 83.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       2     15.00
     F       6      9.00
     O    1433      8.00
     N    1314      7.00
     C    5800      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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 642 "
      " NAG D   1 " - " ASN B 642 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 959.7 milliseconds
  

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      74.4% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 399
    Processing helix  chain 'A' and resid 402 through 432
      removed outlier: 3.882A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 483
      removed outlier: 3.711A  pdb=" N   THR A 481 " --> pdb=" O   SER A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 507
      removed outlier: 4.143A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL A 502 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 516
      removed outlier: 3.527A  pdb=" N   VAL A 513 " --> pdb=" O   SER A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.901A  pdb=" N   ILE A 543 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
      removed outlier: 3.572A  pdb=" N   LEU A 573 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
      removed outlier: 3.737A  pdb=" N   VAL A 604 " --> pdb=" O   LYS A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.526A  pdb=" N   MET A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP A 621 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.595A  pdb=" N   MET A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A 665 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 690
      removed outlier: 3.741A  pdb=" N   ILE A 684 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 719
      removed outlier: 3.966A  pdb=" N   LEU A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE A 719 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 738
    Processing helix  chain 'A' and resid 760 through 773
      removed outlier: 3.584A  pdb=" N   ALA A 767 " --> pdb=" O   GLY A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.564A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 791 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 810
    Processing helix  chain 'A' and resid 811 through 813
      No H-bonds generated for 'chain 'A' and resid 811 through 813'
    Processing helix  chain 'A' and resid 815 through 819
      removed outlier: 3.737A  pdb=" N   HIS A 819 " --> pdb=" O   PRO A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
    Processing helix  chain 'A' and resid 829 through 853
      removed outlier: 3.604A  pdb=" N   LEU A 835 " --> pdb=" O   TRP A 831 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 852 " --> pdb=" O   TRP A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 864
    Processing helix  chain 'A' and resid 865 through 872
      removed outlier: 3.559A  pdb=" N   LEU A 869 " --> pdb=" O   LEU A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 878
    Processing helix  chain 'A' and resid 879 through 887
    Processing helix  chain 'B' and resid 379 through 390
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 394 through 399
    Processing helix  chain 'B' and resid 402 through 432
      removed outlier: 3.882A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 483
      removed outlier: 3.711A  pdb=" N   THR B 481 " --> pdb=" O   SER B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 507
      removed outlier: 4.157A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B 502 " --> pdb=" O   ILE B 498 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE B 507 " --> pdb=" O   LEU B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.528A  pdb=" N   VAL B 513 " --> pdb=" O   SER B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.903A  pdb=" N   ILE B 543 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 593
      removed outlier: 3.565A  pdb=" N   LEU B 573 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN B 593 " --> pdb=" O   ARG B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 608
      removed outlier: 3.737A  pdb=" N   VAL B 604 " --> pdb=" O   LYS B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 623
      removed outlier: 3.525A  pdb=" N   MET B 617 " --> pdb=" O   SER B 613 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP B 621 " --> pdb=" O   MET B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 3.595A  pdb=" N   MET B 664 " --> pdb=" O   PRO B 660 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 665 " --> pdb=" O   ILE B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 690
      removed outlier: 3.743A  pdb=" N   ILE B 684 " --> pdb=" O   LEU B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 719
      removed outlier: 3.964A  pdb=" N   LEU B 718 " --> pdb=" O   GLY B 714 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE B 719 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 727 through 738
    Processing helix  chain 'B' and resid 760 through 773
