Starting phenix.real_space_refine
on Thu Feb 13 16:54:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ty7_26168/02_2025/7ty7_26168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty7_26168/02_2025/7ty7_26168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ty7_26168/02_2025/7ty7_26168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty7_26168/02_2025/7ty7_26168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty7_26168/02_2025/7ty7_26168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty7_26168/02_2025/7ty7_26168.cif"
  }
  resolution = 3.37
  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=   0.028
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
     P       2      5.49       5
     S      36      5.16       5
     C    5757      2.51       5
     N    1312      2.21       5
     O    1431      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8538
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4075
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4075
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          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: 170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 170
          Unusual residues: {'BCT': 1, 'CLR': 4, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 142
          Unusual residues: {'BCT': 1, 'CLR': 3, 'PC1': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 5.90, per 1000 atoms: 0.69
  Number of scatterers: 8538
  At special positions: 0
  Unit cell: (121.588, 89.308, 85.004, 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)
     S      36     16.00
     P       2     15.00
     O    1431      8.00
     N    1312      7.00
     C    5757      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: 2.34
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      73.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
    Processing helix  chain 'A' and resid 392 through 400
      removed outlier: 3.623A  pdb=" N   ALA A 400 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 431
      removed outlier: 3.692A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
      removed outlier: 3.585A  pdb=" N   GLY A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 483
    Processing helix  chain 'A' and resid 485 through 508
      removed outlier: 3.691A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.706A  pdb=" N   LEU A 540 " --> pdb=" O   THR A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
      removed outlier: 3.535A  pdb=" N   LEU A 573 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
      removed outlier: 3.561A  pdb=" N   ARG A 603 " --> pdb=" O   GLY A 599 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A 604 " --> pdb=" O   LYS A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 624
      removed outlier: 3.511A  pdb=" N   ILE A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 666
      removed outlier: 4.082A  pdb=" N   MET A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE A 665 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 690
      removed outlier: 3.562A  pdb=" N   LEU A 673 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR A 685 " --> pdb=" O   GLU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 719
      removed outlier: 4.016A  pdb=" N   LEU A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   PHE A 719 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 739
    Processing helix  chain 'A' and resid 760 through 772
    Processing helix  chain 'A' and resid 773 through 775
      No H-bonds generated for 'chain 'A' and resid 773 through 775'
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.887A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 812
    Processing helix  chain 'A' and resid 822 through 827
    Processing helix  chain 'A' and resid 829 through 853
    Processing helix  chain 'A' and resid 858 through 865
    Processing helix  chain 'A' and resid 865 through 872
      removed outlier: 3.599A  pdb=" N   LEU A 869 " --> pdb=" O   LEU A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 878
      removed outlier: 3.766A  pdb=" N   LEU A 876 " --> pdb=" O   VAL A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 887
      removed outlier: 3.519A  pdb=" N   LEU A 883 " --> pdb=" O   ARG A 879 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   CYS A 885 " --> pdb=" O   VAL A 881 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 390
