Starting phenix.real_space_refine
on Wed Feb 12 00:03:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wi0_32517/02_2025/7wi0_32517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wi0_32517/02_2025/7wi0_32517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wi0_32517/02_2025/7wi0_32517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wi0_32517/02_2025/7wi0_32517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wi0_32517/02_2025/7wi0_32517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wi0_32517/02_2025/7wi0_32517.cif"
  }
  resolution = 3.82
  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      30      5.16       5
     C    4303      2.51       5
     N    1148      2.21       5
     O    1342      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6823
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1558
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 940
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
    Chain: "C"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 929
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "D"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 817
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "E"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 830
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 935
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 800
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.19, per 1000 atoms: 0.76
  Number of scatterers: 6823
  At special positions: 0
  Unit cell: (86.358, 94.916, 122.146, 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      30     16.00
     O    1342      8.00
     N    1148      7.00
     C    4303      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " 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
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
  Time building additional restraints: 1.53
  Conformation dependent library (CDL) restraints added in 915.5 milliseconds
  

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1606

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 22 sheets defined
      2.7% alpha, 29.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 341
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.848A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 389
      removed outlier: 3.620A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 386 through 389'
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.563A  pdb=" N   ASP C  90 " --> pdb=" O   ARG C  87 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA C  91 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 87 through 91'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.807A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   CYS A 432 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR A 380 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.726A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454
      removed outlier: 3.608A  pdb=" N   ARG A 493 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.636A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 20
      removed outlier: 3.689A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  83 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET B  83 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP B  73 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   TYR B  80 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7
      removed outlier: 3.508A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  83 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR C  69 " --> pdb=" O   GLN C  82 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 7.932A  pdb=" N   MET C  34 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   SER C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C  48 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7
      removed outlier: 6.722A  pdb=" N   THR D  69 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
    Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 54
      removed outlier: 5.405A  pdb=" N   LEU D  46 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   GLN D  37 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE D  48 " --> pdb=" O   TRP D  35 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN D  38 " --> pdb=" O   THR D  85 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR D  85 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 7
      removed outlier: 3.603A  pdb=" N   PHE E  71 " --> pdb=" O   CYS E  23 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.674A  pdb=" N   LEU E  11 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54
      removed outlier: 3.522A  pdb=" N   GLN E  37 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   LEU E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN E  89 " --> pdb=" O   ALA E  34 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR E  85 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.909A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.054A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 120 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL H 119 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA H  92 " --> pdb=" O   VAL H 119 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 18 through 19
      removed outlier: 3.506A  pdb=" N   ASP H  82 " --> pdb=" O   THR H  69 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 72 through 73
      removed outlier: 3.561A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.646A  pdb=" N   TYR L  88 " --> pdb=" O   THR L 105 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL L 107 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA L  86 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.646A  pdb=" N   TYR L  88 " --> pdb=" O   THR L 105 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL L 107 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA L  86 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER L  92 " --> pdb=" O   VAL L 100 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL L 100 " --> pdb=" O   SER L  92 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 17 through 21

    158 hydrogen bonds defined for protein.
