Starting phenix.real_space_refine
on Tue Mar 11 21:57:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afe_15395/03_2025/8afe_15395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afe_15395/03_2025/8afe_15395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afe_15395/03_2025/8afe_15395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afe_15395/03_2025/8afe_15395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afe_15395/03_2025/8afe_15395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afe_15395/03_2025/8afe_15395.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      23      5.16       5
     C    4124      2.51       5
     N    1282      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6785
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 739
          Classifications: {'peptide': 96}
          Link IDs: {'TRANS': 95}
    Chain: "B"
      Number of atoms: 747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 747
          Classifications: {'peptide': 97}
          Link IDs: {'TRANS': 96}
    Chain: "D"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 600
          Classifications: {'peptide': 79}
          Link IDs: {'TRANS': 78}
    Chain: "F"
      Number of atoms: 600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 600
          Classifications: {'peptide': 79}
          Link IDs: {'TRANS': 78}
    Chain: "G"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 333
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
    Chain: "H"
      Number of atoms: 299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 299
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "I"
      Number of atoms: 860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 860
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 2, 'TRANS': 108}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
  Time building chain proxies: 4.87, per 1000 atoms: 0.72
  Number of scatterers: 6785
  At special positions: 0
  Unit cell: (63.6, 242.475, 88.775, 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      23     16.00
     O    1356      8.00
     N    1282      7.00
     C    4124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 795 " - pdb=" SG  CYS D 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 795 " - pdb=" SG  CYS C 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 795 " - pdb=" SG  CYS I 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 795 " - pdb=" SG  CYS J 868 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 950.6 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 13 sheets defined
      50.3% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 350 through 357
      removed outlier: 3.961A  pdb=" N   ASP A 354 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 441
      removed outlier: 3.647A  pdb=" N   GLU A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ARG A 363 " --> pdb=" O   THR A 359 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   GLU A 426 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 432
      removed outlier: 3.877A  pdb=" N   ALA B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU B 367 " --> pdb=" O   ARG B 363 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL B 372 " --> pdb=" O   ALA B 368 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU B 383 " --> pdb=" O   LYS B 379 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ARG B 404 " --> pdb=" O   ASP B 400 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B 429 " --> pdb=" O   SER B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 442
    Processing helix  chain 'B' and resid 443 through 446
    Processing helix  chain 'D' and resid 859 through 863
      removed outlier: 3.554A  pdb=" N   THR D 863 " --> pdb=" O   PRO D 860 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 859 through 863
      removed outlier: 3.892A  pdb=" N   THR C 863 " --> pdb=" O   PRO C 860 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 163
      removed outlier: 3.828A  pdb=" N   LEU E 115 " --> pdb=" O   VAL E 111 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ALA E 116 " --> pdb=" O   SER E 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 163
      removed outlier: 3.591A  pdb=" N   ALA F  92 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ASN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 404 through 439
      removed outlier: 3.796A  pdb=" N   ALA G 411 " --> pdb=" O   ALA G 407 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS G 412 " --> pdb=" O   THR G 408 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA G 418 " --> pdb=" O   ALA G 414 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU G 426 " --> pdb=" O   ARG G 422 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA G 427 " --> pdb=" O   LEU G 423 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU G 429 " --> pdb=" O   SER G 425 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA G 433 " --> pdb=" O   LEU G 429 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 440 through 444
