Starting phenix.real_space_refine
on Thu Feb 13 17:38:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ubf_42085/02_2025/8ubf_42085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ubf_42085/02_2025/8ubf_42085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ubf_42085/02_2025/8ubf_42085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ubf_42085/02_2025/8ubf_42085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ubf_42085/02_2025/8ubf_42085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ubf_42085/02_2025/8ubf_42085.cif"
  }
  resolution = 3.61
  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=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     102      5.49       5
     S      36      5.16       5
     C    5560      2.51       5
     N    1682      2.21       5
     O    1911      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 9291
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2593
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 10, 'TRANS': 306}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 976
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "D"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "E"
      Number of atoms: 876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 876
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "F"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "H"
      Number of atoms: 209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 209
          Classifications: {'RNA': 10}
          Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6}
          Link IDs: {'rna3p': 9}
    Chain: "I"
      Number of atoms: 1973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1973
          Classifications: {'RNA': 92}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 16, 'rna3p': 75}
          Chain breaks: 2
  Time building chain proxies: 6.20, per 1000 atoms: 0.67
  Number of scatterers: 9291
  At special positions: 0
  Unit cell: (85, 87, 132, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P     102     15.00
     O    1911      8.00
     N    1682      7.00
     C    5560      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.04
  Conformation dependent library (CDL) restraints added in 806.7 milliseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1654

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 2 sheets defined
      76.2% alpha, 1.8% beta
      32 base pairs and 60 stacking pairs defined.
    Time for finding SS restraints: 3.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 13
    Processing helix  chain 'A' and resid 14 through 27
      removed outlier: 3.558A  pdb=" N   ASP A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 40
      removed outlier: 3.993A  pdb=" N   GLU A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 54
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.558A  pdb=" N   GLY A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.591A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 183 through 199
      removed outlier: 3.733A  pdb=" N   GLN A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL A 197 " --> pdb=" O   TYR A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 241
    Processing helix  chain 'A' and resid 275 through 289
      removed outlier: 4.021A  pdb=" N   ARG A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 307
      removed outlier: 3.892A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.901A  pdb=" N   TYR A 323 " --> pdb=" O   MET A 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 32
      removed outlier: 3.748A  pdb=" N   ARG B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      Proline residue:  B  29  - end of helix
    Processing helix  chain 'B' and resid 38 through 62
      removed outlier: 4.269A  pdb=" N   VAL B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLU B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 87
      removed outlier: 3.880A  pdb=" N   LEU B  68 " --> pdb=" O   GLN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 122
    Processing helix  chain 'C' and resid 12 through 34
      removed outlier: 3.880A  pdb=" N   ARG C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 35 through 37
      No H-bonds generated for 'chain 'C' and resid 35 through 37'
    Processing helix  chain 'C' and resid 38 through 50
    Processing helix  chain 'C' and resid 51 through 60
      removed outlier: 3.519A  pdb=" N   LEU C  55 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 88
      removed outlier: 3.584A  pdb=" N   LEU C  68 " --> pdb=" O   GLN C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 121
    Processing helix  chain 'D' and resid 14 through 32
      removed outlier: 3.825A  pdb=" N   ARG D  22 " --> pdb=" O   GLU D  18 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL D  23 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      Proline residue:  D  29  - end of helix
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 51 through 62
      removed outlier: 3.560A  pdb=" N   LEU D  55 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 86
    Processing helix  chain 'D' and resid 95 through 121
    Processing helix  chain 'E' and resid 13 through 34
      removed outlier: 3.716A  pdb=" N   ARG E  22 " --> pdb=" O   GLU E  18 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      Proline residue:  E  29  - end of helix
    Processing helix  chain 'E' and resid 35 through 37
      No H-bonds generated for 'chain 'E' and resid 35 through 37'
    Processing helix  chain 'E' and resid 38 through 50
    Processing helix  chain 'E' and resid 51 through 61
    Processing helix  chain 'E' and resid 65 through 86
      removed outlier: 3.637A  pdb=" N   ASP E  72 " --> pdb=" O   LEU E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 121
    Processing helix  chain 'F' and resid 14 through 32
      removed outlier: 4.502A  pdb=" N   ARG F  22 " --> pdb=" O   GLU F  18 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL F  23 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      Proline residue:  F  29  - end of helix
    Processing helix  chain 'F' and resid 35 through 37
      No H-bonds generated for 'chain 'F' and resid 35 through 37'
    Processing helix  chain 'F' and resid 38 through 50
    Processing helix  chain 'F' and resid 51 through 61
      removed outlier: 3.523A  pdb=" N   LEU F  55 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 87
      removed outlier: 3.613A  pdb=" N   GLY F  87 " --> pdb=" O   ARG F  83 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 89 through 93
      removed outlier: 3.935A  pdb=" N   HIS F  92 " --> pdb=" O   GLN F  89 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ALA F  93 " --> pdb=" O   LYS F  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 89 through 93'
    Processing helix  chain 'F' and resid 95 through 122
      removed outlier: 4.293A  pdb=" N   LEU F 105 " --> pdb=" O   THR F 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213
      removed outlier: 3.657A  pdb=" N   HIS A 133 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 252 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265

    471 hydrogen bonds defined for protein.