    384 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: 1.82

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1101
        1.26 -     1.40: 1858
        1.40 -     1.54: 3952
        1.54 -     1.68: 39
        1.68 -     1.83: 40
  Bond restraints: 6990
  Sorted by residual:
  bond pdb=" C   THR C  78 "
       pdb=" O   THR C  78 "
    ideal  model  delta    sigma   weight residual
    1.234  1.462 -0.228 1.22e-02 6.72e+03 3.49e+02
  bond pdb=" C   SER B 106 "
       pdb=" O   SER B 106 "
    ideal  model  delta    sigma   weight residual
    1.234  1.117  0.117 1.19e-02 7.06e+03 9.66e+01
  bond pdb=" C   VAL B 101 "
       pdb=" O   VAL B 101 "
    ideal  model  delta    sigma   weight residual
    1.235  1.150  0.084 1.45e-02 4.76e+03 3.38e+01
  bond pdb=" CA  SER B 106 "
       pdb=" C   SER B 106 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 1.22e-02 6.72e+03 3.22e+01
  bond pdb=" C   THR C  78 "
       pdb=" N   LEU C  79 "
    ideal  model  delta    sigma   weight residual
    1.331  1.401 -0.070 1.29e-02 6.01e+03 2.94e+01
  ... (remaining 6985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.67: 9380
        3.67 -     7.34: 101
        7.34 -    11.01: 15
       11.01 -    14.68: 1
       14.68 -    18.36: 2
  Bond angle restraints: 9499
  Sorted by residual:
  angle pdb=" N   GLY B 105 "
        pdb=" CA  GLY B 105 "
        pdb=" C   GLY B 105 "
      ideal   model   delta    sigma   weight residual
     112.49  130.85  -18.36 1.21e+00 6.83e-01 2.30e+02
  angle pdb=" N   VAL B 101 "
        pdb=" CA  VAL B 101 "
        pdb=" C   VAL B 101 "
      ideal   model   delta    sigma   weight residual
     112.29  121.27   -8.98 9.40e-01 1.13e+00 9.12e+01
  angle pdb=" N   ASP B 112 "
        pdb=" CA  ASP B 112 "
        pdb=" C   ASP B 112 "
      ideal   model   delta    sigma   weight residual
     111.36  120.42   -9.06 1.09e+00 8.42e-01 6.91e+01
  angle pdb=" N   ALA B 102 "
        pdb=" CA  ALA B 102 "
        pdb=" C   ALA B 102 "
      ideal   model   delta    sigma   weight residual
     109.59   98.35   11.24 1.47e+00 4.63e-01 5.85e+01
  angle pdb=" O   SER B 106 "
        pdb=" C   SER B 106 "
        pdb=" N   SER B 107 "
      ideal   model   delta    sigma   weight residual
     123.46  116.86    6.60 9.90e-01 1.02e+00 4.44e+01
  ... (remaining 9494 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3694
       17.97 -    35.95: 350
       35.95 -    53.92: 53
       53.92 -    71.89: 9
       71.89 -    89.87: 8
  Dihedral angle restraints: 4114
    sinusoidal: 1576
      harmonic: 2538
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.43  -56.43     1      1.00e+01 1.00e-02 4.29e+01
  dihedral pdb=" CA  SER E  93 "
           pdb=" C   SER E  93 "
           pdb=" N   TYR E  94 "
           pdb=" CA  TYR E  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.77  -21.23     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  88 "
           pdb=" CB  CYS D  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.59   35.59     1      1.00e+01 1.00e-02 1.79e+01
  ... (remaining 4111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 916
       0.095 -    0.189: 97
       0.189 -    0.284: 13
       0.284 -    0.379: 1
       0.379 -    0.474: 1
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" CA  VAL B 101 "
            pdb=" N   VAL B 101 "
            pdb=" C   VAL B 101 "
            pdb=" CB  VAL B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.97    0.47 2.00e-01 2.50e+01 5.61e+00
  chirality pdb=" CA  SER B 107 "
            pdb=" N   SER B 107 "
            pdb=" C   SER B 107 "
            pdb=" CB  SER B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  TYR E  94 "
            pdb=" N   TYR E  94 "
            pdb=" C   TYR E  94 "
            pdb=" CB  TYR E  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  ... (remaining 1025 not shown)

  Planarity restraints: 1227
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  77 "    0.013 2.00e-02 2.50e+03   2.67e-02 7.11e+00
        pdb=" C   ASN C  77 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ASN C  77 "    0.018 2.00e-02 2.50e+03
        pdb=" N   THR C  78 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 372 "    0.043 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO A 373 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  45 "    0.042 5.00e-02 4.00e+02   6.34e-02 6.43e+00
        pdb=" N   PRO L  46 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO L  46 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L  46 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1224 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1858
