Starting phenix.real_space_refine
on Wed Sep 17 07:25:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dun_47171/09_2025/9dun_47171.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dun_47171/09_2025/9dun_47171.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dun_47171/09_2025/9dun_47171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dun_47171/09_2025/9dun_47171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dun_47171/09_2025/9dun_47171.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dun_47171/09_2025/9dun_47171.cif"
  }
  resolution = 3.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.065
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4309      2.51       5
     N    1133      2.21       5
     O    1180      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6672
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2041
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 22, 'TRANS': 238}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 2021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2021
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 22, 'TRANS': 235}
          Chain breaks: 7
    Chain: "C"
      Number of atoms: 1028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1028
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1032
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1032
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 258
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 292
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
          Chain breaks: 1
  Time building chain proxies: 2.01, per 1000 atoms: 0.30
  Number of scatterers: 6672
  At special positions: 0
  Unit cell: (83.391, 131.043, 69.312, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1180      8.00
     N    1133      7.00
     C    4309      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 446.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 6 sheets defined
      38.0% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 312 through 327
      removed outlier: 3.782A  pdb=" N   ASN A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ARG A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 5.230A  pdb=" N   TYR A 318 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASN A 325 " --> pdb=" O   ASN A 321 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER A 326 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 364
      removed outlier: 3.669A  pdb=" N   HIS A 364 " --> pdb=" O   PRO A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 395
      removed outlier: 3.713A  pdb=" N   LYS A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TYR A 392 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 424
    Processing helix  chain 'A' and resid 517 through 528
      removed outlier: 3.749A  pdb=" N   ASP A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A 523 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE A 524 " --> pdb=" O   ARG A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 532
      removed outlier: 3.589A  pdb=" N   GLN A 532 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 529 through 532'
    Processing helix  chain 'A' and resid 566 through 570
      removed outlier: 3.644A  pdb=" N   ILE A 569 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LEU A 570 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 566 through 570'
    Processing helix  chain 'A' and resid 628 through 633
      removed outlier: 4.205A  pdb=" N   ARG A 633 " --> pdb=" O   PRO A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 651
      removed outlier: 3.509A  pdb=" N   LEU A 650 " --> pdb=" O   PRO A 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 327
      removed outlier: 3.876A  pdb=" N   ASN B 325 " --> pdb=" O   ASN B 321 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   SER B 326 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 395
      removed outlier: 3.867A  pdb=" N   LYS B 391 " --> pdb=" O   ILE B 387 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR B 392 " --> pdb=" O   ASP B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
    Processing helix  chain 'B' and resid 519 through 529
      removed outlier: 3.531A  pdb=" N   SER B 523 " --> pdb=" O   LEU B 519 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ILE B 524 " --> pdb=" O   ARG B 520 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU B 525 " --> pdb=" O   ASP B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 532
      No H-bonds generated for 'chain 'B' and resid 530 through 532'
    Processing helix  chain 'B' and resid 566 through 568
      No H-bonds generated for 'chain 'B' and resid 566 through 568'
    Processing helix  chain 'B' and resid 569 through 574
      removed outlier: 3.578A  pdb=" N   VAL B 573 " --> pdb=" O   ILE B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 633
      removed outlier: 4.324A  pdb=" N   ARG B 633 " --> pdb=" O   PRO B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 646 through 651
      removed outlier: 3.574A  pdb=" N   LEU B 650 " --> pdb=" O   PRO B 646 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 60
      removed outlier: 4.288A  pdb=" N   PHE C  59 " --> pdb=" O   THR C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 69
    Processing helix  chain 'C' and resid 74 through 79
      removed outlier: 4.037A  pdb=" N   SER C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 104
      removed outlier: 3.730A  pdb=" N   LYS C  98 " --> pdb=" O   LEU C  94 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU C 100 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR C 103 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 126
    Processing helix  chain 'C' and resid 153 through 160
      removed outlier: 3.766A  pdb=" N   GLU C 157 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 184