    Processing helix  chain 'B' and resid 392 through 400
      removed outlier: 3.622A  pdb=" N   ALA B 400 " --> pdb=" O   ASP B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 431
      removed outlier: 3.694A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
      removed outlier: 3.585A  pdb=" N   GLY B 424 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 483
    Processing helix  chain 'B' and resid 485 through 508
      removed outlier: 3.692A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 516
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.706A  pdb=" N   LEU B 540 " --> pdb=" O   THR B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 593
      removed outlier: 3.534A  pdb=" N   LEU B 573 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN B 593 " --> pdb=" O   ARG B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 608
      removed outlier: 3.560A  pdb=" N   ARG B 603 " --> pdb=" O   GLY B 599 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B 604 " --> pdb=" O   LYS B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 624
      removed outlier: 3.511A  pdb=" N   ILE B 624 " --> pdb=" O   VAL B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 4.083A  pdb=" N   MET B 664 " --> pdb=" O   PRO B 660 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE B 665 " --> pdb=" O   ILE B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 690
      removed outlier: 3.562A  pdb=" N   LEU B 673 " --> pdb=" O   LEU B 669 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR B 685 " --> pdb=" O   GLU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 719
      removed outlier: 4.016A  pdb=" N   LEU B 718 " --> pdb=" O   GLY B 714 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE B 719 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 739
    Processing helix  chain 'B' and resid 760 through 772
    Processing helix  chain 'B' and resid 773 through 775
      No H-bonds generated for 'chain 'B' and resid 773 through 775'
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.885A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 812
    Processing helix  chain 'B' and resid 822 through 827
    Processing helix  chain 'B' and resid 829 through 853
    Processing helix  chain 'B' and resid 858 through 865
    Processing helix  chain 'B' and resid 865 through 872
      removed outlier: 3.598A  pdb=" N   LEU B 869 " --> pdb=" O   LEU B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 878
      removed outlier: 3.765A  pdb=" N   LEU B 876 " --> pdb=" O   VAL B 872 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 887
      removed outlier: 3.518A  pdb=" N   LEU B 883 " --> pdb=" O   ARG B 879 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   CYS B 885 " --> pdb=" O   VAL B 881 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463
      removed outlier: 4.798A  pdb=" N   VAL A 461 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 461 through 463
      removed outlier: 4.798A  pdb=" N   VAL B 461 " --> pdb=" O   THR B 727 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1488 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: 2.49

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1323
        1.32 -     1.45: 2194
        1.45 -     1.57: 5154
        1.57 -     1.69: 4
        1.69 -     1.82: 66
  Bond restraints: 8741
  Sorted by residual:
  bond pdb=" N   ILE A 783 "
       pdb=" CA  ILE A 783 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.038 7.50e-03 1.78e+04 2.50e+01
  bond pdb=" N   ILE B 783 "
       pdb=" CA  ILE B 783 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 7.50e-03 1.78e+04 2.42e+01
  bond pdb=" N   HIS B 819 "
       pdb=" CA  HIS B 819 "
    ideal  model  delta    sigma   weight residual
    1.453  1.492 -0.038 8.30e-03 1.45e+04 2.14e+01
  bond pdb=" N   HIS A 819 "
       pdb=" CA  HIS A 819 "
    ideal  model  delta    sigma   weight residual
    1.453  1.491 -0.038 8.30e-03 1.45e+04 2.07e+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 1.65e+01
  ... (remaining 8736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8031
        1.70 -     3.39: 3032
        3.39 -     5.09: 745
        5.09 -     6.79: 88
        6.79 -     8.48: 4
  Bond angle restraints: 11900
  Sorted by residual:
  angle pdb=" N   LEU B 680 "
        pdb=" CA  LEU B 680 "
        pdb=" C   LEU B 680 "
