Starting phenix.real_space_refine
on Sat May 10 14:00:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ygn_33817/05_2025/7ygn_33817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ygn_33817/05_2025/7ygn_33817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ygn_33817/05_2025/7ygn_33817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ygn_33817/05_2025/7ygn_33817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ygn_33817/05_2025/7ygn_33817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ygn_33817/05_2025/7ygn_33817.cif"
  }
  resolution = 3.0
  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=   0.200
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       9      5.49       5
     Mg      2      5.21       5
     S      43      5.16       5
     C    3896      2.51       5
     N    1057      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6133
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 5945
          Classifications: {'peptide': 739}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 701}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 186
          Classifications: {'RNA': 9}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 5}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.15, per 1000 atoms: 0.68
  Number of scatterers: 6133
  At special positions: 0
  Unit cell: (76.09, 84.786, 113.048, 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      43     16.00
     P       9     15.00
     Mg      2     11.99
     O    1126      8.00
     N    1057      7.00
     C    3896      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 839.0 milliseconds
  

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1402

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      39.2% alpha, 24.6% beta
      0 base pairs and 3 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 262
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 3.678A  pdb=" N   THR A 266 " --> pdb=" O   HIS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 316
      No H-bonds generated for 'chain 'A' and resid 314 through 316'
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 344 through 347
      removed outlier: 3.518A  pdb=" N   ALA A 347 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 344 through 347'
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 402 through 414
      removed outlier: 4.603A  pdb=" N   GLY A 413 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   SER A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 458
    Processing helix  chain 'A' and resid 502 through 508
      removed outlier: 3.727A  pdb=" N   LYS A 506 " --> pdb=" O   PRO A 502 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS A 507 " --> pdb=" O   GLU A 503 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP A 508 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 502 through 508'
    Processing helix  chain 'A' and resid 509 through 520
    Processing helix  chain 'A' and resid 522 through 540
    Processing helix  chain 'A' and resid 540 through 549
    Processing helix  chain 'A' and resid 586 through 593
      removed outlier: 3.579A  pdb=" N   VAL A 590 " --> pdb=" O   TRP A 586 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 591 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 612 through 631
      removed outlier: 4.401A  pdb=" N   GLY A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      Proline residue:  A 629  - end of helix
    Processing helix  chain 'A' and resid 646 through 661
    Processing helix  chain 'A' and resid 675 through 688
    Processing helix  chain 'A' and resid 699 through 704
      removed outlier: 3.894A  pdb=" N   GLN A 704 " --> pdb=" O   ARG A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 724
    Processing helix  chain 'A' and resid 781 through 802
      removed outlier: 4.294A  pdb=" N   SER A 785 " --> pdb=" O   GLU A 781 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 788 " --> pdb=" O   ASP A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 818
      No H-bonds generated for 'chain 'A' and resid 816 through 818'
    Processing helix  chain 'A' and resid 819 through 826
    Processing helix  chain 'A' and resid 826 through 833
      removed outlier: 3.512A  pdb=" N   LYS A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 838
    Processing helix  chain 'A' and resid 914 through 926
    Processing helix  chain 'A' and resid 939 through 955
    Processing helix  chain 'A' and resid 961 through 967
      removed outlier: 4.081A  pdb=" N   GLY A 966 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 775
      removed outlier: 3.908A  pdb=" N   ASP A 743 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL A 739 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   VAL A 744 " --> pdb=" O   ASP A 813 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE A 808 " --> pdb=" O   VAL A 846 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   PHE A 848 " --> pdb=" O   ILE A 808 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 810 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   VAL A 850 " --> pdb=" O   VAL A 810 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG A 812 " --> pdb=" O   VAL A 850 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 908 " --> pdb=" O   VAL A 847 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   VAL A 849 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   CYS A 906 " --> pdb=" O   VAL A 849 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 851 " --> pdb=" O   TYR A 904 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   TYR A 904 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A 885 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   SER A 223 " --> pdb=" O   ALA A 861 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337
      removed outlier: 3.614A  pdb=" N   ASN A 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337
      removed outlier: 3.614A  pdb=" N   ASN A 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU A 372 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272
      removed outlier: 5.825A  pdb=" N   HIS A 242 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LEU A 306 " --> pdb=" O   HIS A 242 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   THR A 244 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE A 304 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   SER A 246 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ILE A 302 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 425
      removed outlier: 3.514A  pdb=" N   ARG A 423 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431
    Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 440
    Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 572
    Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 641

    289 hydrogen bonds defined for protein.