      removed outlier: 3.583A  pdb=" N   ALA B 767 " --> pdb=" O   GLY B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.564A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 791 " --> pdb=" O   VAL B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 810
    Processing helix  chain 'B' and resid 811 through 813
      No H-bonds generated for 'chain 'B' and resid 811 through 813'
    Processing helix  chain 'B' and resid 815 through 819
      removed outlier: 3.734A  pdb=" N   HIS B 819 " --> pdb=" O   PRO B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 822 through 827
    Processing helix  chain 'B' and resid 829 through 853
      removed outlier: 3.605A  pdb=" N   LEU B 835 " --> pdb=" O   TRP B 831 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER B 852 " --> pdb=" O   TRP B 848 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 858 through 864
    Processing helix  chain 'B' and resid 865 through 872
      removed outlier: 3.556A  pdb=" N   LEU B 869 " --> pdb=" O   LEU B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 878
    Processing helix  chain 'B' and resid 879 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742
      removed outlier: 7.592A  pdb=" N   VAL A 740 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN A 754 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742
      removed outlier: 7.591A  pdb=" N   VAL B 740 " --> pdb=" O   GLN B 754 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLN B 754 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1446 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: 2.36

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1392
        1.33 -     1.45: 2156
        1.45 -     1.58: 5174
        1.58 -     1.70: 4
        1.70 -     1.83: 66
  Bond restraints: 8792
  Sorted by residual:
  bond pdb=" N   ILE B 783 "
       pdb=" CA  ILE B 783 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 7.60e-03 1.73e+04 2.36e+01
  bond pdb=" N   ILE A 783 "
       pdb=" CA  ILE A 783 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 7.60e-03 1.73e+04 2.24e+01
  bond pdb=" N   VAL B 634 "
       pdb=" CA  VAL B 634 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 8.70e-03 1.32e+04 1.60e+01
  bond pdb=" N   VAL A 634 "
       pdb=" CA  VAL A 634 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 8.70e-03 1.32e+04 1.60e+01
  bond pdb=" N   LEU A 669 "
       pdb=" CA  LEU A 669 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 8.50e-03 1.38e+04 1.27e+01
  ... (remaining 8787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 7968
        1.64 -     3.28: 3171
        3.28 -     4.91: 728
        4.91 -     6.55: 108
        6.55 -     8.19: 5
  Bond angle restraints: 11980
  Sorted by residual:
  angle pdb=" C   PRO B 598 "
        pdb=" N   GLY B 599 "
        pdb=" CA  GLY B 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.80   -5.77 1.12e+00 7.97e-01 2.65e+01
  angle pdb=" C   PRO A 598 "
        pdb=" N   GLY A 599 "
        pdb=" CA  GLY A 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.79   -5.76 1.12e+00 7.97e-01 2.65e+01
  angle pdb=" C   GLY B 380 "
        pdb=" N   GLY B 381 "
        pdb=" CA  GLY B 381 "
      ideal   model   delta    sigma   weight residual
     120.00  125.62   -5.62 1.10e+00 8.26e-01 2.61e+01
  angle pdb=" C   GLY A 380 "
        pdb=" N   GLY A 381 "
        pdb=" CA  GLY A 381 "
      ideal   model   delta    sigma   weight residual
     120.00  125.61   -5.61 1.10e+00 8.26e-01 2.60e+01
  angle pdb=" N   LEU A 873 "
        pdb=" CA  LEU A 873 "
        pdb=" C   LEU A 873 "
      ideal   model   delta    sigma   weight residual
     111.07  116.05   -4.98 1.07e+00 8.73e-01 2.17e+01
  ... (remaining 11975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 5094
       17.32 -    34.64: 380
       34.64 -    51.96: 106
       51.96 -    69.28: 33
       69.28 -    86.61: 13
  Dihedral angle restraints: 5626
    sinusoidal: 2656
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" CA  ARG A 388 "
           pdb=" C   ARG A 388 "
           pdb=" N   ARG A 389 "
           pdb=" CA  ARG A 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.60  -19.40     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ARG B 388 "
           pdb=" C   ARG B 388 "
           pdb=" N   ARG B 389 "
           pdb=" CA  ARG B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.62  -19.38     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  TYR A 628 "
           pdb=" C   TYR A 628 "
           pdb=" N   THR A 629 "
           pdb=" CA  THR A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.42   16.58     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 5623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 488
       0.043 -    0.086: 398
       0.086 -    0.129: 366
       0.129 -    0.172: 163
       0.172 -    0.215: 19
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.16e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.35   -0.05 2.00e-02 2.50e+03 7.08e+00
  chirality pdb=" CA  LEU B 484 "
            pdb=" N   LEU B 484 "
            pdb=" C   LEU B 484 "