      ideal   model   delta    sigma   weight residual
     111.36  105.56    5.80 1.09e+00 8.42e-01 2.83e+01
  angle pdb=" N   LEU A 680 "
        pdb=" CA  LEU A 680 "
        pdb=" C   LEU A 680 "
      ideal   model   delta    sigma   weight residual
     111.36  105.58    5.78 1.09e+00 8.42e-01 2.81e+01
  angle pdb=" C   THR A 837 "
        pdb=" N   GLY A 838 "
        pdb=" CA  GLY A 838 "
      ideal   model   delta    sigma   weight residual
     119.98  125.81   -5.83 1.11e+00 8.12e-01 2.76e+01
  angle pdb=" C   THR B 837 "
        pdb=" N   GLY B 838 "
        pdb=" CA  GLY B 838 "
      ideal   model   delta    sigma   weight residual
     119.98  125.80   -5.82 1.11e+00 8.12e-01 2.75e+01
  angle pdb=" C   LEU A 427 "
        pdb=" N   GLY A 428 "
        pdb=" CA  GLY A 428 "
      ideal   model   delta    sigma   weight residual
     119.94  125.58   -5.64 1.11e+00 8.12e-01 2.58e+01
  ... (remaining 11895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.43: 5287
       25.43 -    50.86: 245
       50.86 -    76.29: 26
       76.29 -   101.71: 2
      101.71 -   127.14: 3
  Dihedral angle restraints: 5563
    sinusoidal: 2587
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C6  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -61.70 -127.14     1      3.00e+01 1.11e-03 1.71e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   61.63 -125.74     1      3.00e+01 1.11e-03 1.69e+01
  dihedral pdb=" CA  GLN A 625 "
           pdb=" C   GLN A 625 "
           pdb=" N   ASP A 626 "
           pdb=" CA  ASP A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.49  -20.51     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 5560 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 602
       0.058 -    0.116: 509
       0.116 -    0.174: 285
       0.174 -    0.231: 28
       0.231 -    0.289: 4
  Chirality restraints: 1428
  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   -2.11   -0.29 2.00e-02 2.50e+03 2.09e+02
  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   -2.14   -0.26 2.00e-02 2.50e+03 1.66e+02
  chirality pdb=" CA  LEU B 680 "
            pdb=" N   LEU B 680 "
            pdb=" C   LEU B 680 "
            pdb=" CB  LEU B 680 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1425 not shown)

  Planarity restraints: 1404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.350 2.00e-02 2.50e+03   3.01e-01 1.13e+03
        pdb=" C7  NAG C   1 "   -0.084 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.147 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.535 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.123 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.345 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG D   1 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.091 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.530 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.174 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.337 2.00e-02 2.50e+03   2.91e-01 1.06e+03
        pdb=" C7  NAG D   2 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.043 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.509 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.205 2.00e-02 2.50e+03
  ... (remaining 1401 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1264
        2.82 -     3.34: 9215
        3.34 -     3.86: 13300
        3.86 -     4.38: 17762
        4.38 -     4.90: 28719
  Nonbonded interactions: 70260
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 561 "
            pdb=" CG  LYS A 562 "
     model   vdw
     2.304 3.440
  nonbonded pdb=" O   PRO B 561 "
            pdb=" CG  LYS B 562 "
     model   vdw
     2.305 3.440
  nonbonded pdb=" O   LEU A 577 "
            pdb=" OG1 THR A 581 "
     model   vdw
     2.412 3.040
  nonbonded pdb=" O   LEU B 577 "
            pdb=" OG1 THR B 581 "
     model   vdw
     2.412 3.040
  nonbonded pdb=" NH2 ARG B 832 "
            pdb=" OE1 GLU B 882 "
     model   vdw
     2.457 3.120
  ... (remaining 70255 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 369 through 891 or resid 2101 through 2103))
  selection = (chain 'B' and (resid 369 through 891 or resid 2101 through 2103))
}
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:             2.350
  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:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.980