    801 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      3 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 963
        1.30 -     1.43: 1632
        1.43 -     1.56: 3607
        1.56 -     1.69: 16
        1.69 -     1.82: 67
  Bond restraints: 6285
  Sorted by residual:
  bond pdb=" C2  OMC B  26 "
       pdb=" N3  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.350  1.491 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" C4  OMC B  26 "
       pdb=" N4  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.332  1.471 -0.139 2.00e-02 2.50e+03 4.81e+01
  bond pdb=" N3  OMC B  26 "
       pdb=" C4  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.317  1.454 -0.137 2.00e-02 2.50e+03 4.66e+01
  bond pdb=" C5  OMC B  26 "
       pdb=" C6  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.346  1.481 -0.135 2.00e-02 2.50e+03 4.59e+01
  bond pdb=" O3'   U B   2 "
       pdb=" P     A B   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.528  0.079 1.50e-02 4.44e+03 2.78e+01
  ... (remaining 6280 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.32: 8507
        4.32 -     8.64: 41
        8.64 -    12.96: 1
       12.96 -    17.28: 2
       17.28 -    21.60: 2
  Bond angle restraints: 8553
  Sorted by residual:
  angle pdb=" O3'   U B  25 "
        pdb=" P   OMC B  26 "
        pdb=" OP1 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     108.00   86.40   21.60 3.00e+00 1.11e-01 5.18e+01
  angle pdb=" O3'   U B  25 "
        pdb=" P   OMC B  26 "
        pdb=" OP2 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     108.00   90.04   17.96 3.00e+00 1.11e-01 3.58e+01
  angle pdb=" N   GLN A 263 "
        pdb=" CA  GLN A 263 "
        pdb=" C   GLN A 263 "
      ideal   model   delta    sigma   weight residual
     111.28  105.23    6.05 1.09e+00 8.42e-01 3.09e+01
  angle pdb=" OP2 OMC B  26 "
        pdb=" P   OMC B  26 "
        pdb=" O5' OMC B  26 "
      ideal   model   delta    sigma   weight residual
     100.81  116.44  -15.63 3.00e+00 1.11e-01 2.71e+01
  angle pdb=" OP1 OMC B  26 "
        pdb=" P   OMC B  26 "
        pdb=" OP2 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     115.29  128.88  -13.59 3.00e+00 1.11e-01 2.05e+01
  ... (remaining 8548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3353
       17.79 -    35.59: 355
       35.59 -    53.38: 67
       53.38 -    71.17: 20
       71.17 -    88.97: 7
  Dihedral angle restraints: 3802
    sinusoidal: 1637
      harmonic: 2165
  Sorted by residual:
  dihedral pdb=" C4'   U B   2 "
           pdb=" C3'   U B   2 "
           pdb=" C2'   U B   2 "
           pdb=" C1'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00    5.39   30.61     1      8.00e+00 1.56e-02 2.09e+01
  dihedral pdb=" O4'   U B   2 "
           pdb=" C2'   U B   2 "
           pdb=" C1'   U B   2 "
           pdb=" C3'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -2.36   27.36     1      8.00e+00 1.56e-02 1.68e+01
  dihedral pdb=" C5'   U B   2 "
           pdb=" C4'   U B   2 "
           pdb=" C3'   U B   2 "
           pdb=" O3'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  109.29  -27.29     1      8.00e+00 1.56e-02 1.67e+01
  ... (remaining 3799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 837
       0.068 -    0.135: 125
       0.135 -    0.203: 13
       0.203 -    0.271: 1
       0.271 -    0.339: 1
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" P     U B   2 "
            pdb=" OP1   U B   2 "
            pdb=" OP2   U B   2 "
            pdb=" O5'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.07    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" C3'   U B   2 "
            pdb=" C4'   U B   2 "
            pdb=" O3'   U B   2 "
            pdb=" C2'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.22   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE A 905 "
            pdb=" N   ILE A 905 "
            pdb=" C   ILE A 905 "
            pdb=" CB  ILE A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.73e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   2 "   -0.044 2.00e-02 2.50e+03   2.47e-02 1.38e+01
        pdb=" N1    U B   2 "    0.056 2.00e-02 2.50e+03
        pdb=" C2    U B   2 "    0.014 2.00e-02 2.50e+03