    Processing helix  chain 'H' and resid 405 through 431
      removed outlier: 3.648A  pdb=" N   HIS H 409 " --> pdb=" O   ASP H 405 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU H 410 " --> pdb=" O   SER H 406 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE H 420 " --> pdb=" O   LEU H 416 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU H 421 " --> pdb=" O   GLN H 417 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 432 through 441
      removed outlier: 3.589A  pdb=" N   ASP H 440 " --> pdb=" O   ALA H 436 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG H 441 " --> pdb=" O   ALA H 437 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 859 through 863
      removed outlier: 3.602A  pdb=" N   THR I 863 " --> pdb=" O   PRO I 860 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 859 through 863
      removed outlier: 3.819A  pdb=" N   THR J 863 " --> pdb=" O   PRO J 860 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7
      removed outlier: 3.711A  pdb=" N   VAL D 851 " --> pdb=" O   CYS D 795 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR D 850 " --> pdb=" O   ASP D 845 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.212A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 885 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   MET D 807 " --> pdb=" O   VAL D 823 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   VAL D 823 " --> pdb=" O   MET D 807 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP D 809 " --> pdb=" O   VAL D 821 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872
    Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.550A  pdb=" N   VAL C  12 " --> pdb=" O   THR C 885 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832
      removed outlier: 7.030A  pdb=" N   TRP C 809 " --> pdb=" O   VAL C 821 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   VAL C 823 " --> pdb=" O   MET C 807 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   MET C 807 " --> pdb=" O   VAL C 823 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6
      removed outlier: 3.613A  pdb=" N   VAL I 851 " --> pdb=" O   CYS I 795 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12
      removed outlier: 6.809A  pdb=" N   MET I 807 " --> pdb=" O   VAL I 823 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   VAL I 823 " --> pdb=" O   MET I 807 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TRP I 809 " --> pdb=" O   VAL I 821 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872
      removed outlier: 3.571A  pdb=" N   TYR I 872 " --> pdb=" O   SER I 875 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.544A  pdb=" N   GLY J  10 " --> pdb=" O   THR J 885 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.544A  pdb=" N   GLY J  10 " --> pdb=" O   THR J 885 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793

    463 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.87 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: 2430
        1.34 -     1.46: 1083
        1.46 -     1.58: 3290
        1.58 -     1.70: 0
        1.70 -     1.81: 38
  Bond restraints: 6841
  Sorted by residual:
  bond pdb=" CB  TRP C 827 "
       pdb=" CG  TRP C 827 "
    ideal  model  delta    sigma   weight residual
    1.498  1.446  0.052 3.10e-02 1.04e+03 2.78e+00
  bond pdb=" CG1 ILE D 806 "
       pdb=" CD1 ILE D 806 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.67e+00
  bond pdb=" C   TYR J 832 "
       pdb=" N   VAL J 833 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.016 1.29e-02 6.01e+03 1.62e+00
  bond pdb=" CB  ASN I 869 "
       pdb=" CG  ASN I 869 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.59e+00
  bond pdb=" C   LYS D 859 "
       pdb=" N   PRO D 860 "
    ideal  model  delta    sigma   weight residual
    1.337  1.323  0.014 1.11e-02 8.12e+03 1.49e+00
  ... (remaining 6836 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 8401
        1.17 -     2.34: 683
        2.34 -     3.51: 99
        3.51 -     4.68: 19
        4.68 -     5.85: 7
  Bond angle restraints: 9209
  Sorted by residual:
  angle pdb=" N   ILE J 806 "
        pdb=" CA  ILE J 806 "
        pdb=" C   ILE J 806 "
      ideal   model   delta    sigma   weight residual
     108.93  113.36   -4.43 1.35e+00 5.49e-01 1.08e+01
  angle pdb=" N   ILE D 806 "
        pdb=" CA  ILE D 806 "
        pdb=" C   ILE D 806 "
      ideal   model   delta    sigma   weight residual
     109.30  113.38   -4.08 1.31e+00 5.83e-01 9.70e+00
  angle pdb=" C   ALA E 118 "
        pdb=" N   GLU E 119 "
        pdb=" CA  GLU E 119 "
      ideal   model   delta    sigma   weight residual
     120.68  115.81    4.87 1.70e+00 3.46e-01 8.22e+00
  angle pdb=" C   SER E 112 "
        pdb=" N   ALA E 113 "