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
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   0.081   8741  Z= 0.853
  Angle     :  1.814   8.482  11900  Z= 1.380
  Chirality :  0.088   0.289   1428
  Planarity :  0.014   0.301   1402
  Dihedral  : 13.973 127.141   3643
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  4.57 %
    Favored  : 94.99 %
  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: -3.03 (0.21), residues: 1024
  helix: -1.79 (0.16), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.14 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 492 
 HIS   0.006   0.002   HIS B 834 
 PHE   0.014   0.002   PHE A 471 
 TYR   0.017   0.002   TYR B 824 
 ARG   0.006   0.001   ARG A 827 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A  479 CYS cc_start: 0.8762 (m) cc_final: 0.8481 (m)
REVERT: A  626 ASP cc_start: 0.8246 (m-30) cc_final: 0.7950 (m-30)
REVERT: A  821 ASP cc_start: 0.8875 (t0) cc_final: 0.8625 (t0)
REVERT: B  479 CYS cc_start: 0.8730 (m) cc_final: 0.8473 (m)
REVERT: B  626 ASP cc_start: 0.8182 (m-30) cc_final: 0.7895 (m-30)
REVERT: B  821 ASP cc_start: 0.8901 (t0) cc_final: 0.8643 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1512
  time to fit residues: 32.6670
Evaluate side-chains
  74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.052451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.045980 restraints weight = 36561.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 3.64
r_work: 0.2659 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8741  Z= 0.221
  Angle     :  0.657  10.390  11900  Z= 0.317
  Chirality :  0.043   0.330   1428
  Planarity :  0.005   0.041   1402
  Dihedral  :  9.969  97.302   1737
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.58 %
    Favored  : 88.53 %
  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:  0.33 (0.25), residues: 1024
  helix:  0.86 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.03 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 831 
 HIS   0.005   0.001   HIS A 819 
 PHE   0.021   0.001   PHE B 411 
 TYR   0.014   0.001   TYR A 824 
 ARG   0.005   0.001   ARG B 490 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A  479 CYS cc_start: 0.9263 (m) cc_final: 0.9045 (m)
REVERT: A  626 ASP cc_start: 0.8473 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  696 MET cc_start: 0.8915 (mmm) cc_final: 0.8704 (mmm)
REVERT: A  776 MET cc_start: 0.9444 (ptp) cc_final: 0.9118 (ptp)
REVERT: A  805 LEU cc_start: 0.9357 (tp) cc_final: 0.9116 (tp)
REVERT: A  821 ASP cc_start: 0.9145 (t0) cc_final: 0.8926 (t0)
REVERT: A  880 ASN cc_start: 0.9432 (p0) cc_final: 0.8993 (t0)
REVERT: B  617 MET cc_start: 0.9458 (mmm) cc_final: 0.9256 (mmm)
REVERT: B  626 ASP cc_start: 0.8449 (m-30) cc_final: 0.8155 (m-30)
REVERT: B  696 MET cc_start: 0.8956 (mmm) cc_final: 0.8743 (mmm)
REVERT: B  805 LEU cc_start: 0.9364 (tp) cc_final: 0.9118 (tp)
REVERT: B  821 ASP cc_start: 0.9232 (t0) cc_final: 0.8999 (t0)
REVERT: B  880 ASN cc_start: 0.9410 (p0) cc_final: 0.8935 (t0)
  outliers start: 17
  outliers final: 8
  residues processed: 92
  average time/residue: 0.1413
  time to fit residues: 20.9002
Evaluate side-chains
  69 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  765 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.2886 r_free = 0.2886 target = 0.048597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.042309 restraints weight = 39528.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 3.71
r_work: 0.2562 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   8741  Z= 0.412
  Angle     :  0.711  11.059  11900  Z= 0.333
  Chirality :  0.043   0.211   1428
  Planarity :  0.005   0.038   1402
  Dihedral  :  9.446  83.008   1737
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 10.36 %
    Favored  : 86.30 %
  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 (0.27), residues: 1024
  helix:  1.66 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.90 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 492 
 HIS   0.006   0.002   HIS B 819 
 PHE   0.016   0.002   PHE A 471 
 TYR   0.013   0.001   TYR B 824 
 ARG   0.005   0.001   ARG B 490 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 62
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A  617 MET cc_start: 0.9521 (mmm) cc_final: 0.9138 (mmm)
REVERT: A  626 ASP cc_start: 0.8567 (m-30) cc_final: 0.8275 (m-30)
REVERT: A  821 ASP cc_start: 0.9242 (t0) cc_final: 0.9003 (t0)