        pdb=" O2    U B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U B   2 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4    U B   2 "   -0.013 2.00e-02 2.50e+03
        pdb=" O4    U B   2 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    U B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U B   2 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 220 "   -0.038 5.00e-02 4.00e+02   5.66e-02 5.12e+00
        pdb=" N   PRO A 221 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 221 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 221 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 246 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO A 247 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 247 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 247 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 29
        2.49 -     3.10: 4032
        3.10 -     3.70: 8648
        3.70 -     4.30: 12746
        4.30 -     4.90: 21940
  Nonbonded interactions: 47395
  Sorted by model distance:
  nonbonded pdb=" OP1   U B   1 "
            pdb="MG    MG A1001 "
     model   vdw
     1.892 2.170
  nonbonded pdb=" O   LEU A 971 "
            pdb="MG    MG A1001 "
     model   vdw
     1.900 2.170
  nonbonded pdb=" OD2 ASP A 743 "
            pdb="MG    MG A1002 "
     model   vdw
     2.039 2.170
  nonbonded pdb=" OP1   A B   3 "
            pdb="MG    MG A1001 "
     model   vdw
     2.114 2.170
  nonbonded pdb=" OG  SER A 439 "
            pdb=" OE2 GLU A 447 "
     model   vdw
     2.209 3.040
  ... (remaining 47390 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.390
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:12.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.006   0.141   6285  Z= 0.291
  Angle     :  0.854  21.598   8553  Z= 0.441
  Chirality :  0.049   0.339    977
  Planarity :  0.006   0.058   1051
  Dihedral  : 15.418  88.968   2400
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.11 (0.31), residues: 733
  helix:  1.28 (0.36), residues: 234
  sheet:  0.54 (0.36), residues: 198
  loop : -1.22 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 728 
 HIS   0.010   0.001   HIS A 353 
 PHE   0.017   0.002   PHE A 578 
 TYR   0.013   0.002   TYR A 239 
 ARG   0.008   0.001   ARG A 570 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15886 (  284)
  hydrogen bonds       : angle       6.85611 (  801)
  covalent geometry    : bond        0.00595 ( 6285)
  covalent geometry    : angle       0.85402 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.650 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 1.1551
  time to fit residues: 93.9039
Evaluate side-chains
  63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 240 GLN
A 535 GLN
A 746 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.191760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142328 restraints weight = 6688.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 3.25
r_work: 0.3440 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6285  Z= 0.141
  Angle     :  0.553   4.870   8553  Z= 0.287
  Chirality :  0.045   0.152    977
  Planarity :  0.005   0.057   1051
  Dihedral  :  9.424  81.209    918
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.22 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.49 (0.31), residues: 733
  helix:  1.67 (0.35), residues: 238
  sheet:  0.68 (0.36), residues: 196
  loop : -1.04 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 884 
 HIS   0.005   0.001   HIS A 927 
 PHE   0.022   0.002   PHE A 320 
 TYR   0.015   0.001   TYR A 239 
 ARG   0.006   0.000   ARG A 570 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  284)
  hydrogen bonds       : angle       5.31099 (  801)
  covalent geometry    : bond        0.00333 ( 6285)
  covalent geometry    : angle       0.55253 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6521 (mmp) cc_final: 0.6146 (mtm)
REVERT: A  505 MET cc_start: 0.6163 (mmt) cc_final: 0.5760 (mmt)
REVERT: A  520 ASN cc_start: 0.7802 (m110) cc_final: 0.7557 (m110)
REVERT: A  624 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7540 (mt-10)
REVERT: A  643 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7421 (mmtt)
REVERT: A  663 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7479 (mtmm)