        2.79 -     3.32: 5543
        3.32 -     3.85: 10966
        3.85 -     4.37: 11967
        4.37 -     4.90: 21668
  Nonbonded interactions: 52002
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN H   6 "
            pdb=" OG1 THR H 117 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER D  63 "
            pdb=" O   THR D  74 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OD1 ASP B  90 "
            pdb=" OH  TYR B  94 "
     model   vdw
     2.317 3.040
  ... (remaining 51997 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 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ 
 through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ 
 or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 
 107))
  selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ 
 through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ 
 or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 
 107))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             5.620
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.630
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
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      :  0.008   0.228   6990  Z= 0.528
  Angle     :  1.048  18.355   9499  Z= 0.635
  Chirality :  0.064   0.474   1028
  Planarity :  0.007   0.064   1226
  Dihedral  : 14.368  89.866   2487
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.60 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.08 %
    Favored  : 89.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -4.32 (0.24), residues: 872
  helix: -5.25 (0.15), residues: 30
  sheet: -2.73 (0.25), residues: 349
  loop : -2.85 (0.23), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 114 
 HIS   0.005   0.002   HIS L  36 
 PHE   0.019   0.002   PHE B  27 
 TYR   0.023   0.002   TYR C  95 
 ARG   0.005   0.000   ARG D  61 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 226
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7452 (ttpt)
REVERT: B   50 VAL cc_start: 0.9168 (p) cc_final: 0.8790 (p)
REVERT: B   51 MET cc_start: 0.8872 (mmm) cc_final: 0.8489 (mmt)
REVERT: B  116 GLN cc_start: 0.8414 (tp40) cc_final: 0.8191 (mm-40)
REVERT: C   65 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7657 (ttpt)
REVERT: E    2 ILE cc_start: 0.7706 (mp) cc_final: 0.7208 (mp)
REVERT: E   85 THR cc_start: 0.8060 (t) cc_final: 0.7840 (m)
REVERT: E   90 GLN cc_start: 0.8712 (pp30) cc_final: 0.8374 (pp30)
REVERT: H   62 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8251 (tm-30)
REVERT: H   89 GLU cc_start: 0.7658 (mp0) cc_final: 0.7446 (mt-10)
REVERT: L   63 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7772 (mtp-110)
  outliers start: 3
  outliers final: 1
  residues processed: 227
  average time/residue: 0.2109
  time to fit residues: 62.1525
Evaluate side-chains
  167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
B  39 GLN
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 HIS
D  31 ASN
D  38 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
L   1 GLN
L  36 HIS
L  39 GLN
L  40 GLN
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.128924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.105433 restraints weight = 11801.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.108496 restraints weight = 7172.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.110668 restraints weight = 5134.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6990  Z= 0.233
  Angle     :  0.645   7.658   9499  Z= 0.343
  Chirality :  0.046   0.205   1028
  Planarity :  0.005   0.050   1226
  Dihedral  :  5.528  38.983   1001
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.22 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.26), residues: 872
  helix: -5.02 (0.20), residues: 18
  sheet: -2.29 (0.26), residues: 347
  loop : -2.29 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  47 
 HIS   0.003   0.001   HIS H 107 
 PHE   0.021   0.002   PHE B  29 
 TYR   0.026   0.002   TYR L  51 
 ARG   0.004   0.001   ARG D  24 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: B   16 ARG cc_start: 0.8132 (ttm170) cc_final: 0.7912 (tpp80)
REVERT: B   47 TRP cc_start: 0.8353 (t60) cc_final: 0.7766 (t60)
REVERT: C   36 TRP cc_start: 0.7921 (m100) cc_final: 0.7495 (m100)
REVERT: C   45 LEU cc_start: 0.8469 (mt) cc_final: 0.8245 (mt)
REVERT: C   65 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7642 (ttpt)
REVERT: E    2 ILE cc_start: 0.7500 (mp) cc_final: 0.7250 (mp)