        pdb=" CA  ALA E 113 "
      ideal   model   delta    sigma   weight residual
     122.42  118.24    4.18 1.55e+00 4.16e-01 7.29e+00
  angle pdb=" CA  TRP C 827 "
        pdb=" CB  TRP C 827 "
        pdb=" CG  TRP C 827 "
      ideal   model   delta    sigma   weight residual
     113.60  108.52    5.08 1.90e+00 2.77e-01 7.16e+00
  ... (remaining 9204 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 3786
       17.25 -    34.51: 381
       34.51 -    51.76: 46
       51.76 -    69.02: 6
       69.02 -    86.27: 14
  Dihedral angle restraints: 4233
    sinusoidal: 1691
      harmonic: 2542
  Sorted by residual:
  dihedral pdb=" CB  CYS C 795 "
           pdb=" SG  CYS C 795 "
           pdb=" SG  CYS C 868 "
           pdb=" CB  CYS C 868 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.73   49.27     1      1.00e+01 1.00e-02 3.34e+01
  dihedral pdb=" CB  CYS I 795 "
           pdb=" SG  CYS I 795 "
           pdb=" SG  CYS I 868 "
           pdb=" CB  CYS I 868 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.90   48.10     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" CA  HIS A 350 "
           pdb=" C   HIS A 350 "
           pdb=" N   ALA A 351 "
           pdb=" CA  ALA A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.67  -25.33     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 4230 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 711
       0.039 -    0.079: 242
       0.079 -    0.118: 79
       0.118 -    0.158: 4
       0.158 -    0.197: 5
  Chirality restraints: 1041
  Sorted by residual:
  chirality pdb=" CB  ILE J 842 "
            pdb=" CA  ILE J 842 "
            pdb=" CG1 ILE J 842 "
            pdb=" CG2 ILE J 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CB  ILE I 842 "
            pdb=" CA  ILE I 842 "
            pdb=" CG1 ILE I 842 "
            pdb=" CG2 ILE I 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CB  VAL J 823 "
            pdb=" CA  VAL J 823 "
            pdb=" CG1 VAL J 823 "
            pdb=" CG2 VAL J 823 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.18 2.00e-01 2.50e+01 8.50e-01
  ... (remaining 1038 not shown)

  Planarity restraints: 1219
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 859 "    0.057 5.00e-02 4.00e+02   8.65e-02 1.20e+01
        pdb=" N   PRO C 860 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO C 860 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 860 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 417 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.12e+00
        pdb=" CD  GLN B 417 "    0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 417 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 417 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 859 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO J 860 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO J 860 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO J 860 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1216 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 272
        2.71 -     3.26: 6877
        3.26 -     3.80: 10416
        3.80 -     4.35: 13277
        4.35 -     4.90: 22214
  Nonbonded interactions: 53056
  Sorted by model distance:
  nonbonded pdb=" O   THR B 424 "
            pdb=" ND2 ASN C 831 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" NH1 ARG D 799 "
            pdb=" OG  SER D 800 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OD1 ASP I 802 "
            pdb=" NH2 ARG I 844 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" NH1 ARG I 808 "
            pdb=" OH  TYR I 810 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   ASP C 862 "
            pdb=" OH  TYR C 866 "
     model   vdw
     2.255 3.040
  ... (remaining 53051 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 350 through 445)
}
ncs_group {
  reference = (chain 'C' and resid 2 through 887)
  selection = (chain 'D' and resid 2 through 887)
  selection = chain 'I'
  selection = (chain 'J' and resid 2 through 887)
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'G' and resid 403 through 441)
  selection = chain 'H'
}

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:             1.330
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.540
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6057
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   6841  Z= 0.377
  Angle     :  0.699   5.850   9209  Z= 0.430
  Chirality :  0.044   0.197   1041
  Planarity :  0.004   0.086   1219
  Dihedral  : 14.166  86.270   2573
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.28), residues: 852
  helix: -0.24 (0.25), residues: 379
  sheet: -2.06 (0.31), residues: 239
  loop :  0.03 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP C 827 
 HIS   0.005   0.002   HIS A 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.018   0.002   TYR J  13 