REVERT: A  763 ASN cc_start: 0.8338 (t0) cc_final: 0.8104 (t0)
REVERT: A  764 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8154 (tp)
REVERT: A  827 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6715 (mp0)
REVERT: A  845 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7845 (ttt)
REVERT: A  886 ASP cc_start: 0.8714 (p0) cc_final: 0.8439 (p0)
REVERT: A  895 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5994 (ptp90)
  outliers start: 13
  outliers final: 1
  residues processed: 83
  average time/residue: 1.2856
  time to fit residues: 111.8921
Evaluate side-chains
  65 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  845 MET
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0970
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
A 539 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.178192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.132045 restraints weight = 6787.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.57
r_work: 0.3152 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6285  Z= 0.142
  Angle     :  0.523   4.900   8553  Z= 0.273
  Chirality :  0.044   0.155    977
  Planarity :  0.005   0.056   1051
  Dihedral  :  9.113  81.310    918
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 12.37 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.62 (0.31), residues: 733
  helix:  1.77 (0.35), residues: 240
  sheet:  0.79 (0.37), residues: 191
  loop : -0.96 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 927 
 PHE   0.019   0.002   PHE A 320 
 TYR   0.013   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 753 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (  284)
  hydrogen bonds       : angle       5.06618 (  801)
  covalent geometry    : bond        0.00344 ( 6285)
  covalent geometry    : angle       0.52346 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  520 ASN cc_start: 0.7647 (m110) cc_final: 0.7142 (m-40)
REVERT: A  618 GLU cc_start: 0.7863 (tt0) cc_final: 0.7038 (mm-30)
REVERT: A  624 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7730 (mt-10)
REVERT: A  643 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7495 (mmtt)
REVERT: A  666 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8789 (ttp)
REVERT: A  700 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7153 (ttp80)
REVERT: A  707 ARG cc_start: 0.7411 (mtm110) cc_final: 0.7082 (ptm-80)
REVERT: A  763 ASN cc_start: 0.8573 (t0) cc_final: 0.8317 (t0)
REVERT: A  764 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8074 (tp)
REVERT: A  827 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6601 (mp0)
REVERT: A  845 MET cc_start: 0.8281 (ttm) cc_final: 0.8015 (ttt)
REVERT: A  895 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6036 (ptp90)
  outliers start: 21
  outliers final: 5
  residues processed: 84
  average time/residue: 1.3601
  time to fit residues: 119.4645
Evaluate side-chains
  73 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.169637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.122724 restraints weight = 6910.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 3.08
r_work: 0.3081 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6285  Z= 0.198
  Angle     :  0.574   5.711   8553  Z= 0.298
  Chirality :  0.046   0.176    977
  Planarity :  0.005   0.054   1051
  Dihedral  :  9.038  80.759    918
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.16 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.34 (0.31), residues: 733
  helix:  1.65 (0.34), residues: 241
  sheet:  0.45 (0.35), residues: 196
  loop : -1.13 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 604 
 HIS   0.006   0.001   HIS A 927 
 PHE   0.021   0.002   PHE A 320 
 TYR   0.014   0.002   TYR A 239 
 ARG   0.002   0.000   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04581 (  284)
  hydrogen bonds       : angle       5.12878 (  801)
  covalent geometry    : bond        0.00490 ( 6285)
  covalent geometry    : angle       0.57431 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.8179 (tttt) cc_final: 0.7363 (tptp)
REVERT: A  309 ILE cc_start: 0.7378 (mt) cc_final: 0.7172 (mt)
REVERT: A  313 CYS cc_start: 0.8398 (p) cc_final: 0.8180 (p)
REVERT: A  520 ASN cc_start: 0.7611 (m110) cc_final: 0.7317 (m110)