      removed outlier: 3.598A  pdb=" N   CYS C 169 " --> pdb=" O   HIS C 165 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   TYR C 174 " --> pdb=" O   ARG C 170 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASP C 178 " --> pdb=" O   TYR C 174 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN C 181 " --> pdb=" O   LEU C 177 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS C 182 " --> pdb=" O   ASP C 178 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR C 183 " --> pdb=" O   TRP C 179 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR C 184 " --> pdb=" O   LEU C 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 58
      removed outlier: 3.637A  pdb=" N   VAL D  54 " --> pdb=" O   GLU D  50 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   THR D  55 " --> pdb=" O   TRP D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 69
    Processing helix  chain 'D' and resid 74 through 79
      removed outlier: 3.983A  pdb=" N   SER D  78 " --> pdb=" O   THR D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 102
      removed outlier: 3.554A  pdb=" N   LYS D  98 " --> pdb=" O   LEU D  94 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU D 100 " --> pdb=" O   ARG D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 126
      removed outlier: 3.591A  pdb=" N   LEU D 113 " --> pdb=" O   ASP D 109 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR D 115 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 161
      removed outlier: 3.805A  pdb=" N   LEU D 154 " --> pdb=" O   TRP D 150 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG D 155 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   HIS D 156 " --> pdb=" O   VAL D 152 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS D 161 " --> pdb=" O   GLU D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 184
      removed outlier: 3.871A  pdb=" N   ASP D 178 " --> pdb=" O   TYR D 174 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TRP D 179 " --> pdb=" O   PHE D 175 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU D 180 " --> pdb=" O   VAL D 176 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN D 181 " --> pdb=" O   LEU D 177 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS D 182 " --> pdb=" O   ASP D 178 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR D 184 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 303
      removed outlier: 3.536A  pdb=" N   VAL A 330 " --> pdb=" O   ILE A 353 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A 349 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A 370 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 556 through 559
      removed outlier: 6.311A  pdb=" N   ALA A 556 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   VAL A 640 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ARG A 558 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   CYS A 637 " --> pdb=" O   CYS A 581 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A 639 " --> pdb=" O   GLY A 579 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER A 576 " --> pdb=" O   CYS A 611 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   CYS A 611 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 301 through 303
      removed outlier: 3.524A  pdb=" N   VAL B 330 " --> pdb=" O   ILE B 353 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 350
      removed outlier: 3.696A  pdb=" N   LYS B 370 " --> pdb=" O   LEU B 350 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 559
      removed outlier: 6.294A  pdb=" N   ALA B 556 " --> pdb=" O   LEU B 638 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   VAL B 640 " --> pdb=" O   ALA B 556 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ARG B 558 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 577 through 578

    168 hydrogen bonds defined for protein.
    495 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2103
        1.34 -     1.46: 1359
        1.46 -     1.58: 3298
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 6826
  Sorted by residual:
  bond pdb=" CA  ILE A 559 "
       pdb=" CB  ILE A 559 "
    ideal  model  delta    sigma   weight residual
    1.528  1.540 -0.012 1.34e-02 5.57e+03 7.85e-01
  bond pdb=" N   PRO A 628 "
       pdb=" CA  PRO A 628 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.31e-02 5.83e+03 7.14e-01
  bond pdb=" CA  ASN B 592 "
       pdb=" CB  ASN B 592 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.66e-01
  bond pdb=" CB  PRO F 651 "
       pdb=" CG  PRO F 651 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 5.98e-01
  bond pdb=" CA  HIS C  63 "
       pdb=" C   HIS C  63 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.34e-02 5.57e+03 5.48e-01
  ... (remaining 6821 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 8817
        1.18 -     2.37: 354
        2.37 -     3.55: 92
        3.55 -     4.73: 18
        4.73 -     5.91: 4
  Bond angle restraints: 9285
  Sorted by residual:
  angle pdb=" N   ILE C  95 "
        pdb=" CA  ILE C  95 "
        pdb=" C   ILE C  95 "
      ideal   model   delta    sigma   weight residual
     112.96  109.14    3.82 1.00e+00 1.00e+00 1.46e+01
  angle pdb=" N   LEU B 596 "
        pdb=" CA  LEU B 596 "
        pdb=" C   LEU B 596 "
      ideal   model   delta    sigma   weight residual
     110.24  114.25   -4.01 1.30e+00 5.92e-01 9.51e+00
  angle pdb=" N   ILE A 518 "
        pdb=" CA  ILE A 518 "
        pdb=" C   ILE A 518 "
      ideal   model   delta    sigma   weight residual
     111.58  108.32    3.26 1.06e+00 8.90e-01 9.48e+00
  angle pdb=" C   ASP D  61 "
        pdb=" N   ASP D  62 "
        pdb=" CA  ASP D  62 "
      ideal   model   delta    sigma   weight residual
     121.54  126.67   -5.13 1.91e+00 2.74e-01 7.22e+00
  angle pdb=" C   ILE B 595 "
        pdb=" N   LEU B 596 "
        pdb=" CA  LEU B 596 "
      ideal   model   delta    sigma   weight residual
     120.82  124.33   -3.51 1.47e+00 4.63e-01 5.69e+00
  ... (remaining 9280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 3394
       17.16 -    34.33: 434
       34.33 -    51.49: 188
       51.49 -    68.65: 36
       68.65 -    85.82: 11
  Dihedral angle restraints: 4063
    sinusoidal: 1630
      harmonic: 2433
  Sorted by residual:
  dihedral pdb=" CA  CYS C  60 "