 ARG   0.013   0.001   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: C  865 VAL cc_start: 0.7852 (m) cc_final: 0.7637 (p)
REVERT: I  862 ASP cc_start: 0.7207 (m-30) cc_final: 0.6998 (m-30)
REVERT: J  807 MET cc_start: 0.6494 (mmm) cc_final: 0.5574 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2072
  time to fit residues: 32.9012
Evaluate side-chains
  116 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 62 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.177255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.166935 restraints weight = 9383.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 1.55
r_work: 0.4051 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3925 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6841  Z= 0.337
  Angle     :  0.642   7.694   9209  Z= 0.351
  Chirality :  0.043   0.176   1041
  Planarity :  0.005   0.067   1219
  Dihedral  :  5.384  26.140    981
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.88 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.29), residues: 852
  helix:  0.92 (0.26), residues: 385
  sheet: -2.01 (0.32), residues: 223
  loop :  0.01 (0.44), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 827 
 HIS   0.005   0.001   HIS B 350 
 PHE   0.006   0.001   PHE D 840 
 TYR   0.014   0.002   TYR C  13 
 ARG   0.007   0.001   ARG E 129 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.739 
Fit side-chains
REVERT: D  839 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7724 (ttp-110)
REVERT: C  865 VAL cc_start: 0.8138 (m) cc_final: 0.7911 (p)
REVERT: E  128 ARG cc_start: 0.6041 (ttm110) cc_final: 0.5797 (ttm170)
REVERT: E  139 ASN cc_start: 0.6547 (t0) cc_final: 0.6341 (t0)
REVERT: F  143 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7118 (mt)
REVERT: H  426 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6960 (mt-10)
REVERT: I  817 GLN cc_start: 0.7002 (mp10) cc_final: 0.6622 (mp10)
REVERT: I  862 ASP cc_start: 0.7491 (m-30) cc_final: 0.7103 (m-30)
REVERT: J  807 MET cc_start: 0.7780 (mmm) cc_final: 0.7493 (mmp)
  outliers start: 15
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2163
  time to fit residues: 31.9125
Evaluate side-chains
  119 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.176888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.166514 restraints weight = 9416.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.57
r_work: 0.4054 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6841  Z= 0.312
  Angle     :  0.590   5.816   9209  Z= 0.324
  Chirality :  0.042   0.161   1041
  Planarity :  0.005   0.059   1219
  Dihedral  :  5.214  24.396    981
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 12.75 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.29), residues: 852
  helix:  1.35 (0.26), residues: 381
  sheet: -1.97 (0.32), residues: 224
  loop :  0.09 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP I 827 
 HIS   0.005   0.001   HIS B 350 
 PHE   0.004   0.001   PHE I 840 
 TYR   0.015   0.002   TYR C  13 
 ARG   0.006   0.001   ARG E 129 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 HIS cc_start: 0.4171 (OUTLIER) cc_final: 0.3501 (m-70)
REVERT: B  397 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7452 (tp30)
REVERT: E  139 ASN cc_start: 0.6472 (t0) cc_final: 0.6183 (t0)
REVERT: F  143 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7074 (mt)
REVERT: H  426 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6911 (mt-10)
REVERT: I  817 GLN cc_start: 0.6994 (mp10) cc_final: 0.6595 (mp10)
REVERT: J  807 MET cc_start: 0.7906 (mmm) cc_final: 0.7487 (mmm)
REVERT: J  810 TYR cc_start: 0.6607 (m-80) cc_final: 0.6346 (m-80)
REVERT: J  859 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6870 (mtmm)
  outliers start: 20
  outliers final: 11
  residues processed: 118
  average time/residue: 0.2015
  time to fit residues: 31.3977
Evaluate side-chains
  126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain D residue  834 ASP
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  807 MET
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 61 optimal weight:    0.0270
   chunk 65 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0870
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN
E 139 ASN
I 883 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.185689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.174218 restraints weight = 9449.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 1.82
r_work: 0.4127 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3988 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6841  Z= 0.182
  Angle     :  0.494   5.223   9209  Z= 0.275
  Chirality :  0.039   0.142   1041
  Planarity :  0.004   0.053   1219
  Dihedral  :  4.712  21.437    981
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.47 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.30), residues: 852