REVERT: A  532 CYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7447 (p)
REVERT: A  610 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8030 (mptt)
REVERT: A  611 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7625 (pmm-80)
REVERT: A  624 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7510 (mt-10)
REVERT: A  666 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8767 (ttp)
REVERT: A  700 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7278 (ttp80)
REVERT: A  827 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6661 (mp0)
REVERT: A  845 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7906 (ttt)
REVERT: A  895 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5969 (ptp90)
  outliers start: 24
  outliers final: 6
  residues processed: 91
  average time/residue: 1.3603
  time to fit residues: 129.2924
Evaluate side-chains
  76 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  845 MET
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0670
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.2522

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 GLN
A 539 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.170907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.114518 restraints weight = 6813.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.34
r_work: 0.3115 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6285  Z= 0.142
  Angle     :  0.519   6.734   8553  Z= 0.270
  Chirality :  0.044   0.155    977
  Planarity :  0.005   0.053   1051
  Dihedral  :  8.943  79.923    918
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.73 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.52 (0.31), residues: 733
  helix:  1.86 (0.34), residues: 241
  sheet:  0.56 (0.35), residues: 194
  loop : -1.08 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.019   0.002   PHE A 320 
 TYR   0.012   0.001   TYR A 239 
 ARG   0.009   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  284)
  hydrogen bonds       : angle       5.00157 (  801)
  covalent geometry    : bond        0.00351 ( 6285)
  covalent geometry    : angle       0.51858 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.8195 (tttt) cc_final: 0.7268 (tptp)
REVERT: A  309 ILE cc_start: 0.7395 (mt) cc_final: 0.7138 (mt)
REVERT: A  348 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7396 (ptp)
REVERT: A  505 MET cc_start: 0.5653 (mmt) cc_final: 0.5081 (mmt)
REVERT: A  520 ASN cc_start: 0.7555 (m110) cc_final: 0.7240 (m110)
REVERT: A  532 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7653 (p)
REVERT: A  611 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7586 (pmm-80)
REVERT: A  618 GLU cc_start: 0.7999 (tt0) cc_final: 0.7101 (mm-30)
REVERT: A  624 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7587 (mt-10)
REVERT: A  700 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7326 (ttp80)
REVERT: A  707 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7111 (ptm-80)
REVERT: A  763 ASN cc_start: 0.8551 (t0) cc_final: 0.8228 (t0)
REVERT: A  827 GLU cc_start: 0.7696 (mt-10) cc_final: 0.6687 (mp0)
REVERT: A  895 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.5960 (ptp90)
  outliers start: 17
  outliers final: 8
  residues processed: 75
  average time/residue: 1.2749
  time to fit residues: 100.4097
Evaluate side-chains
  72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 896 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.168607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.123308 restraints weight = 6795.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.02
r_work: 0.3079 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6285  Z= 0.178
  Angle     :  0.549   7.139   8553  Z= 0.284
  Chirality :  0.045   0.164    977
  Planarity :  0.005   0.052   1051
  Dihedral  :  8.936  79.601    918
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.18 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.46 (0.31), residues: 733
  helix:  1.85 (0.34), residues: 240
  sheet:  0.53 (0.35), residues: 194
  loop : -1.14 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 927 
 PHE   0.028   0.002   PHE A 272 
 TYR   0.013   0.002   TYR A 239 
 ARG   0.006   0.000   ARG A 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04215 (  284)
  hydrogen bonds       : angle       5.06092 (  801)