            pdb=" CB  LEU B 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 1404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.305 2.00e-02 2.50e+03   2.57e-01 8.25e+02
        pdb=" C7  NAG D   1 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.441 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.304 2.00e-02 2.50e+03   2.56e-01 8.21e+02
        pdb=" C7  NAG C   1 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.439 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "   -0.072 2.00e-02 2.50e+03   5.89e-02 4.33e+01
        pdb=" C7  NAG C   2 "    0.019 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "   -0.054 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "    0.093 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1401 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 2694
        2.91 -     3.40: 9413
        3.40 -     3.90: 15126
        3.90 -     4.40: 17228
        4.40 -     4.90: 28434
  Nonbonded interactions: 72895
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU B 874 "
            pdb=" CD2 PHE B 878 "
     model   vdw
     2.407 3.760
  nonbonded pdb=" CD1 LEU A 874 "
            pdb=" CD2 PHE A 878 "
     model   vdw
     2.430 3.760
  nonbonded pdb=" OH  TYR A 555 "
            pdb=" OH  TYR B 555 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   VAL B 729 "
            pdb=" OG1 THR B 733 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" O   VAL A 729 "
            pdb=" OG1 THR A 733 "
     model   vdw
     2.486 3.040
  ... (remaining 72890 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'
  selection = chain 'B'
}
ncs_group {
  reference = 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.220
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.090
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
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      :  0.013   0.049   8792  Z= 0.854
  Angle     :  1.782   8.189  11980  Z= 1.347
  Chirality :  0.085   0.215   1434
  Planarity :  0.010   0.257   1402
  Dihedral  : 14.152  86.606   3710
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.37 %
    Favored  : 91.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.22), residues: 1022
  helix: -2.25 (0.16), residues: 676
  sheet:  None (None), residues: 0
  loop : -1.83 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 662 
 HIS   0.004   0.001   HIS A 819 
 PHE   0.016   0.002   PHE A 495 
 TYR   0.014   0.002   TYR B 628 
 ARG   0.004   0.001   ARG B 514 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 201
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A  641 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7207 (p)
REVERT: A  696 MET cc_start: 0.7845 (mmm) cc_final: 0.7568 (mmt)
REVERT: A  833 MET cc_start: 0.8496 (tmm) cc_final: 0.8162 (tmm)
REVERT: B  696 MET cc_start: 0.7842 (mmm) cc_final: 0.7557 (mmt)
REVERT: B  833 MET cc_start: 0.8457 (tmm) cc_final: 0.8101 (tmm)
  outliers start: 7
  outliers final: 2
  residues processed: 208
  average time/residue: 0.2227
  time to fit residues: 63.0398
Evaluate side-chains
  115 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  641 SER
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  650 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 683 GLN
B 550 GLN
B 683 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.082699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074813 restraints weight = 27660.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.35
r_work: 0.3219 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8792  Z= 0.237
  Angle     :  0.656   7.021  11980  Z= 0.325
  Chirality :  0.042   0.160   1434
  Planarity :  0.005   0.042   1402
  Dihedral  : 10.323  88.605   1813
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.61 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.25), residues: 1022
  helix:  0.37 (0.18), residues: 700
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 492 
 HIS   0.004   0.001   HIS B 651 
 PHE   0.024   0.002   PHE A 411 
 TYR   0.010   0.001   TYR A 486 
 ARG   0.006   0.001   ARG A 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A  399 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8035 (t0)
REVERT: A  413 TYR cc_start: 0.9215 (t80) cc_final: 0.8993 (t80)
REVERT: A  812 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8640 (mp)
REVERT: B  399 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8039 (t0)
REVERT: B  413 TYR cc_start: 0.9251 (t80) cc_final: 0.9051 (t80)
REVERT: B  681 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8353 (mm-30)
  outliers start: 19
  outliers final: 6
  residues processed: 143
  average time/residue: 0.1499
  time to fit residues: 32.8887
Evaluate side-chains
  112 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  681 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 457 GLN
A 834 HIS
B 457 GLN
B 834 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.081920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.073701 restraints weight = 28454.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.50
r_work: 0.3198 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8792  Z= 0.246