REVERT: E   78 LEU cc_start: 0.8290 (mm) cc_final: 0.7887 (tt)
REVERT: E   90 GLN cc_start: 0.8820 (pp30) cc_final: 0.8307 (pp30)
REVERT: H   43 GLN cc_start: 0.8555 (mp10) cc_final: 0.7937 (mp10)
REVERT: H   87 ARG cc_start: 0.6971 (mtm110) cc_final: 0.6614 (mtm110)
REVERT: L   63 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7501 (ttp-110)
  outliers start: 16
  outliers final: 5
  residues processed: 204
  average time/residue: 0.1900
  time to fit residues: 51.1267
Evaluate side-chains
  177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 172
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   96 CYS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue    9 SER
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
D   6 GLN
** D  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 100 GLN
H  62 GLN
H 108 ASN
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  81 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 = 0.3613 r_free = 0.3613 target = 0.123163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099347 restraints weight = 12276.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.102314 restraints weight = 7538.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.104376 restraints weight = 5444.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   6990  Z= 0.429
  Angle     :  0.737   8.265   9499  Z= 0.390
  Chirality :  0.048   0.282   1028
  Planarity :  0.005   0.055   1226
  Dihedral  :  5.634  40.889    996
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.83 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.27), residues: 872
  helix: -5.14 (0.20), residues: 24
  sheet: -2.25 (0.26), residues: 355
  loop : -2.02 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  47 
 HIS   0.007   0.002   HIS L  36 
 PHE   0.024   0.002   PHE A 490 
 TYR   0.024   0.002   TYR E  94 
 ARG   0.005   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
REVERT: B   47 TRP cc_start: 0.8463 (t60) cc_final: 0.7711 (t60)
REVERT: C   36 TRP cc_start: 0.7986 (m100) cc_final: 0.7577 (m100)
REVERT: C   45 LEU cc_start: 0.8545 (mt) cc_final: 0.8328 (mt)
REVERT: C   80 TYR cc_start: 0.6840 (m-80) cc_final: 0.6613 (m-80)
REVERT: C   86 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7972 (pp)
REVERT: C   89 GLU cc_start: 0.8531 (mp0) cc_final: 0.8315 (mp0)
REVERT: E   90 GLN cc_start: 0.8947 (pp30) cc_final: 0.8417 (pp30)
REVERT: H   43 GLN cc_start: 0.8635 (mp10) cc_final: 0.8067 (mp10)
REVERT: L   63 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7692 (mtm-85)
  outliers start: 32
  outliers final: 26
  residues processed: 192
  average time/residue: 0.2123
  time to fit residues: 53.4546
Evaluate side-chains
  187 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   96 CYS
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   36 HIS
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0270
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
E 100 GLN
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.128753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.105010 restraints weight = 12061.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.108130 restraints weight = 7231.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110344 restraints weight = 5152.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6990  Z= 0.183
  Angle     :  0.628   8.494   9499  Z= 0.324
  Chirality :  0.044   0.188   1028
  Planarity :  0.004   0.050   1226
  Dihedral  :  5.063  34.293    996
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.06 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.27), residues: 872
  helix: -4.82 (0.26), residues: 18
  sheet: -1.94 (0.26), residues: 372
  loop : -1.86 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  47 
 HIS   0.003   0.001   HIS H 107 
 PHE   0.012   0.001   PHE A 490 
 TYR   0.026   0.001   TYR E  94 
 ARG   0.005   0.000   ARG A 346 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: B   16 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7831 (tpp80)
REVERT: B   47 TRP cc_start: 0.8195 (t60) cc_final: 0.7737 (t60)
REVERT: C    3 GLN cc_start: 0.7129 (pp30) cc_final: 0.6919 (tm-30)
REVERT: C   36 TRP cc_start: 0.7864 (m100) cc_final: 0.7509 (m100)
REVERT: C   45 LEU cc_start: 0.8489 (mt) cc_final: 0.8276 (mt)
REVERT: C   86 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7900 (pp)
REVERT: E   90 GLN cc_start: 0.8791 (pp30) cc_final: 0.8364 (pp30)
REVERT: H   43 GLN cc_start: 0.8605 (mp10) cc_final: 0.8133 (mp10)
REVERT: H  104 TYR cc_start: 0.8390 (m-80) cc_final: 0.8094 (m-80)