           pdb=" C   CYS C  60 "
           pdb=" N   ASP C  61 "
           pdb=" CA  ASP C  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  THR B 625 "
           pdb=" C   THR B 625 "
           pdb=" N   PRO B 626 "
           pdb=" CA  PRO B 626 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.10   17.90     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  CYS D  60 "
           pdb=" C   CYS D  60 "
           pdb=" N   ASP D  61 "
           pdb=" CA  ASP D  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.18  -17.82     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 4060 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 588
       0.028 -    0.056: 333
       0.056 -    0.085: 93
       0.085 -    0.113: 52
       0.113 -    0.141: 14
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  ILE B 643 "
            pdb=" N   ILE B 643 "
            pdb=" C   ILE B 643 "
            pdb=" CB  ILE B 643 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  VAL B 627 "
            pdb=" N   VAL B 627 "
            pdb=" C   VAL B 627 "
            pdb=" CB  VAL B 627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CB  ILE A 595 "
            pdb=" CA  ILE A 595 "
            pdb=" CG1 ILE A 595 "
            pdb=" CG2 ILE A 595 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 1149
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F 661 "   -0.041 5.00e-02 4.00e+02   6.32e-02 6.38e+00
        pdb=" N   PRO F 662 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO F 662 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F 662 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 625 "    0.031 5.00e-02 4.00e+02   4.64e-02 3.44e+00
        pdb=" N   PRO A 626 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 626 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 626 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 627 "    0.024 5.00e-02 4.00e+02   3.69e-02 2.17e+00
        pdb=" N   PRO A 628 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 628 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 628 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1146 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1345
        2.78 -     3.31: 5854
        3.31 -     3.84: 10407
        3.84 -     4.37: 11885
        4.37 -     4.90: 21207
  Nonbonded interactions: 50698
  Sorted by model distance:
  nonbonded pdb=" O   SER A 427 "
            pdb=" OG  SER A 427 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG  SER F 636 "
            pdb=" N   ALA F 637 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OH  TYR B 571 "
            pdb=" O   ALA D  44 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" NZ  LYS B 312 "
            pdb=" O   THR B 407 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" NH1 ARG C 121 "
            pdb=" O   LEU D 158 "
     model   vdw
     2.271 3.120
  ... (remaining 50693 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 299 through 408 or resid 420 through 435 or resid 494 thro \ 
ugh 654))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and resid 41 through 185)
}
ncs_group {
  reference = (chain 'E' and resid 636 through 674)
  selection = (chain 'F' and (resid 636 through 644 or resid 647 through 655 or resid 663 thro \ 
ugh 674))
}

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:             1.830
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.920
  Find NCS groups from input model:        0.140
  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:1.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
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      :  0.003   0.039   6826  Z= 0.126
  Angle     :  0.593   5.914   9285  Z= 0.316
  Chirality :  0.041   0.141   1080
  Planarity :  0.005   0.063   1149
  Dihedral  : 18.866  85.818   2479
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 31.61 %
    Favored  : 63.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.29), residues: 784
  helix: -1.47 (0.30), residues: 265
  sheet: -0.87 (0.55), residues: 89
  loop : -2.18 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 171 
 TYR   0.011   0.001   TYR B 383 
 PHE   0.013   0.002   PHE B 394 
 TRP   0.008   0.001   TRP F 647 
 HIS   0.006   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6826)
  covalent geometry    : angle       0.59271 ( 9285)
  hydrogen bonds       : bond        0.21650 (  168)
  hydrogen bonds       : angle       8.40560 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  316 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5928 (m-40)
REVERT: A  339 GLN cc_start: 0.8087 (mp10) cc_final: 0.7561 (mt0)
REVERT: A  369 GLN cc_start: 0.7330 (tt0) cc_final: 0.6955 (mt0)
REVERT: A  391 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6852 (mmmt)
REVERT: A  419 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3176 (pt)
REVERT: A  517 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7400 (tmtt)
REVERT: A  610 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6870 (mm)
REVERT: B  339 GLN cc_start: 0.8138 (mp10) cc_final: 0.7610 (mt0)
REVERT: B  369 GLN cc_start: 0.7160 (tt0) cc_final: 0.6885 (mt0)
REVERT: B  383 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6707 (m-80)
REVERT: B  391 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6875 (mmmt)
REVERT: B  520 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6765 (mtp-110)
REVERT: C  162 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7629 (mtpt)
REVERT: D   48 ARG cc_start: 0.7096 (mmt90) cc_final: 0.6561 (mmt180)
REVERT: D   83 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7876 (mt-10)
REVERT: D  162 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7795 (mtpt)
REVERT: D  179 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.4677 (t60)
REVERT: E  666 MET cc_start: 0.7337 (mmm) cc_final: 0.6891 (mmm)
  outliers start: 35
  outliers final: 25
  residues processed: 135
  average time/residue: 0.0814
  time to fit residues: 15.1035
Evaluate side-chains
  134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  326 SER