  covalent geometry    : bond        0.00445 ( 6285)
  covalent geometry    : angle       0.54871 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.8166 (tttt) cc_final: 0.7264 (tptp)
REVERT: A  309 ILE cc_start: 0.7435 (mt) cc_final: 0.7216 (mt)
REVERT: A  348 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7212 (ptp)
REVERT: A  505 MET cc_start: 0.5774 (mmt) cc_final: 0.5057 (mmt)
REVERT: A  520 ASN cc_start: 0.7295 (m110) cc_final: 0.6910 (m110)
REVERT: A  532 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7547 (p)
REVERT: A  611 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7635 (pmm-80)
REVERT: A  618 GLU cc_start: 0.7857 (tt0) cc_final: 0.7024 (mm-30)
REVERT: A  624 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7459 (mt-10)
REVERT: A  700 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7304 (ttp80)
REVERT: A  707 ARG cc_start: 0.7282 (mtm110) cc_final: 0.7055 (ptm-80)
REVERT: A  827 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6796 (mp0)
REVERT: A  895 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.5850 (ptp90)
  outliers start: 18
  outliers final: 7
  residues processed: 76
  average time/residue: 1.3534
  time to fit residues: 107.6660
Evaluate side-chains
  68 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.170278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.123848 restraints weight = 6768.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.63
r_work: 0.3083 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6285  Z= 0.130
  Angle     :  0.514   7.391   8553  Z= 0.265
  Chirality :  0.044   0.159    977
  Planarity :  0.004   0.052   1051
  Dihedral  :  8.872  78.558    918
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.48 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.61 (0.31), residues: 733
  helix:  1.97 (0.35), residues: 242
  sheet:  0.65 (0.36), residues: 189
  loop : -1.08 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.019   0.001   PHE A 320 
 TYR   0.012   0.001   TYR A 239 
 ARG   0.007   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  284)
  hydrogen bonds       : angle       4.93675 (  801)
  covalent geometry    : bond        0.00322 ( 6285)
  covalent geometry    : angle       0.51386 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8066 (tttt) cc_final: 0.7108 (tptp)
REVERT: A  258 MET cc_start: 0.6555 (mmp) cc_final: 0.6290 (mtm)
REVERT: A  309 ILE cc_start: 0.7430 (mt) cc_final: 0.7177 (mt)
REVERT: A  348 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6785 (ppp)
REVERT: A  423 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.6862 (ttm110)
REVERT: A  505 MET cc_start: 0.5622 (mmt) cc_final: 0.5101 (mmt)
REVERT: A  520 ASN cc_start: 0.7607 (m110) cc_final: 0.7200 (m110)
REVERT: A  532 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7659 (p)
REVERT: A  546 GLU cc_start: 0.7685 (tp30) cc_final: 0.7347 (tm-30)
REVERT: A  593 ASP cc_start: 0.7540 (m-30) cc_final: 0.6921 (t70)
REVERT: A  611 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7535 (pmm-80)
REVERT: A  618 GLU cc_start: 0.7948 (tt0) cc_final: 0.7039 (mm-30)
REVERT: A  624 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7506 (mt-10)
REVERT: A  645 ASP cc_start: 0.8124 (p0) cc_final: 0.7730 (p0)
REVERT: A  700 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7306 (ttp80)
REVERT: A  763 ASN cc_start: 0.8562 (t0) cc_final: 0.8195 (t0)
REVERT: A  827 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6685 (mp0)
REVERT: A  895 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.5952 (ptp90)
  outliers start: 16
  outliers final: 8
  residues processed: 79
  average time/residue: 1.4499
  time to fit residues: 119.9681
Evaluate side-chains
  74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 285 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.170286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.122288 restraints weight = 6712.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.65
r_work: 0.3098 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6285  Z= 0.124
  Angle     :  0.509   7.693   8553  Z= 0.262
  Chirality :  0.043   0.150    977
  Planarity :  0.004   0.053   1051
  Dihedral  :  8.839  77.713    918
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.93 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.65 (0.31), residues: 733