REVERT: L   63 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7601 (ttp-110)
  outliers start: 21
  outliers final: 13
  residues processed: 187
  average time/residue: 0.1965
  time to fit residues: 48.2635
Evaluate side-chains
  172 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   96 CYS
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   93 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
E  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.125026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.101146 restraints weight = 11991.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.104027 restraints weight = 7373.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106152 restraints weight = 5360.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6990  Z= 0.329
  Angle     :  0.673   7.580   9499  Z= 0.350
  Chirality :  0.046   0.242   1028
  Planarity :  0.005   0.056   1226
  Dihedral  :  5.219  35.783    996
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 23.12 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.27), residues: 872
  helix: -4.97 (0.28), residues: 24
  sheet: -1.92 (0.26), residues: 364
  loop : -1.79 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  47 
 HIS   0.005   0.002   HIS L  36 
 PHE   0.018   0.002   PHE A 490 
 TYR   0.021   0.002   TYR E  94 
 ARG   0.005   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8126 (t)
REVERT: B   47 TRP cc_start: 0.8266 (t60) cc_final: 0.7847 (t60)
REVERT: C   34 MET cc_start: 0.8947 (mmt) cc_final: 0.8676 (mmt)
REVERT: C   36 TRP cc_start: 0.7965 (m100) cc_final: 0.7485 (m100)
REVERT: C   86 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8019 (pp)
REVERT: E   90 GLN cc_start: 0.8822 (pp30) cc_final: 0.8158 (pp30)
REVERT: H   43 GLN cc_start: 0.8629 (mp10) cc_final: 0.8140 (mp10)
REVERT: H   87 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6943 (mtm110)
REVERT: L   63 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.6976 (mtp180)
  outliers start: 32
  outliers final: 21
  residues processed: 185
  average time/residue: 0.1941
  time to fit residues: 47.2243
Evaluate side-chains
  181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   93 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.126540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102483 restraints weight = 12010.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.105512 restraints weight = 7404.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.107529 restraints weight = 5349.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6990  Z= 0.265
  Angle     :  0.672   7.944   9499  Z= 0.346
  Chirality :  0.045   0.225   1028
  Planarity :  0.004   0.046   1226
  Dihedral  :  5.111  34.617    996
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.00 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.27), residues: 872
  helix: -4.45 (0.46), residues: 18
  sheet: -1.81 (0.26), residues: 370
  loop : -1.71 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  47 
 HIS   0.003   0.001   HIS L  36 
 PHE   0.016   0.001   PHE A 490 
 TYR   0.024   0.001   TYR E  94 
 ARG   0.007   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: B   47 TRP cc_start: 0.8200 (t60) cc_final: 0.7826 (t60)
REVERT: B  118 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8400 (p)
REVERT: C   34 MET cc_start: 0.8998 (mmt) cc_final: 0.8736 (mmt)
REVERT: C   36 TRP cc_start: 0.7920 (m100) cc_final: 0.7499 (m100)
REVERT: C   86 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8002 (pp)
REVERT: E   90 GLN cc_start: 0.8773 (pp30) cc_final: 0.8294 (pp30)
REVERT: H   43 GLN cc_start: 0.8622 (mp10) cc_final: 0.8146 (mp10)
REVERT: H   48 MET cc_start: 0.8135 (mtt) cc_final: 0.7839 (mtp)
REVERT: L   63 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7450 (ttp-110)
REVERT: L   81 GLN cc_start: 0.8467 (mp10) cc_final: 0.8186 (mp10)
  outliers start: 28
  outliers final: 18
  residues processed: 176
  average time/residue: 0.2357
  time to fit residues: 55.3378
Evaluate side-chains
  172 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   93 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN
D  27 GLN
** E  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.127565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103823 restraints weight = 11803.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.106822 restraints weight = 7269.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.108972 restraints weight = 5258.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6990  Z= 0.217
  Angle     :  0.651   8.468   9499  Z= 0.332