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  391 LYS
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  652 LEU
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.0050
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0040
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 382 ASN
B 316 ASN
B 385 ASN
B 549 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.221859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.193747 restraints weight = 6728.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 1.80
r_work: 0.3962 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
moved from start:          0.0725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6826  Z= 0.103
  Angle     :  0.559   6.089   9285  Z= 0.287
  Chirality :  0.041   0.154   1080
  Planarity :  0.005   0.051   1149
  Dihedral  :  8.734  57.423    964
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 30.82 %
    Favored  : 63.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.30), residues: 784
  helix: -1.02 (0.30), residues: 293
  sheet: -0.65 (0.52), residues: 93
  loop : -2.38 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 612 
 TYR   0.013   0.001   TYR B 383 
 PHE   0.013   0.001   PHE A 362 
 TRP   0.010   0.001   TRP D 179 
 HIS   0.006   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6826)
  covalent geometry    : angle       0.55877 ( 9285)
  hydrogen bonds       : bond        0.03581 (  168)
  hydrogen bonds       : angle       5.71234 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  339 GLN cc_start: 0.7940 (mp10) cc_final: 0.7333 (mt0)
REVERT: A  369 GLN cc_start: 0.7335 (tt0) cc_final: 0.6924 (mt0)
REVERT: A  383 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6684 (m-80)
REVERT: A  391 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6382 (mmmt)
REVERT: A  517 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7248 (tmtt)
REVERT: B  339 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7382 (mt0)
REVERT: B  369 GLN cc_start: 0.7204 (tt0) cc_final: 0.6921 (mt0)
REVERT: B  520 ARG cc_start: 0.7063 (mtm110) cc_final: 0.6611 (mtp-110)
REVERT: B  592 ASN cc_start: 0.5615 (t0) cc_final: 0.5409 (t0)
REVERT: C   50 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7151 (mt-10)
REVERT: C  162 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7441 (mtpt)
REVERT: D   83 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7697 (mt-10)
REVERT: D  162 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7425 (mtpt)
REVERT: D  179 TRP cc_start: 0.5852 (OUTLIER) cc_final: 0.4769 (t60)
REVERT: E  666 MET cc_start: 0.7362 (mmm) cc_final: 0.6903 (mmm)
  outliers start: 43
  outliers final: 22
  residues processed: 141
  average time/residue: 0.0758
  time to fit residues: 14.5988
Evaluate side-chains
  126 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  652 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 385 ASN
A 636 ASN
B 385 ASN
B 433 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.215590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.187325 restraints weight = 6724.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 1.82
r_work: 0.3903 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6826  Z= 0.153
  Angle     :  0.609   6.564   9285  Z= 0.308
  Chirality :  0.043   0.166   1080
  Planarity :  0.005   0.059   1149
  Dihedral  :  8.495  59.660    939
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 30.82 %
    Favored  : 63.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.29), residues: 784
  helix: -1.01 (0.30), residues: 288
  sheet: -0.48 (0.54), residues: 87
  loop : -2.50 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 612 
 TYR   0.014   0.002   TYR A 332 
 PHE   0.014   0.002   PHE A 362 
 TRP   0.009   0.001   TRP A 577 
 HIS   0.007   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6826)
  covalent geometry    : angle       0.60912 ( 9285)
  hydrogen bonds       : bond        0.03962 (  168)
  hydrogen bonds       : angle       5.27860 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 104
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  339 GLN cc_start: 0.7971 (mp10) cc_final: 0.7389 (mt0)
REVERT: A  369 GLN cc_start: 0.7385 (tt0) cc_final: 0.6955 (mt0)
REVERT: A  383 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6779 (m-80)
REVERT: A  391 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6210 (mmtt)
REVERT: A  517 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7405 (tmtt)
REVERT: A  519 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7231 (mp)
REVERT: B  339 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7387 (mt0)
REVERT: B  369 GLN cc_start: 0.7257 (tt0) cc_final: 0.6978 (mt0)
REVERT: B  520 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6715 (mtp-110)
REVERT: C   50 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: C  162 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7573 (mtpt)
REVERT: D  162 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7453 (mtpt)
REVERT: D  170 ARG cc_start: 0.6843 (mtt180) cc_final: 0.6625 (mtt180)
REVERT: D  179 TRP cc_start: 0.5870 (OUTLIER) cc_final: 0.4758 (t60)
  outliers start: 42
  outliers final: 25
  residues processed: 140
  average time/residue: 0.0818
  time to fit residues: 15.5344
Evaluate side-chains
  129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  549 GLN
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  652 LEU
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 69 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0770
   chunk 77 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 382 ASN
A 385 ASN
B 385 ASN
D  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.218887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.190232 restraints weight = 6774.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 1.84
r_work: 0.3923 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6826  Z= 0.111
  Angle     :  0.553   6.407   9285  Z= 0.283
  Chirality :  0.042   0.154   1080
  Planarity :  0.005   0.059   1149