REVERT: A  833 MET cc_start: 0.9347 (ppp) cc_final: 0.9046 (tmm)
REVERT: B  559 MET cc_start: 0.9325 (mpp) cc_final: 0.8909 (mmp)
REVERT: B  626 ASP cc_start: 0.8513 (m-30) cc_final: 0.8229 (m-30)
REVERT: B  821 ASP cc_start: 0.9259 (t0) cc_final: 0.9013 (t0)
REVERT: B  833 MET cc_start: 0.9374 (ppp) cc_final: 0.9066 (tmm)
  outliers start: 30
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1421
  time to fit residues: 19.4351
Evaluate side-chains
  70 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  842 ILE
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  850 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 683 GLN
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 GLN
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.050049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.043763 restraints weight = 38460.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.2731 rms_B_bonded: 3.77
r_work: 0.2605 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8741  Z= 0.212
  Angle     :  0.591  10.863  11900  Z= 0.276
  Chirality :  0.039   0.214   1428
  Planarity :  0.005   0.042   1402
  Dihedral  :  8.608  59.785   1737
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.14 %
    Favored  : 85.97 %
  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:  1.48 (0.26), residues: 1024
  helix:  1.84 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -0.93 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 831 
 HIS   0.002   0.001   HIS B 819 
 PHE   0.015   0.001   PHE A 471 
 TYR   0.015   0.001   TYR A 824 
 ARG   0.003   0.000   ARG A 490 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  559 MET cc_start: 0.9371 (mpp) cc_final: 0.9013 (mmp)
REVERT: A  617 MET cc_start: 0.9520 (mmm) cc_final: 0.9216 (mmm)
REVERT: A  626 ASP cc_start: 0.8462 (m-30) cc_final: 0.8175 (m-30)
REVERT: A  821 ASP cc_start: 0.9210 (t0) cc_final: 0.8982 (t0)
REVERT: A  833 MET cc_start: 0.9356 (ppp) cc_final: 0.9035 (tmm)
REVERT: A  880 ASN cc_start: 0.9508 (p0) cc_final: 0.9018 (t0)
REVERT: B  559 MET cc_start: 0.9331 (mpp) cc_final: 0.8998 (mmp)
REVERT: B  617 MET cc_start: 0.9532 (mmm) cc_final: 0.9245 (mmm)
REVERT: B  626 ASP cc_start: 0.8434 (m-30) cc_final: 0.8161 (m-30)
REVERT: B  821 ASP cc_start: 0.9198 (t0) cc_final: 0.8937 (t0)
REVERT: B  833 MET cc_start: 0.9360 (ppp) cc_final: 0.9036 (tmm)
REVERT: B  880 ASN cc_start: 0.9449 (p0) cc_final: 0.8933 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 75
  average time/residue: 0.1441
  time to fit residues: 17.3272
Evaluate side-chains
  67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  664 MET
Chi-restraints excluded: chain B residue  842 ILE
Chi-restraints excluded: chain B residue  843 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 71 optimal weight:   20.0000
   chunk 95 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 834 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.049727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.043393 restraints weight = 38262.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 3.76
r_work: 0.2587 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8741  Z= 0.253
  Angle     :  0.594   9.397  11900  Z= 0.277
  Chirality :  0.039   0.216   1428
  Planarity :  0.004   0.043   1402
  Dihedral  :  8.258  59.302   1737
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 11.92 %
    Favored  : 85.19 %
  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:  1.71 (0.27), residues: 1024
  helix:  2.04 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.88 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 492 
 HIS   0.003   0.001   HIS B 819 
 PHE   0.014   0.001   PHE A 471 
 TYR   0.014   0.001   TYR A 824 
 ARG   0.002   0.000   ARG B 490 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 65
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A  557 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8617 (m)
REVERT: A  617 MET cc_start: 0.9533 (mmm) cc_final: 0.9238 (mmm)
REVERT: A  626 ASP cc_start: 0.8450 (m-30) cc_final: 0.8164 (m-30)
REVERT: A  821 ASP cc_start: 0.9134 (t0) cc_final: 0.8886 (t0)
REVERT: A  833 MET cc_start: 0.9361 (ppp) cc_final: 0.9005 (tmm)
REVERT: B  557 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8524 (m)
REVERT: B  559 MET cc_start: 0.9363 (mpp) cc_final: 0.9130 (mpp)
REVERT: B  626 ASP cc_start: 0.8421 (m-30) cc_final: 0.8137 (m-30)