  Chirality :  0.045   0.204   1028
  Planarity :  0.004   0.052   1226
  Dihedral  :  4.909  32.137    996
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 25.40 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.28), residues: 872
  helix: -4.47 (0.44), residues: 12
  sheet: -1.67 (0.26), residues: 370
  loop : -1.62 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C  99 
 PHE   0.014   0.001   PHE A 490 
 TYR   0.022   0.001   TYR E  94 
 ARG   0.007   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 161
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: B   47 TRP cc_start: 0.8067 (t60) cc_final: 0.7833 (t60)
REVERT: B  118 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8305 (p)
REVERT: C   34 MET cc_start: 0.8996 (mmt) cc_final: 0.8777 (mmt)
REVERT: C   36 TRP cc_start: 0.7910 (m100) cc_final: 0.7514 (m100)
REVERT: C   86 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8020 (pp)
REVERT: E   90 GLN cc_start: 0.8730 (pp30) cc_final: 0.8142 (pp30)
REVERT: H   43 GLN cc_start: 0.8607 (mp10) cc_final: 0.8128 (mp10)
REVERT: H   48 MET cc_start: 0.8099 (mtt) cc_final: 0.7852 (mtp)
REVERT: L   63 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7431 (ttp-110)
REVERT: L   81 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8214 (mp10)
  outliers start: 31
  outliers final: 20
  residues processed: 181
  average time/residue: 0.2109
  time to fit residues: 50.1666
Evaluate side-chains
  177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   81 GLN
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
D  27 GLN
** E  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 108 ASN
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.128021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.104252 restraints weight = 11927.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.107322 restraints weight = 7277.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.109428 restraints weight = 5208.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6990  Z= 0.229
  Angle     :  0.674  10.513   9499  Z= 0.341
  Chirality :  0.045   0.202   1028
  Planarity :  0.004   0.047   1226
  Dihedral  :  4.865  30.916    996
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 26.08 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.28), residues: 872
  helix: -4.43 (0.47), residues: 12
  sheet: -1.52 (0.27), residues: 365
  loop : -1.61 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C  99 
 PHE   0.013   0.001   PHE A 490 
 TYR   0.027   0.002   TYR B  60 
 ARG   0.008   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 TRP cc_start: 0.8068 (t60) cc_final: 0.7849 (t60)
REVERT: C   34 MET cc_start: 0.9002 (mmt) cc_final: 0.8790 (mmt)
REVERT: C   36 TRP cc_start: 0.7930 (m100) cc_final: 0.7538 (m100)
REVERT: C   86 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8044 (pp)
REVERT: E    4 MET cc_start: 0.6358 (mmm) cc_final: 0.5903 (mmt)
REVERT: E   90 GLN cc_start: 0.8729 (pp30) cc_final: 0.8397 (pp30)
REVERT: H   43 GLN cc_start: 0.8613 (mp10) cc_final: 0.8185 (mp10)
REVERT: H   48 MET cc_start: 0.8108 (mtt) cc_final: 0.7899 (mtp)
  outliers start: 28
  outliers final: 21
  residues processed: 176
  average time/residue: 0.1967
  time to fit residues: 45.6772
Evaluate side-chains
  177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 155
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 70 optimal weight:    0.0980
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E  37 GLN
E  79 GLN
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.123179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.100085 restraints weight = 12008.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103156 restraints weight = 7015.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.105203 restraints weight = 4880.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6990  Z= 0.222
  Angle     :  0.675  11.756   9499  Z= 0.339
  Chirality :  0.044   0.196   1028
  Planarity :  0.004   0.051   1226
  Dihedral  :  4.842  28.952    996
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.61 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.28), residues: 872
  helix: -4.41 (0.48), residues: 12
  sheet: -1.45 (0.27), residues: 365
  loop : -1.53 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  47 
 HIS   0.002   0.001   HIS C  99 
 PHE   0.012   0.001   PHE A 490 
 TYR   0.024   0.001   TYR C  80 
 ARG   0.008   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: B   47 TRP cc_start: 0.8027 (t60) cc_final: 0.7805 (t60)