  Dihedral  :  8.235  58.288    937
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.84 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 31.08 %
    Favored  : 63.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.29), residues: 784
  helix: -0.82 (0.30), residues: 289
  sheet: -0.24 (0.56), residues: 87
  loop : -2.50 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 612 
 TYR   0.012   0.001   TYR B 383 
 PHE   0.015   0.002   PHE D  59 
 TRP   0.008   0.001   TRP A 577 
 HIS   0.005   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6826)
  covalent geometry    : angle       0.55322 ( 9285)
  hydrogen bonds       : bond        0.03227 (  168)
  hydrogen bonds       : angle       4.99076 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 101
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  339 GLN cc_start: 0.7864 (mp10) cc_final: 0.7284 (mt0)
REVERT: A  369 GLN cc_start: 0.7250 (tt0) cc_final: 0.6847 (mt0)
REVERT: A  383 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6702 (m-80)
REVERT: A  391 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6134 (mmtt)
REVERT: A  517 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7344 (tmtt)
REVERT: A  519 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7159 (mp)
REVERT: B  339 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7308 (mt0)
REVERT: B  369 GLN cc_start: 0.7102 (tt0) cc_final: 0.6843 (mt0)
REVERT: B  520 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6644 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7003 (ttt90)
REVERT: C   50 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7198 (mt-10)
REVERT: C  162 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7484 (mtpt)
REVERT: C  184 TYR cc_start: 0.5706 (t80) cc_final: 0.5431 (t80)
REVERT: D   83 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7553 (mt-10)
REVERT: D  162 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7456 (mtpt)
REVERT: D  170 ARG cc_start: 0.6910 (mtt180) cc_final: 0.6705 (mtt180)
REVERT: D  179 TRP cc_start: 0.5940 (OUTLIER) cc_final: 0.4837 (t60)
  outliers start: 43
  outliers final: 29
  residues processed: 137
  average time/residue: 0.0879
  time to fit residues: 16.2050
Evaluate side-chains
  134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   66 GLN
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  664 GLU
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0770
   chunk 47 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0040
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5152

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

Flipped N/Q/H residues before XYZ refinement:
A 385 ASN
B 385 ASN
D  66 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.219143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.190426 restraints weight = 6814.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 1.85
r_work: 0.3941 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6483
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6826  Z= 0.108
  Angle     :  0.541   5.579   9285  Z= 0.276
  Chirality :  0.041   0.151   1080
  Planarity :  0.005   0.061   1149
  Dihedral  :  8.203  59.369    937
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.97 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 30.29 %
    Favored  : 63.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.30), residues: 784
  helix: -0.66 (0.30), residues: 290
  sheet: -0.16 (0.57), residues: 87
  loop : -2.44 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  67 
 TYR   0.012   0.001   TYR A 332 
 PHE   0.013   0.001   PHE A 362 
 TRP   0.008   0.001   TRP A 577 
 HIS   0.005   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6826)
  covalent geometry    : angle       0.54062 ( 9285)
  hydrogen bonds       : bond        0.03129 (  168)
  hydrogen bonds       : angle       4.81542 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 101
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  339 GLN cc_start: 0.7893 (mp10) cc_final: 0.7296 (mt0)
REVERT: A  369 GLN cc_start: 0.7192 (tt0) cc_final: 0.6852 (mt0)
REVERT: A  383 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6756 (m-80)
REVERT: A  391 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6140 (mmtt)
REVERT: A  517 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7295 (tmtt)
REVERT: A  519 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7126 (mp)
REVERT: B  339 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7306 (mt0)
REVERT: B  369 GLN cc_start: 0.7099 (tt0) cc_final: 0.6846 (mt0)
REVERT: B  520 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6651 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7016 (ttt90)
REVERT: B  653 GLN cc_start: 0.4500 (OUTLIER) cc_final: 0.4216 (mt0)
REVERT: C   50 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: C  162 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7487 (mtpt)
REVERT: C  184 TYR cc_start: 0.5715 (t80) cc_final: 0.5422 (t80)
REVERT: D  162 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7449 (mtpt)
REVERT: D  170 ARG cc_start: 0.6890 (mtt180) cc_final: 0.6686 (mtt180)
REVERT: D  179 TRP cc_start: 0.5926 (OUTLIER) cc_final: 0.4793 (t60)
  outliers start: 49
  outliers final: 31
  residues processed: 143
  average time/residue: 0.0813
  time to fit residues: 15.7992
Evaluate side-chains
  139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 99
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  653 GLN
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   66 GLN
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  652 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
A 382 ASN
A 385 ASN
B 325 ASN
B 385 ASN
D  66 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.214333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.187912 restraints weight = 6985.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 1.76
r_work: 0.3886 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6826  Z= 0.178
  Angle     :  0.629   6.408   9285  Z= 0.318
  Chirality :  0.044   0.170   1080
  Planarity :  0.006   0.065   1149