  Angle     :  0.605   7.259  11980  Z= 0.295
  Chirality :  0.040   0.164   1434
  Planarity :  0.005   0.045   1402
  Dihedral  :  9.875  87.975   1808
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 12.95 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.25), residues: 1022
  helix:  1.00 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.96 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 492 
 HIS   0.003   0.001   HIS B 834 
 PHE   0.015   0.001   PHE B 411 
 TYR   0.014   0.001   TYR B 486 
 ARG   0.005   0.001   ARG A 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A  413 TYR cc_start: 0.9197 (t80) cc_final: 0.8997 (t80)
REVERT: A  664 MET cc_start: 0.8466 (mtm) cc_final: 0.8137 (mtp)
REVERT: B  399 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8181 (t0)
REVERT: B  413 TYR cc_start: 0.9204 (t80) cc_final: 0.9003 (t80)
REVERT: B  486 TYR cc_start: 0.7956 (t80) cc_final: 0.7672 (t80)
REVERT: B  664 MET cc_start: 0.8414 (mtm) cc_final: 0.8096 (mtp)
  outliers start: 30
  outliers final: 17
  residues processed: 131
  average time/residue: 0.1403
  time to fit residues: 29.1533
Evaluate side-chains
  118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0980
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 884 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.082030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.073898 restraints weight = 28264.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 3.49
r_work: 0.3209 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8792  Z= 0.204
  Angle     :  0.601   8.544  11980  Z= 0.288
  Chirality :  0.040   0.214   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  9.555  85.170   1808
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.40 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1022
  helix:  1.24 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.74 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 492 
 HIS   0.001   0.001   HIS B 651 
 PHE   0.013   0.001   PHE A 836 
 TYR   0.015   0.001   TYR B 486 
 ARG   0.004   0.001   ARG A 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 TYR cc_start: 0.9215 (t80) cc_final: 0.8990 (t80)
REVERT: A  664 MET cc_start: 0.8352 (mtm) cc_final: 0.7994 (mtp)
REVERT: A  696 MET cc_start: 0.7967 (mmm) cc_final: 0.7653 (mmt)
REVERT: A  812 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8599 (mp)
REVERT: A  820 PRO cc_start: 0.8874 (Cg_exo) cc_final: 0.8606 (Cg_endo)
REVERT: B  399 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8320 (t70)
REVERT: B  413 TYR cc_start: 0.9230 (t80) cc_final: 0.9005 (t80)
REVERT: B  486 TYR cc_start: 0.7796 (t80) cc_final: 0.7552 (t80)
REVERT: B  664 MET cc_start: 0.8331 (mtm) cc_final: 0.7984 (mtp)
REVERT: B  696 MET cc_start: 0.8045 (mmm) cc_final: 0.7741 (mmt)
  outliers start: 25
  outliers final: 14
  residues processed: 124
  average time/residue: 0.1442
  time to fit residues: 28.2246
Evaluate side-chains
  117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  874 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0370
   chunk 87 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.081947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.073958 restraints weight = 28536.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 3.46
r_work: 0.3214 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8792  Z= 0.186
  Angle     :  0.584   9.343  11980  Z= 0.279
  Chirality :  0.039   0.163   1434
  Planarity :  0.005   0.047   1402
  Dihedral  :  9.388  82.769   1808
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.40 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1022
  helix:  1.36 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.56 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 662 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.012   0.001   PHE A 836 
 TYR   0.015   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A  664 MET cc_start: 0.8243 (mtm) cc_final: 0.7871 (mtp)
REVERT: A  812 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: A  820 PRO cc_start: 0.8771 (Cg_exo) cc_final: 0.8516 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7273 (ppp) cc_final: 0.6858 (tmm)
REVERT: B  399 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8365 (t70)
REVERT: B  486 TYR cc_start: 0.7789 (t80) cc_final: 0.7518 (t80)
REVERT: B  664 MET cc_start: 0.8228 (mtm) cc_final: 0.7858 (mtp)
REVERT: B  696 MET cc_start: 0.8065 (mmm) cc_final: 0.7814 (mmt)
REVERT: B  820 PRO cc_start: 0.8885 (Cg_exo) cc_final: 0.8620 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7229 (ppp) cc_final: 0.6946 (tmm)
  outliers start: 26
  outliers final: 18
  residues processed: 129
  average time/residue: 0.1452
  time to fit residues: 29.2084
Evaluate side-chains
  125 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  399 ASP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.080754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.072861 restraints weight = 28452.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 3.39