REVERT: B  118 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8276 (p)
REVERT: C   34 MET cc_start: 0.8992 (mmt) cc_final: 0.8766 (mmt)
REVERT: C   36 TRP cc_start: 0.7969 (m100) cc_final: 0.7464 (m100)
REVERT: C   86 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8020 (pp)
REVERT: E    4 MET cc_start: 0.6414 (mmm) cc_final: 0.5985 (mmt)
REVERT: H   43 GLN cc_start: 0.8611 (mp10) cc_final: 0.8087 (mp10)
REVERT: H   48 MET cc_start: 0.8164 (mtt) cc_final: 0.7857 (mtp)
REVERT: H   81 MET cc_start: 0.7986 (tmm) cc_final: 0.7372 (tmm)
REVERT: H   89 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8214 (pt0)
REVERT: L   63 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7549 (ttp-110)
  outliers start: 27
  outliers final: 23
  residues processed: 176
  average time/residue: 0.1963
  time to fit residues: 45.5039
Evaluate side-chains
  179 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   81 GLN
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0470
   chunk 15 optimal weight:    0.0370
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
L  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.123342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100451 restraints weight = 12058.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.103523 restraints weight = 6975.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.105671 restraints weight = 4827.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6990  Z= 0.224
  Angle     :  0.688  12.967   9499  Z= 0.347
  Chirality :  0.045   0.193   1028
  Planarity :  0.004   0.048   1226
  Dihedral  :  4.830  27.926    996
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 27.42 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.28), residues: 872
  helix: -4.43 (0.47), residues: 12
  sheet: -1.48 (0.27), residues: 362
  loop : -1.54 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  47 
 HIS   0.002   0.001   HIS C  99 
 PHE   0.012   0.001   PHE A 490 
 TYR   0.021   0.001   TYR E  94 
 ARG   0.009   0.001   ARG C  87 

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

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

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 TRP cc_start: 0.8019 (t60) cc_final: 0.7785 (t60)
REVERT: B  118 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8272 (p)
REVERT: C   34 MET cc_start: 0.8992 (mmt) cc_final: 0.8752 (mmt)
REVERT: C   36 TRP cc_start: 0.7968 (m100) cc_final: 0.7462 (m100)
REVERT: C   86 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8064 (pp)
REVERT: E    4 MET cc_start: 0.6381 (mmm) cc_final: 0.5927 (mmt)
REVERT: E   90 GLN cc_start: 0.8724 (pp30) cc_final: 0.8315 (pp30)
REVERT: H   43 GLN cc_start: 0.8613 (mp10) cc_final: 0.8084 (mp10)
REVERT: H   48 MET cc_start: 0.8146 (mtt) cc_final: 0.7899 (mtp)
REVERT: H   81 MET cc_start: 0.8003 (tmm) cc_final: 0.7420 (tmm)
REVERT: H   89 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8214 (pt0)
  outliers start: 26
  outliers final: 22
  residues processed: 171
  average time/residue: 0.2048
  time to fit residues: 45.7388
Evaluate side-chains
  178 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain L residue   81 GLN
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0030
   chunk 59 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0370
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.7672

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

Flipped N/Q/H residues before XYZ refinement:
E  79 GLN
L  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.123721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.101179 restraints weight = 12002.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.104160 restraints weight = 6910.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.106294 restraints weight = 4797.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6990  Z= 0.230
  Angle     :  0.706  13.203   9499  Z= 0.355
  Chirality :  0.044   0.193   1028
  Planarity :  0.005   0.051   1226
  Dihedral  :  4.857  27.294    996
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.42 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.28), residues: 872
  helix: -4.42 (0.48), residues: 12
  sheet: -1.44 (0.27), residues: 370
  loop : -1.50 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  47 
 HIS   0.002   0.001   HIS C  99 
 PHE   0.012   0.001   PHE A 490 
 TYR   0.025   0.001   TYR C  80 
 ARG   0.009   0.001   ARG C  87 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2774.11 seconds
wall clock time: 50 minutes 36.43 seconds (3036.43 seconds total)