  helix:  2.05 (0.26), residues: 379
  sheet: -1.72 (0.31), residues: 243
  loop :  0.49 (0.46), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 878 
 HIS   0.002   0.001   HIS A 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.010   0.001   TYR C  13 
 ARG   0.005   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.3640 (OUTLIER) cc_final: 0.3215 (m-70)
REVERT: H  426 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6884 (mt-10)
REVERT: I  817 GLN cc_start: 0.6883 (mp10) cc_final: 0.6556 (mp10)
REVERT: I  872 TYR cc_start: 0.8711 (t80) cc_final: 0.8448 (t80)
REVERT: J  807 MET cc_start: 0.7988 (mmm) cc_final: 0.7671 (mpp)
REVERT: J  810 TYR cc_start: 0.6650 (m-80) cc_final: 0.6425 (m-80)
  outliers start: 14
  outliers final: 7
  residues processed: 114
  average time/residue: 0.2032
  time to fit residues: 30.5198
Evaluate side-chains
  114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain I residue  807 MET
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 72 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0270
   chunk 13 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.184974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.173611 restraints weight = 9240.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 1.79
r_work: 0.4118 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3976 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6841  Z= 0.216
  Angle     :  0.504   5.541   9209  Z= 0.280
  Chirality :  0.039   0.138   1041
  Planarity :  0.004   0.050   1219
  Dihedral  :  4.705  20.611    981
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.19 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.30), residues: 852
  helix:  2.25 (0.25), residues: 382
  sheet: -1.71 (0.31), residues: 246
  loop :  0.65 (0.48), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 878 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.013   0.001   TYR C  13 
 ARG   0.009   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.785 
Fit side-chains
REVERT: B  397 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7537 (tp30)
REVERT: B  404 ARG cc_start: 0.6775 (ptt-90) cc_final: 0.6550 (ptp-170)
REVERT: I  872 TYR cc_start: 0.8723 (t80) cc_final: 0.8453 (t80)
REVERT: J  807 MET cc_start: 0.8011 (mmm) cc_final: 0.7787 (mmm)
REVERT: J  810 TYR cc_start: 0.6755 (m-80) cc_final: 0.6430 (m-80)
  outliers start: 22
  outliers final: 14
  residues processed: 116
  average time/residue: 0.2023
  time to fit residues: 31.0959
Evaluate side-chains
  121 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  865 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain I residue  807 MET
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain J residue  823 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN
E 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.183795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.172482 restraints weight = 9259.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 1.78
r_work: 0.4106 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3962 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6841  Z= 0.268
  Angle     :  0.535   6.043   9209  Z= 0.296
  Chirality :  0.040   0.143   1041
  Planarity :  0.004   0.050   1219
  Dihedral  :  4.849  23.022    981
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.48 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.30), residues: 852
  helix:  2.17 (0.25), residues: 383
  sheet: -1.74 (0.30), residues: 253
  loop :  0.50 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 878 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.013   0.002   TYR J  13 
 ARG   0.007   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  350 HIS cc_start: 0.4269 (OUTLIER) cc_final: 0.3606 (m-70)
REVERT: B  397 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7539 (tp30)
REVERT: E  139 ASN cc_start: 0.6413 (t0) cc_final: 0.6150 (t0)
REVERT: I  817 GLN cc_start: 0.7094 (mp10) cc_final: 0.6877 (mp10)
REVERT: I  851 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7385 (m)
REVERT: I  872 TYR cc_start: 0.8743 (t80) cc_final: 0.8499 (t80)
REVERT: J  807 MET cc_start: 0.8031 (mmm) cc_final: 0.7808 (mmm)
REVERT: J  810 TYR cc_start: 0.6877 (m-80) cc_final: 0.6526 (m-80)
  outliers start: 28
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1888
  time to fit residues: 30.8170
Evaluate side-chains
  127 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  865 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain I residue  807 MET
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 73 optimal weight:    0.2980
   chunk 41 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 67 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.184094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.173078 restraints weight = 9071.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 1.72