r_work: 0.3200 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8792  Z= 0.221
  Angle     :  0.603  10.353  11980  Z= 0.286
  Chirality :  0.040   0.163   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  9.193  83.728   1808
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.30 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1022
  helix:  1.47 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.41 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 662 
 HIS   0.001   0.001   HIS A 547 
 PHE   0.012   0.001   PHE A 836 
 TYR   0.020   0.001   TYR B 413 
 ARG   0.003   0.000   ARG A 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  664 MET cc_start: 0.8234 (mtm) cc_final: 0.7870 (mtp)
REVERT: A  812 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8612 (mp)
REVERT: A  820 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8573 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7372 (ppp) cc_final: 0.6960 (tmm)
REVERT: B  664 MET cc_start: 0.8202 (mtm) cc_final: 0.7839 (mtp)
REVERT: B  820 PRO cc_start: 0.8748 (Cg_exo) cc_final: 0.8478 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7305 (ppp) cc_final: 0.6977 (tmm)
  outliers start: 22
  outliers final: 17
  residues processed: 126
  average time/residue: 0.1426
  time to fit residues: 28.9139
Evaluate side-chains
  122 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  595 SER
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  874 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    0.0870
   chunk 67 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.081513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.073719 restraints weight = 28417.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 3.40
r_work: 0.3210 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8792  Z= 0.188
  Angle     :  0.610  11.742  11980  Z= 0.285
  Chirality :  0.040   0.163   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.959  83.571   1808
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.42 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1022
  helix:  1.52 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.31 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 662 
 HIS   0.001   0.001   HIS A 547 
 PHE   0.012   0.001   PHE A 836 
 TYR   0.015   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A  664 MET cc_start: 0.8172 (mtm) cc_final: 0.7771 (mtp)
REVERT: A  812 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8590 (mp)
REVERT: A  820 PRO cc_start: 0.8699 (Cg_exo) cc_final: 0.8465 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7409 (ppp) cc_final: 0.7013 (tmm)
REVERT: B  587 MET cc_start: 0.8127 (mmp) cc_final: 0.7917 (mmp)
REVERT: B  617 MET cc_start: 0.7682 (mmm) cc_final: 0.7340 (mtp)
REVERT: B  664 MET cc_start: 0.8129 (mtm) cc_final: 0.7749 (mtp)
REVERT: B  820 PRO cc_start: 0.8757 (Cg_exo) cc_final: 0.8493 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7226 (ppp) cc_final: 0.6893 (tmm)
  outliers start: 19
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1415
  time to fit residues: 26.8328
Evaluate side-chains
  118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 10 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7744

-------------------------------------------------------------------------------
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 = 0.3513 r_free = 0.3513 target = 0.081137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.073225 restraints weight = 28890.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.44
r_work: 0.3201 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8792  Z= 0.208
  Angle     :  0.617  12.435  11980  Z= 0.289
  Chirality :  0.040   0.199   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.788  83.018   1808
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.53 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1022
  helix:  1.55 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.26 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 662 
 HIS   0.001   0.001   HIS A 547 
 PHE   0.012   0.001   PHE A 836 
 TYR   0.022   0.001   TYR A 390 
 ARG   0.003   0.000   ARG B 694 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8832 (t)
REVERT: A  578 MET cc_start: 0.8763 (ttt) cc_final: 0.8312 (ttt)
REVERT: A  664 MET cc_start: 0.8164 (mtm) cc_final: 0.7784 (mtp)
REVERT: A  812 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (mp)
REVERT: A  820 PRO cc_start: 0.8721 (Cg_exo) cc_final: 0.8491 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7506 (ppp) cc_final: 0.7133 (tmm)
REVERT: B  513 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8829 (t)
REVERT: B  587 MET cc_start: 0.8244 (mmp) cc_final: 0.8018 (mmp)
REVERT: B  664 MET cc_start: 0.8124 (mtm) cc_final: 0.7738 (mtp)
REVERT: B  820 PRO cc_start: 0.8730 (Cg_exo) cc_final: 0.8477 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7311 (ppp) cc_final: 0.6966 (tmm)
  outliers start: 23
  outliers final: 17
  residues processed: 119
  average time/residue: 0.1401
  time to fit residues: 26.3713
Evaluate side-chains