  helix:  2.08 (0.35), residues: 241
  sheet:  0.61 (0.36), residues: 189
  loop : -1.07 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.023   0.002   PHE A 272 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.007   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  284)
  hydrogen bonds       : angle       4.86919 (  801)
  covalent geometry    : bond        0.00304 ( 6285)
  covalent geometry    : angle       0.50940 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8049 (tttt) cc_final: 0.7082 (tptp)
REVERT: A  258 MET cc_start: 0.6548 (mmp) cc_final: 0.5982 (mmp)
REVERT: A  309 ILE cc_start: 0.7400 (mt) cc_final: 0.7164 (mt)
REVERT: A  348 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6648 (ppp)
REVERT: A  423 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.6705 (ttm110)
REVERT: A  505 MET cc_start: 0.5597 (mmt) cc_final: 0.5327 (mmt)
REVERT: A  508 ASP cc_start: 0.7005 (m-30) cc_final: 0.6205 (t0)
REVERT: A  520 ASN cc_start: 0.7523 (m110) cc_final: 0.7124 (m110)
REVERT: A  532 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7647 (p)
REVERT: A  546 GLU cc_start: 0.7675 (tp30) cc_final: 0.7324 (tm-30)
REVERT: A  610 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7759 (mptt)
REVERT: A  611 ARG cc_start: 0.7847 (mtt90) cc_final: 0.7512 (pmm-80)
REVERT: A  618 GLU cc_start: 0.7921 (tt0) cc_final: 0.7006 (mm-30)
REVERT: A  624 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7482 (mt-10)
REVERT: A  645 ASP cc_start: 0.8108 (p0) cc_final: 0.7790 (p0)
REVERT: A  700 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7281 (ttp80)
REVERT: A  763 ASN cc_start: 0.8543 (t0) cc_final: 0.8152 (t0)
REVERT: A  820 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7708 (tp)
REVERT: A  827 GLU cc_start: 0.7643 (mt-10) cc_final: 0.6693 (mp0)
REVERT: A  895 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5974 (ptp90)
  outliers start: 17
  outliers final: 9
  residues processed: 82
  average time/residue: 1.3010
  time to fit residues: 111.7311
Evaluate side-chains
  80 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.170158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.123475 restraints weight = 6821.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.58
r_work: 0.3094 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6285  Z= 0.141
  Angle     :  0.515   7.878   8553  Z= 0.265
  Chirality :  0.044   0.156    977
  Planarity :  0.005   0.053   1051
  Dihedral  :  8.822  76.999    918
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.93 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.64 (0.31), residues: 733
  helix:  2.09 (0.34), residues: 241
  sheet:  0.60 (0.36), residues: 189
  loop : -1.09 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.020   0.001   PHE A 320 
 TYR   0.012   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  284)
  hydrogen bonds       : angle       4.90584 (  801)
  covalent geometry    : bond        0.00350 ( 6285)
  covalent geometry    : angle       0.51487 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8111 (tttt) cc_final: 0.7143 (tptp)
REVERT: A  258 MET cc_start: 0.6649 (mmp) cc_final: 0.6094 (mmp)
REVERT: A  309 ILE cc_start: 0.7452 (mt) cc_final: 0.7194 (mt)
REVERT: A  348 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6739 (ppp)
REVERT: A  423 ARG cc_start: 0.7425 (mtp-110) cc_final: 0.6629 (ttm110)
REVERT: A  505 MET cc_start: 0.5680 (mmt) cc_final: 0.5387 (mmt)
REVERT: A  508 ASP cc_start: 0.7098 (m-30) cc_final: 0.6286 (t0)
REVERT: A  520 ASN cc_start: 0.7331 (m110) cc_final: 0.6965 (m110)
REVERT: A  532 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7697 (p)
REVERT: A  546 GLU cc_start: 0.7749 (tp30) cc_final: 0.7381 (tm-30)
REVERT: A  610 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7812 (mptt)
REVERT: A  611 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7429 (pmm-80)
REVERT: A  618 GLU cc_start: 0.7965 (tt0) cc_final: 0.7078 (mm-30)
REVERT: A  624 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7540 (mt-10)
REVERT: A  645 ASP cc_start: 0.8174 (p0) cc_final: 0.7867 (p0)
REVERT: A  700 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7343 (ttp80)
REVERT: A  763 ASN cc_start: 0.8527 (t0) cc_final: 0.8152 (t0)