r_work: 0.4115 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3974 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6841  Z= 0.238
  Angle     :  0.518   6.561   9209  Z= 0.286
  Chirality :  0.039   0.142   1041
  Planarity :  0.003   0.048   1219
  Dihedral  :  4.731  20.959    981
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.91 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.30), residues: 852
  helix:  2.28 (0.25), residues: 383
  sheet: -1.75 (0.30), residues: 253
  loop :  0.52 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 878 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.005   0.001   PHE I 840 
 TYR   0.013   0.002   TYR C  13 
 ARG   0.007   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 HIS cc_start: 0.3978 (OUTLIER) cc_final: 0.3350 (m-70)
REVERT: B  397 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7516 (tp30)
REVERT: E  139 ASN cc_start: 0.6356 (t0) cc_final: 0.6067 (t0)
REVERT: I  851 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7347 (m)
REVERT: I  872 TYR cc_start: 0.8659 (t80) cc_final: 0.8430 (t80)
REVERT: J  807 MET cc_start: 0.8035 (mmm) cc_final: 0.7781 (mmm)
REVERT: J  810 TYR cc_start: 0.6882 (m-80) cc_final: 0.6476 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1837
  time to fit residues: 28.8605
Evaluate side-chains
  128 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue  868 CYS
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  865 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain I residue  807 MET
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Chi-restraints excluded: chain J residue  833 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 24 optimal weight:    0.4980
   chunk 75 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.182991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.171920 restraints weight = 9244.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 1.76
r_work: 0.4104 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3964 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6841  Z= 0.261
  Angle     :  0.537   6.860   9209  Z= 0.295
  Chirality :  0.040   0.142   1041
  Planarity :  0.003   0.048   1219
  Dihedral  :  4.794  22.195    981
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 16.91 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.30), residues: 852
  helix:  2.25 (0.25), residues: 383
  sheet: -1.79 (0.30), residues: 253
  loop :  0.50 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 878 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.012   0.002   TYR C  13 
 ARG   0.009   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 HIS cc_start: 0.4007 (OUTLIER) cc_final: 0.3410 (m-70)
REVERT: B  397 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7535 (tp30)
REVERT: E  139 ASN cc_start: 0.6354 (t0) cc_final: 0.6060 (t0)
REVERT: I  851 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7336 (m)
REVERT: J  807 MET cc_start: 0.7986 (mmm) cc_final: 0.7762 (mmm)
REVERT: J  810 TYR cc_start: 0.6924 (m-80) cc_final: 0.6445 (m-80)
  outliers start: 32
  outliers final: 25
  residues processed: 121
  average time/residue: 0.2066
  time to fit residues: 32.9578
Evaluate side-chains
  132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue  868 CYS
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  851 VAL
Chi-restraints excluded: chain C residue  865 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain I residue  824 VAL
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain I residue  886 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Chi-restraints excluded: chain J residue  833 VAL
Chi-restraints excluded: chain J residue  859 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.183664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.172590 restraints weight = 9287.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 1.75
r_work: 0.4106 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3966 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6841  Z= 0.262
  Angle     :  0.543   7.132   9209  Z= 0.297
  Chirality :  0.040   0.143   1041
  Planarity :  0.003   0.047   1219
  Dihedral  :  4.775  20.957    981
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 16.91 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.30), residues: 852
  helix:  2.22 (0.25), residues: 383
  sheet: -1.78 (0.30), residues: 253
  loop :  0.52 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 878 
 HIS   0.004   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.012   0.002   TYR C  13 
 ARG   0.007   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 HIS cc_start: 0.3998 (OUTLIER) cc_final: 0.3355 (m-70)
REVERT: B  397 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7489 (tp30)
REVERT: E  139 ASN cc_start: 0.6332 (t0) cc_final: 0.5923 (t0)
REVERT: I  851 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7329 (m)