  118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.080822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.073185 restraints weight = 28767.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.38
r_work: 0.3202 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8792  Z= 0.207
  Angle     :  0.620  12.997  11980  Z= 0.290
  Chirality :  0.040   0.177   1434
  Planarity :  0.005   0.049   1402
  Dihedral  :  8.589  82.377   1808
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.97 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1022
  helix:  1.52 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.20 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 662 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.011   0.001   PHE B 836 
 TYR   0.021   0.001   TYR A 390 
 ARG   0.002   0.000   ARG B 646 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8838 (t)
REVERT: A  578 MET cc_start: 0.8807 (ttt) cc_final: 0.8345 (ttt)
REVERT: A  587 MET cc_start: 0.8149 (mmp) cc_final: 0.7900 (mmp)
REVERT: A  664 MET cc_start: 0.8112 (mtm) cc_final: 0.7750 (mtp)
REVERT: A  812 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8711 (mp)
REVERT: A  820 PRO cc_start: 0.8729 (Cg_exo) cc_final: 0.8496 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7496 (ppp) cc_final: 0.7093 (tmm)
REVERT: B  486 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7433 (t80)
REVERT: B  513 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8835 (t)
REVERT: B  587 MET cc_start: 0.8314 (mmp) cc_final: 0.8103 (mmp)
REVERT: B  664 MET cc_start: 0.8035 (mtm) cc_final: 0.7672 (mtp)
REVERT: B  820 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8419 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7324 (ppp) cc_final: 0.6975 (tmm)
  outliers start: 25
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1422
  time to fit residues: 27.3118
Evaluate side-chains
  117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 80 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.081764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.074002 restraints weight = 28400.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 3.35
r_work: 0.3225 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8792  Z= 0.178
  Angle     :  0.623  13.271  11980  Z= 0.290
  Chirality :  0.040   0.178   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.468  81.735   1808
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.42 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1022
  helix:  1.56 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.21 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 662 
 HIS   0.001   0.001   HIS B 834 
 PHE   0.011   0.001   PHE A 524 
 TYR   0.019   0.001   TYR A 390 
 ARG   0.003   0.000   ARG B 646 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A  513 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8821 (t)
REVERT: A  578 MET cc_start: 0.8753 (ttt) cc_final: 0.8267 (ttt)
REVERT: A  587 MET cc_start: 0.8104 (mmp) cc_final: 0.7784 (mmp)
REVERT: A  664 MET cc_start: 0.8055 (mtm) cc_final: 0.7654 (mtp)
REVERT: A  812 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8630 (mp)
REVERT: A  820 PRO cc_start: 0.8819 (Cg_exo) cc_final: 0.8597 (Cg_endo)
REVERT: A  833 MET cc_start: 0.7468 (ppp) cc_final: 0.7063 (tmm)
REVERT: B  486 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7440 (t80)
REVERT: B  513 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8813 (t)
REVERT: B  587 MET cc_start: 0.8382 (mmp) cc_final: 0.8144 (mmp)
REVERT: B  664 MET cc_start: 0.8013 (mtm) cc_final: 0.7641 (mtp)
REVERT: B  820 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8442 (Cg_endo)
REVERT: B  833 MET cc_start: 0.7292 (ppp) cc_final: 0.6936 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1363
  time to fit residues: 25.5072
Evaluate side-chains
  117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  831 TRP
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  728 THR
Chi-restraints excluded: chain B residue  809 ILE
Chi-restraints excluded: chain B residue  831 TRP
Chi-restraints excluded: chain B residue  841 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    0.0980
   chunk 41 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.082714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.074854 restraints weight = 28538.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 3.43
r_work: 0.3240 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8792  Z= 0.171
  Angle     :  0.628  13.386  11980  Z= 0.293
  Chirality :  0.039   0.175   1434
  Planarity :  0.005   0.048   1402
  Dihedral  :  8.376  80.804   1808
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.75 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1022
  helix:  1.59 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.22 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 662 
 HIS   0.002   0.001   HIS A 734 
 PHE   0.012   0.001   PHE A 524 
 TYR   0.019   0.001   TYR A 390 
 ARG   0.003   0.000   ARG B 646 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3944.31 seconds
wall clock time: 71 minutes 19.44 seconds (4279.44 seconds total)