  Dihedral  :  8.628  59.768    935
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.73 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 29.76 %
    Favored  : 63.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.29), residues: 784
  helix: -0.92 (0.29), residues: 290
  sheet: -0.42 (0.56), residues: 86
  loop : -2.63 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 612 
 TYR   0.017   0.002   TYR A 332 
 PHE   0.015   0.002   PHE A 362 
 TRP   0.010   0.002   TRP A 577 
 HIS   0.008   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 6826)
  covalent geometry    : angle       0.62853 ( 9285)
  hydrogen bonds       : bond        0.03861 (  168)
  hydrogen bonds       : angle       4.91099 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 105
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.8106 (mp10) cc_final: 0.7475 (mt0)
REVERT: A  369 GLN cc_start: 0.7453 (tt0) cc_final: 0.7006 (mt0)
REVERT: A  371 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.6088 (tpp)
REVERT: A  383 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6822 (m-80)
REVERT: A  391 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6302 (mmtt)
REVERT: A  517 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7457 (tmtt)
REVERT: A  519 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7269 (mp)
REVERT: B  339 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7449 (mt0)
REVERT: B  369 GLN cc_start: 0.7326 (tt0) cc_final: 0.7016 (mt0)
REVERT: B  371 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.6469 (tpp)
REVERT: B  520 ARG cc_start: 0.7278 (mtm110) cc_final: 0.6862 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7209 (ttt90)
REVERT: B  653 GLN cc_start: 0.4793 (OUTLIER) cc_final: 0.4476 (mt0)
REVERT: C  162 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7631 (mtpt)
REVERT: D  162 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7458 (mtpt)
REVERT: D  179 TRP cc_start: 0.6065 (OUTLIER) cc_final: 0.4873 (t60)
REVERT: E  666 MET cc_start: 0.7468 (mmm) cc_final: 0.6924 (tpp)
REVERT: E  671 ASP cc_start: 0.6957 (t0) cc_final: 0.6731 (t0)
REVERT: F  671 ASP cc_start: 0.6805 (t0) cc_final: 0.6600 (t0)
  outliers start: 50
  outliers final: 30
  residues processed: 146
  average time/residue: 0.0837
  time to fit residues: 16.5316
Evaluate side-chains
  143 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 102
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  371 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  653 GLN
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   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 385 ASN
B 325 ASN
B 385 ASN
D  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.216247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.190669 restraints weight = 6842.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 1.69
r_work: 0.3922 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3782 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6826  Z= 0.134
  Angle     :  0.582   5.989   9285  Z= 0.297
  Chirality :  0.043   0.156   1080
  Planarity :  0.006   0.070   1149
  Dihedral  :  8.454  58.246    935
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.10 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 30.29 %
    Favored  : 63.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.29), residues: 784
  helix: -0.78 (0.30), residues: 290
  sheet: -0.35 (0.57), residues: 86
  loop : -2.61 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 612 
 TYR   0.014   0.001   TYR A 332 
 PHE   0.017   0.002   PHE B 434 
 TRP   0.009   0.001   TRP D 179 
 HIS   0.006   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6826)
  covalent geometry    : angle       0.58238 ( 9285)
  hydrogen bonds       : bond        0.03427 (  168)
  hydrogen bonds       : angle       4.82144 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 105
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.8082 (mp10) cc_final: 0.7466 (mt0)
REVERT: A  369 GLN cc_start: 0.7415 (tt0) cc_final: 0.7037 (mt0)
REVERT: A  383 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6802 (m-80)
REVERT: A  391 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6270 (mmtt)
REVERT: A  517 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7409 (tmtt)
REVERT: A  519 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7245 (mp)
REVERT: B  339 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7402 (mt0)
REVERT: B  369 GLN cc_start: 0.7279 (tt0) cc_final: 0.6956 (mt0)
REVERT: B  371 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.6243 (tpp)
REVERT: B  520 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6795 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7175 (ttt90)
REVERT: C  162 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7612 (mtpt)
REVERT: D  162 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7441 (mtpt)
REVERT: D  179 TRP cc_start: 0.6051 (OUTLIER) cc_final: 0.4836 (t60)
REVERT: E  666 MET cc_start: 0.7463 (mmm) cc_final: 0.6979 (tpp)
REVERT: F  671 ASP cc_start: 0.6690 (t0) cc_final: 0.6467 (t0)
REVERT: F  673 MET cc_start: 0.6996 (mtt) cc_final: 0.6519 (mtt)
  outliers start: 46
  outliers final: 30
  residues processed: 142
  average time/residue: 0.0764
  time to fit residues: 14.8953
Evaluate side-chains
  138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  371 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   66 GLN
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  652 LEU
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0670
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 36 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0980
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.3318

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

Flipped N/Q/H residues before XYZ refinement:
A 382 ASN
A 385 ASN
B 385 ASN
D  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.219081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.190946 restraints weight = 6867.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 1.89