REVERT: B  821 ASP cc_start: 0.9154 (t0) cc_final: 0.8907 (t0)
REVERT: B  833 MET cc_start: 0.9411 (ppp) cc_final: 0.9067 (tmm)
  outliers start: 26
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1474
  time to fit residues: 19.7967
Evaluate side-chains
  75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  664 MET
Chi-restraints excluded: chain B residue  842 ILE
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  850 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 564 GLN
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.050546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.044368 restraints weight = 37893.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 3.74
r_work: 0.2623 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8741  Z= 0.183
  Angle     :  0.589   9.517  11900  Z= 0.271
  Chirality :  0.039   0.220   1428
  Planarity :  0.004   0.044   1402
  Dihedral  :  7.986  58.860   1737
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.69 %
    Favored  : 85.19 %
  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:  1.79 (0.27), residues: 1024
  helix:  2.17 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.91 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 831 
 HIS   0.002   0.000   HIS A 819 
 PHE   0.014   0.001   PHE A 471 
 TYR   0.014   0.001   TYR A 824 
 ARG   0.002   0.000   ARG B 389 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  626 ASP cc_start: 0.8451 (m-30) cc_final: 0.8162 (m-30)
REVERT: A  821 ASP cc_start: 0.9125 (t0) cc_final: 0.8881 (t0)
REVERT: A  833 MET cc_start: 0.9367 (ppp) cc_final: 0.8985 (tmm)
REVERT: A  880 ASN cc_start: 0.9484 (p0) cc_final: 0.9123 (t0)
REVERT: B  557 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8630 (m)
REVERT: B  559 MET cc_start: 0.9357 (mpp) cc_final: 0.9071 (mpp)
REVERT: B  617 MET cc_start: 0.9537 (mmm) cc_final: 0.9288 (mmm)
REVERT: B  626 ASP cc_start: 0.8388 (m-30) cc_final: 0.8101 (m-30)
REVERT: B  821 ASP cc_start: 0.9140 (t0) cc_final: 0.8894 (t0)
REVERT: B  833 MET cc_start: 0.9425 (ppp) cc_final: 0.9063 (tmm)
REVERT: B  880 ASN cc_start: 0.9455 (p0) cc_final: 0.9083 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1539
  time to fit residues: 19.2681
Evaluate side-chains
  76 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  664 MET
Chi-restraints excluded: chain B residue  842 ILE
Chi-restraints excluded: chain B residue  843 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 651 HIS
** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 834 HIS
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 651 HIS
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.049022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.042744 restraints weight = 39221.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2706 rms_B_bonded: 3.76
r_work: 0.2574 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8741  Z= 0.327
  Angle     :  0.648   9.335  11900  Z= 0.299
  Chirality :  0.041   0.216   1428
  Planarity :  0.004   0.042   1402
  Dihedral  :  7.989  59.443   1737
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.36 %
    Favored  : 84.19 %
  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:  1.85 (0.27), residues: 1024
  helix:  2.15 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.84 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 492 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.015   0.001   PHE A 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.002   0.000   ARG A 760 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  617 MET cc_start: 0.9538 (mmm) cc_final: 0.9248 (mmm)
REVERT: A  626 ASP cc_start: 0.8389 (m-30) cc_final: 0.8105 (m-30)
REVERT: A  821 ASP cc_start: 0.9121 (t0) cc_final: 0.8883 (t0)
REVERT: A  833 MET cc_start: 0.9430 (ppp) cc_final: 0.9046 (tmm)
REVERT: A  880 ASN cc_start: 0.9484 (p0) cc_final: 0.9099 (t0)
REVERT: B  557 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8687 (m)
REVERT: B  559 MET cc_start: 0.9365 (mpp) cc_final: 0.9132 (mpp)
REVERT: B  617 MET cc_start: 0.9553 (mmm) cc_final: 0.9229 (mmm)
REVERT: B  626 ASP cc_start: 0.8366 (m-30) cc_final: 0.8078 (m-30)
REVERT: B  821 ASP cc_start: 0.9130 (t0) cc_final: 0.8891 (t0)
REVERT: B  833 MET cc_start: 0.9461 (ppp) cc_final: 0.9083 (tmm)
REVERT: B  880 ASN cc_start: 0.9480 (p0) cc_final: 0.9089 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1529