REVERT: J  810 TYR cc_start: 0.6907 (m-80) cc_final: 0.6446 (m-80)
  outliers start: 33
  outliers final: 26
  residues processed: 122
  average time/residue: 0.1984
  time to fit residues: 31.9814
Evaluate side-chains
  130 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue  868 CYS
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  835 SER
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  851 VAL
Chi-restraints excluded: chain C residue  865 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  143 ILE
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain I residue  824 VAL
Chi-restraints excluded: chain I residue  851 VAL
Chi-restraints excluded: chain I residue  886 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Chi-restraints excluded: chain J residue  833 VAL
Chi-restraints excluded: chain J residue  859 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0670
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0980
   chunk 77 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0060
   overall best weight:    0.2934

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

Flipped N/Q/H residues before XYZ refinement:
** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.184038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.172114 restraints weight = 9517.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 1.92
r_work: 0.4093 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6841  Z= 0.178
  Angle     :  0.521   7.836   9209  Z= 0.283
  Chirality :  0.039   0.141   1041
  Planarity :  0.004   0.060   1219
  Dihedral  :  4.551  21.326    981
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.91 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.30), residues: 852
  helix:  2.47 (0.25), residues: 381
  sheet: -1.58 (0.31), residues: 253
  loop :  0.71 (0.49), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 878 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.006   0.001   PHE I 840 
 TYR   0.011   0.001   TYR I 872 
 ARG   0.014   0.000   ARG B 404 

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 HIS cc_start: 0.3647 (OUTLIER) cc_final: 0.3167 (m-70)
REVERT: B  367 LEU cc_start: 0.7934 (mp) cc_final: 0.7655 (mt)
REVERT: B  397 GLU cc_start: 0.7818 (tp30) cc_final: 0.7514 (tp30)
REVERT: E  139 ASN cc_start: 0.6158 (t0) cc_final: 0.5892 (t0)
REVERT: H  422 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7351 (tpp80)
REVERT: H  426 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7080 (mt-10)
REVERT: H  429 LEU cc_start: 0.8376 (mm) cc_final: 0.8107 (mp)
REVERT: I  872 TYR cc_start: 0.8598 (t80) cc_final: 0.8383 (t80)
REVERT: J  810 TYR cc_start: 0.6837 (m-80) cc_final: 0.6390 (m-80)
  outliers start: 28
  outliers final: 23
  residues processed: 117
  average time/residue: 0.2038
  time to fit residues: 31.4678
Evaluate side-chains
  126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 HIS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue  868 CYS
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  821 VAL
Chi-restraints excluded: chain C residue  827 TRP
Chi-restraints excluded: chain C residue  836 VAL
Chi-restraints excluded: chain C residue  846 SER
Chi-restraints excluded: chain C residue  851 VAL
Chi-restraints excluded: chain C residue  865 VAL
Chi-restraints excluded: chain C residue  886 VAL
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain I residue    6 GLU
Chi-restraints excluded: chain I residue  821 VAL
Chi-restraints excluded: chain I residue  824 VAL
Chi-restraints excluded: chain I residue  886 VAL
Chi-restraints excluded: chain J residue  798 SER
Chi-restraints excluded: chain J residue  823 VAL
Chi-restraints excluded: chain J residue  833 VAL
Chi-restraints excluded: chain J residue  859 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 854 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.182775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.171567 restraints weight = 9298.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 1.79
r_work: 0.4097 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3953 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6841  Z= 0.295
  Angle     :  0.601  13.141   9209  Z= 0.321
  Chirality :  0.041   0.164   1041
  Planarity :  0.004   0.047   1219
  Dihedral  :  4.855  21.451    981
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.19 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.30), residues: 852
  helix:  2.21 (0.25), residues: 383
  sheet: -1.70 (0.30), residues: 253
  loop :  0.51 (0.48), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 878 
 HIS   0.004   0.001   HIS B 350 
 PHE   0.006   0.002   PHE I 840 
 TYR   0.013   0.002   TYR D 872 
 ARG   0.011   0.000   ARG B 404 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3874.06 seconds
wall clock time: 66 minutes 59.37 seconds (4019.37 seconds total)