r_work: 0.3930 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6826  Z= 0.101
  Angle     :  0.552   7.178   9285  Z= 0.283
  Chirality :  0.041   0.152   1080
  Planarity :  0.005   0.065   1149
  Dihedral  :  8.174  57.766    935
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.33 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 31.22 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.30), residues: 784
  helix: -0.48 (0.31), residues: 290
  sheet: -0.34 (0.57), residues: 87
  loop : -2.47 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 612 
 TYR   0.011   0.001   TYR B 383 
 PHE   0.015   0.001   PHE B 434 
 TRP   0.008   0.001   TRP D 179 
 HIS   0.005   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6826)
  covalent geometry    : angle       0.55172 ( 9285)
  hydrogen bonds       : bond        0.02989 (  168)
  hydrogen bonds       : angle       4.65546 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 106
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7908 (mp10) cc_final: 0.7301 (mt0)
REVERT: A  369 GLN cc_start: 0.7304 (tt0) cc_final: 0.7006 (mt0)
REVERT: A  371 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6006 (tpp)
REVERT: A  383 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6802 (m-80)
REVERT: A  391 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6155 (mmtt)
REVERT: A  517 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7354 (tmtt)
REVERT: A  519 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7148 (mp)
REVERT: A  558 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6970 (ttt90)
REVERT: B  339 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7314 (mt0)
REVERT: B  369 GLN cc_start: 0.7082 (tt0) cc_final: 0.6847 (mt0)
REVERT: B  408 MET cc_start: 0.7622 (mtt) cc_final: 0.7271 (mtt)
REVERT: B  520 ARG cc_start: 0.7099 (mtm110) cc_final: 0.6671 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7011 (ttt90)
REVERT: C  150 TRP cc_start: 0.7842 (t-100) cc_final: 0.7156 (t60)
REVERT: C  162 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7603 (mtpt)
REVERT: D  106 LEU cc_start: 0.4029 (OUTLIER) cc_final: 0.3331 (pp)
REVERT: D  162 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7465 (mtpt)
REVERT: D  179 TRP cc_start: 0.6005 (OUTLIER) cc_final: 0.4757 (t60)
REVERT: E  668 GLU cc_start: 0.2565 (OUTLIER) cc_final: 0.1891 (mp0)
REVERT: F  673 MET cc_start: 0.7098 (mtt) cc_final: 0.6592 (mtt)
  outliers start: 41
  outliers final: 28
  residues processed: 139
  average time/residue: 0.0854
  time to fit residues: 15.8933
Evaluate side-chains
  142 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 102
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  558 ARG
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  652 LEU
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain E residue  668 GLU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 385 ASN
B 385 ASN
** D  66 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 = 0.4276 r_free = 0.4276 target = 0.216445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.187140 restraints weight = 6909.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 1.93
r_work: 0.3894 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6826  Z= 0.132
  Angle     :  0.587   6.694   9285  Z= 0.298
  Chirality :  0.043   0.152   1080
  Planarity :  0.006   0.068   1149
  Dihedral  :  8.179  57.603    935
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.84 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 29.76 %
    Favored  : 63.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.30), residues: 784
  helix: -0.51 (0.30), residues: 290
  sheet: -0.42 (0.57), residues: 87
  loop : -2.45 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  72 
 TYR   0.015   0.001   TYR A 332 
 PHE   0.014   0.002   PHE B 434 
 TRP   0.008   0.001   TRP D 179 
 HIS   0.005   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6826)
  covalent geometry    : angle       0.58734 ( 9285)
  hydrogen bonds       : bond        0.03270 (  168)
  hydrogen bonds       : angle       4.66150 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 106
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7951 (mp10) cc_final: 0.7340 (mt0)
REVERT: A  364 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7755 (p90)
REVERT: A  371 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.6088 (tpp)
REVERT: A  383 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.6851 (m-80)
REVERT: A  391 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6175 (mmtt)
REVERT: A  517 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7421 (tmtt)
REVERT: A  519 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7177 (mp)
REVERT: A  558 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7009 (ttt90)
REVERT: B  339 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7324 (mt0)
REVERT: B  369 GLN cc_start: 0.7172 (tt0) cc_final: 0.6852 (mt0)
REVERT: B  371 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.6365 (tpp)
REVERT: B  408 MET cc_start: 0.7682 (mtt) cc_final: 0.7335 (mtt)
REVERT: B  520 ARG cc_start: 0.7161 (mtm110) cc_final: 0.6741 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7072 (ttt90)
REVERT: B  653 GLN cc_start: 0.4502 (OUTLIER) cc_final: 0.4233 (mt0)
REVERT: C  162 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7633 (mtpt)
REVERT: D  106 LEU cc_start: 0.4083 (OUTLIER) cc_final: 0.3373 (pp)
REVERT: D  162 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7475 (mtpt)
REVERT: D  179 TRP cc_start: 0.6003 (OUTLIER) cc_final: 0.4732 (t60)
REVERT: E  666 MET cc_start: 0.7542 (mmm) cc_final: 0.6970 (mmm)
REVERT: E  668 GLU cc_start: 0.2549 (OUTLIER) cc_final: 0.1879 (mp0)
REVERT: F  643 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5054 (pp20)
REVERT: F  673 MET cc_start: 0.7083 (mtt) cc_final: 0.6540 (mtt)
  outliers start: 50
  outliers final: 28
  residues processed: 148
  average time/residue: 0.0864
  time to fit residues: 17.1646
Evaluate side-chains
  149 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 105