  time to fit residues: 18.3698
Evaluate side-chains
  78 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  664 MET
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  664 MET
Chi-restraints excluded: chain B residue  842 ILE
Chi-restraints excluded: chain B residue  843 CYS
Chi-restraints excluded: chain B residue  850 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   chunk 49 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0270
   chunk 52 optimal weight:    0.0170
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0770
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.2234

-------------------------------------------------------------------------------
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**
B 564 GLN
** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.050992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.045009 restraints weight = 38673.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 3.63
r_work: 0.2685 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8741  Z= 0.153
  Angle     :  0.594   9.606  11900  Z= 0.269
  Chirality :  0.039   0.222   1428
  Planarity :  0.005   0.046   1402
  Dihedral  :  7.675  59.631   1737
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.70 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.27), residues: 1024
  helix:  2.21 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.80 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 496 
 HIS   0.002   0.000   HIS A 703 
 PHE   0.013   0.001   PHE A 411 
 TYR   0.015   0.001   TYR A 824 
 ARG   0.003   0.000   ARG B 389 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.983 
Fit side-chains
REVERT: A  617 MET cc_start: 0.9553 (mmm) cc_final: 0.9289 (mmm)
REVERT: A  626 ASP cc_start: 0.8166 (m-30) cc_final: 0.7886 (m-30)
REVERT: A  821 ASP cc_start: 0.8841 (t0) cc_final: 0.8493 (t0)
REVERT: A  833 MET cc_start: 0.9469 (ppp) cc_final: 0.9096 (tmm)
REVERT: A  880 ASN cc_start: 0.9451 (p0) cc_final: 0.9075 (t0)
REVERT: B  557 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8531 (p)
REVERT: B  559 MET cc_start: 0.9278 (mpp) cc_final: 0.8990 (mpp)
REVERT: B  626 ASP cc_start: 0.8156 (m-30) cc_final: 0.7871 (m-30)
REVERT: B  821 ASP cc_start: 0.8815 (t0) cc_final: 0.8461 (t0)
REVERT: B  833 MET cc_start: 0.9458 (ppp) cc_final: 0.9087 (tmm)
REVERT: B  880 ASN cc_start: 0.9414 (p0) cc_final: 0.9027 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1507
  time to fit residues: 18.7763
Evaluate side-chains
  74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  664 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0070
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0980
   chunk 75 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4598

-------------------------------------------------------------------------------
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**
** B 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 = 0.2992 r_free = 0.2992 target = 0.051577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.045420 restraints weight = 37377.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 3.56
r_work: 0.2695 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8741  Z= 0.165
  Angle     :  0.612   9.564  11900  Z= 0.276
  Chirality :  0.039   0.221   1428
  Planarity :  0.004   0.042   1402
  Dihedral  :  7.484  59.198   1737
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.70 %
    Favored  : 82.85 %
  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:  1.93 (0.27), residues: 1024
  helix:  2.24 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.78 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 662 
 HIS   0.002   0.000   HIS B 703 
 PHE   0.013   0.001   PHE A 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.002   0.000   ARG A 490 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A  559 MET cc_start: 0.9459 (mpp) cc_final: 0.9231 (mpp)
REVERT: A  587 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8577 (mmm)
REVERT: A  617 MET cc_start: 0.9568 (mmm) cc_final: 0.9284 (mmm)
REVERT: A  626 ASP cc_start: 0.8197 (m-30) cc_final: 0.7917 (m-30)
REVERT: A  672 LEU cc_start: 0.9513 (tp) cc_final: 0.9298 (pp)
REVERT: A  821 ASP cc_start: 0.8834 (t0) cc_final: 0.8567 (t0)
REVERT: A  833 MET cc_start: 0.9472 (ppp) cc_final: 0.9102 (tmm)
REVERT: A  880 ASN cc_start: 0.9450 (p0) cc_final: 0.9078 (t0)