REVERT: A  791 VAL cc_start: 0.7350 (t) cc_final: 0.7040 (t)
REVERT: A  820 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: A  827 GLU cc_start: 0.7667 (mt-10) cc_final: 0.6756 (mp0)
REVERT: A  895 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.5970 (ptp90)
  outliers start: 16
  outliers final: 8
  residues processed: 75
  average time/residue: 1.3131
  time to fit residues: 103.2311
Evaluate side-chains
  77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0470
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7678

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.171479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.115657 restraints weight = 6889.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.33
r_work: 0.3129 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6285  Z= 0.110
  Angle     :  0.495   7.974   8553  Z= 0.254
  Chirality :  0.043   0.146    977
  Planarity :  0.004   0.054   1051
  Dihedral  :  8.774  76.021    918
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.23 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.76 (0.31), residues: 733
  helix:  2.23 (0.35), residues: 242
  sheet:  0.63 (0.36), residues: 189
  loop : -1.05 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.021   0.002   PHE A 950 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (  284)
  hydrogen bonds       : angle       4.78749 (  801)
  covalent geometry    : bond        0.00268 ( 6285)
  covalent geometry    : angle       0.49535 ( 8553)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8070 (tttt) cc_final: 0.7096 (tptp)
REVERT: A  258 MET cc_start: 0.6577 (mmp) cc_final: 0.6045 (mmp)
REVERT: A  309 ILE cc_start: 0.7328 (mt) cc_final: 0.7086 (mt)
REVERT: A  329 MET cc_start: 0.8159 (mmm) cc_final: 0.7916 (mmt)
REVERT: A  348 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6722 (ppp)
REVERT: A  423 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6489 (ttm110)
REVERT: A  505 MET cc_start: 0.5644 (mmt) cc_final: 0.5364 (mmt)
REVERT: A  508 ASP cc_start: 0.7056 (m-30) cc_final: 0.6245 (t0)
REVERT: A  520 ASN cc_start: 0.7249 (m110) cc_final: 0.6975 (m110)
REVERT: A  532 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7644 (p)
REVERT: A  546 GLU cc_start: 0.7679 (tp30) cc_final: 0.7337 (tm-30)
REVERT: A  610 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7836 (mptt)
REVERT: A  611 ARG cc_start: 0.7841 (mtt90) cc_final: 0.7357 (ptp90)
REVERT: A  618 GLU cc_start: 0.7925 (tt0) cc_final: 0.7027 (mm-30)
REVERT: A  624 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7454 (mt-10)
REVERT: A  645 ASP cc_start: 0.8236 (p0) cc_final: 0.7858 (p0)
REVERT: A  700 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7328 (ttp80)
REVERT: A  763 ASN cc_start: 0.8452 (t0) cc_final: 0.8063 (t0)
REVERT: A  820 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7766 (tp)
REVERT: A  827 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6698 (mp0)
  outliers start: 14
  outliers final: 8
  residues processed: 75
  average time/residue: 1.3776
  time to fit residues: 108.1415
Evaluate side-chains
  74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.171175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.115300 restraints weight = 6849.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.32
r_work: 0.3123 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6285  Z= 0.118
  Angle     :  0.501   7.971   8553  Z= 0.256
  Chirality :  0.043   0.149    977
  Planarity :  0.004   0.053   1051
  Dihedral  :  8.761  75.442    918
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.67 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.78 (0.31), residues: 733
  helix:  2.26 (0.35), residues: 242
  sheet:  0.63 (0.36), residues: 189
  loop : -1.04 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 
 PHE   0.019   0.001   PHE A 320 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 423 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  284)
  hydrogen bonds       : angle       4.78644 (  801)
  covalent geometry    : bond        0.00291 ( 6285)
  covalent geometry    : angle       0.50071 ( 8553)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4795.77 seconds
wall clock time: 83 minutes 11.07 seconds (4991.07 seconds total)