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  364 HIS
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  558 ARG
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  371 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  639 LEU
Chi-restraints excluded: chain B residue  653 GLN
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  162 LYS
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  652 LEU
Chi-restraints excluded: chain E residue  665 LEU
Chi-restraints excluded: chain E residue  668 GLU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 369 GLN
A 382 ASN
A 385 ASN
B 385 ASN
C 160 HIS
** D  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.214776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.187082 restraints weight = 6905.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 1.86
r_work: 0.3889 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6662
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6826  Z= 0.148
  Angle     :  0.613   6.646   9285  Z= 0.309
  Chirality :  0.044   0.154   1080
  Planarity :  0.006   0.069   1149
  Dihedral  :  8.065  58.680    933
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.84 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 31.22 %
    Favored  : 63.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.29), residues: 784
  helix: -0.57 (0.30), residues: 290
  sheet: -0.53 (0.57), residues: 86
  loop : -2.49 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 612 
 TYR   0.013   0.002   TYR A 332 
 PHE   0.020   0.002   PHE B 434 
 TRP   0.009   0.001   TRP A 577 
 HIS   0.006   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6826)
  covalent geometry    : angle       0.61326 ( 9285)
  hydrogen bonds       : bond        0.03433 (  168)
  hydrogen bonds       : angle       4.70337 (  495)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 105
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7985 (mp10) cc_final: 0.7379 (mt0)
REVERT: A  371 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6073 (tpp)
REVERT: A  383 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6910 (m-80)
REVERT: A  391 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6311 (mmtt)
REVERT: A  517 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7539 (tmtt)
REVERT: A  519 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7293 (mp)
REVERT: B  339 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7353 (mt0)
REVERT: B  369 GLN cc_start: 0.7170 (tt0) cc_final: 0.6883 (mt0)
REVERT: B  371 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.6455 (tpp)
REVERT: B  408 MET cc_start: 0.7664 (mtt) cc_final: 0.7323 (mtt)
REVERT: B  520 ARG cc_start: 0.7220 (mtm110) cc_final: 0.6801 (mtp-110)
REVERT: B  558 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7170 (ttt90)
REVERT: B  653 GLN cc_start: 0.4541 (OUTLIER) cc_final: 0.4291 (mt0)
REVERT: C  162 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7674 (mtpt)
REVERT: D  106 LEU cc_start: 0.4204 (OUTLIER) cc_final: 0.3441 (pp)
REVERT: D  162 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7548 (mtpt)
REVERT: D  179 TRP cc_start: 0.5987 (OUTLIER) cc_final: 0.4709 (t60)
REVERT: E  666 MET cc_start: 0.7540 (mmm) cc_final: 0.7005 (mmm)
REVERT: E  668 GLU cc_start: 0.2710 (OUTLIER) cc_final: 0.1995 (mp0)
REVERT: F  643 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.4977 (pp20)
REVERT: F  673 MET cc_start: 0.7165 (mtt) cc_final: 0.6669 (mtt)
  outliers start: 43
  outliers final: 27
  residues processed: 141
  average time/residue: 0.0836
  time to fit residues: 16.1354
Evaluate side-chains
  145 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 105
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  383 TYR
Chi-restraints excluded: chain A residue  391 LYS
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  517 LYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  632 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 TYR
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  339 GLN
Chi-restraints excluded: chain B residue  371 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  595 ILE
Chi-restraints excluded: chain B residue  614 ILE
Chi-restraints excluded: chain B residue  632 LEU
Chi-restraints excluded: chain B residue  639 LEU
Chi-restraints excluded: chain B residue  653 GLN
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  179 TRP
Chi-restraints excluded: chain E residue  668 GLU
Chi-restraints excluded: chain F residue  643 GLU
Chi-restraints excluded: chain F residue  647 TRP
Chi-restraints excluded: chain F residue  665 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 1 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 29 optimal weight:    0.7980
   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 385 ASN
B 385 ASN
** D  66 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 = 0.4274 r_free = 0.4274 target = 0.215820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.188232 restraints weight = 6874.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 1.85
r_work: 0.3899 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6826  Z= 0.131
  Angle     :  0.595   6.549   9285  Z= 0.303
  Chirality :  0.043   0.154   1080
  Planarity :  0.006   0.068   1149
  Dihedral  :  7.896  58.815    931
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.10 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 32.28 %
    Favored  : 62.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.29), residues: 784
  helix: -0.60 (0.30), residues: 296
  sheet: -0.51 (0.57), residues: 86
  loop : -2.49 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 435 
 TYR   0.012   0.001   TYR A 332 
 PHE   0.012   0.002   PHE B 362 
 TRP   0.008   0.001   TRP D 179 
 HIS   0.006   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6826)
  covalent geometry    : angle       0.59494 ( 9285)
  hydrogen bonds       : bond        0.03252 (  168)
  hydrogen bonds       : angle       4.60484 (  495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1737.22 seconds
wall clock time: 30 minutes 35.37 seconds (1835.37 seconds total)