REVERT: B  557 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8548 (p)
REVERT: B  559 MET cc_start: 0.9258 (mpp) cc_final: 0.9011 (mpp)
REVERT: B  587 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8558 (mmm)
REVERT: B  626 ASP cc_start: 0.8162 (m-30) cc_final: 0.7841 (m-30)
REVERT: B  672 LEU cc_start: 0.9508 (tp) cc_final: 0.9293 (pp)
REVERT: B  821 ASP cc_start: 0.8814 (t0) cc_final: 0.8540 (t0)
REVERT: B  833 MET cc_start: 0.9450 (ppp) cc_final: 0.9073 (tmm)
REVERT: B  880 ASN cc_start: 0.9405 (p0) cc_final: 0.9034 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 80
  average time/residue: 0.1469
  time to fit residues: 18.9188
Evaluate side-chains
  75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  843 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   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 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.2989 r_free = 0.2989 target = 0.051512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.045417 restraints weight = 37342.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 3.57
r_work: 0.2691 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8741  Z= 0.200
  Angle     :  0.637   9.482  11900  Z= 0.286
  Chirality :  0.039   0.220   1428
  Planarity :  0.004   0.039   1402
  Dihedral  :  7.382  59.293   1737
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.70 %
    Favored  : 82.85 %
  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:  1.99 (0.27), residues: 1024
  helix:  2.24 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.65 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 662 
 HIS   0.002   0.000   HIS A 703 
 PHE   0.013   0.001   PHE A 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.002   0.000   ARG B 432 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A  559 MET cc_start: 0.9458 (mpp) cc_final: 0.9221 (mpp)
REVERT: A  587 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8570 (mmm)
REVERT: A  617 MET cc_start: 0.9566 (mmm) cc_final: 0.9260 (mmm)
REVERT: A  664 MET cc_start: 0.9082 (mtm) cc_final: 0.8749 (mtm)
REVERT: A  672 LEU cc_start: 0.9516 (tp) cc_final: 0.9296 (pp)
REVERT: A  821 ASP cc_start: 0.8836 (t0) cc_final: 0.8575 (t0)
REVERT: A  833 MET cc_start: 0.9478 (ppp) cc_final: 0.9111 (tmm)
REVERT: A  880 ASN cc_start: 0.9445 (p0) cc_final: 0.9078 (t0)
REVERT: B  557 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8564 (p)
REVERT: B  559 MET cc_start: 0.9225 (mpp) cc_final: 0.8973 (mpp)
REVERT: B  587 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8586 (mmm)
REVERT: B  672 LEU cc_start: 0.9513 (tp) cc_final: 0.9292 (pp)
REVERT: B  776 MET cc_start: 0.9581 (ptp) cc_final: 0.9366 (ptp)
REVERT: B  821 ASP cc_start: 0.8785 (t0) cc_final: 0.8525 (t0)
REVERT: B  833 MET cc_start: 0.9466 (ppp) cc_final: 0.9092 (tmm)
REVERT: B  880 ASN cc_start: 0.9422 (p0) cc_final: 0.9055 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1543
  time to fit residues: 17.8945
Evaluate side-chains
  74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 TYR
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  843 CYS
Chi-restraints excluded: chain A residue  889 ASP
Chi-restraints excluded: chain B residue  486 TYR
Chi-restraints excluded: chain B residue  512 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  843 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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**
** B 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 = 0.2928 r_free = 0.2928 target = 0.049859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.043475 restraints weight = 39124.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 3.85
r_work: 0.2607 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8741  Z= 0.276
  Angle     :  0.672  12.261  11900  Z= 0.303
  Chirality :  0.040   0.219   1428
  Planarity :  0.004   0.036   1402
  Dihedral  :  7.442  59.487   1737
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.81 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.27), residues: 1024
  helix:  2.24 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.51 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 662 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.014   0.001   PHE A 471 
 TYR   0.012   0.001   TYR A 824 
 ARG   0.002   0.000   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3379.65 seconds
wall clock time: 61 minutes 21.16 seconds (3681.16 seconds total)