    1392 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      81 hydrogen bonds
      126 hydrogen bond angles
      0 basepair planarities
      32 basepair parallelities
      60 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1251
        1.31 -     1.44: 3278
        1.44 -     1.57: 4914
        1.57 -     1.70: 201
        1.70 -     1.84: 61
  Bond restraints: 9705
  Sorted by residual:
  bond pdb=" N   LYS D  90 "
       pdb=" CA  LYS D  90 "
    ideal  model  delta    sigma   weight residual
    1.463  1.391  0.073 6.90e-03 2.10e+04 1.11e+02
  bond pdb=" CA  LYS D  90 "
       pdb=" C   LYS D  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.596 -0.075 1.08e-02 8.57e+03 4.85e+01
  bond pdb=" C   LYS D  90 "
       pdb=" O   LYS D  90 "
    ideal  model  delta    sigma   weight residual
    1.244  1.181  0.062 9.10e-03 1.21e+04 4.71e+01
  bond pdb=" N   ILE C  88 "
       pdb=" CA  ILE C  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.01e+01
  bond pdb=" CB  TRP A  15 "
       pdb=" CG  TRP A  15 "
    ideal  model  delta    sigma   weight residual
    1.498  1.418  0.080 3.10e-02 1.04e+03 6.62e+00
  ... (remaining 9700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 13178
        2.41 -     4.83: 371
        4.83 -     7.24: 41
        7.24 -     9.66: 12
        9.66 -    12.07: 2
  Bond angle restraints: 13604
  Sorted by residual:
  angle pdb=" N   PRO C  91 "
        pdb=" CA  PRO C  91 "
        pdb=" CB  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     103.25   95.59    7.66 1.05e+00 9.07e-01 5.32e+01
  angle pdb=" O   LYS D  90 "
        pdb=" C   LYS D  90 "
        pdb=" N   PRO D  91 "
      ideal   model   delta    sigma   weight residual
     120.27  125.05   -4.78 6.90e-01 2.10e+00 4.81e+01
  angle pdb=" CA  LYS D  90 "
        pdb=" C   LYS D  90 "
        pdb=" N   PRO D  91 "
      ideal   model   delta    sigma   weight residual
     120.58  116.04    4.54 7.40e-01 1.83e+00 3.76e+01
  angle pdb=" C   LYS D  90 "
        pdb=" N   PRO D  91 "
        pdb=" CA  PRO D  91 "
      ideal   model   delta    sigma   weight residual
     119.84  112.38    7.46 1.25e+00 6.40e-01 3.56e+01
  angle pdb=" N   GLN F  32 "
        pdb=" CA  GLN F  32 "
        pdb=" C   GLN F  32 "
      ideal   model   delta    sigma   weight residual
     113.18  107.68    5.50 1.21e+00 6.83e-01 2.06e+01
  ... (remaining 13599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.29: 5242
       35.29 -    70.58: 648
       70.58 -   105.87: 55
      105.87 -   141.15: 1
      141.15 -   176.44: 3
  Dihedral angle restraints: 5949
    sinusoidal: 3385
      harmonic: 2564
  Sorted by residual:
  dihedral pdb=" O4'   U I  94 "
           pdb=" C1'   U I  94 "
           pdb=" N1    U I  94 "
           pdb=" C2    U I  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   56.23  175.77     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   U I   3 "
           pdb=" C1'   U I   3 "
           pdb=" N1    U I   3 "
           pdb=" C2    U I   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -87.90  -72.10     1      1.50e+01 4.44e-03 2.96e+01
  dihedral pdb=" CA  ALA A 163 "
           pdb=" C   ALA A 163 "
           pdb=" N   THR A 164 "
           pdb=" CA  THR A 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.55   26.45     0      5.00e+00 4.00e-02 2.80e+01
  ... (remaining 5946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1477
       0.087 -    0.174: 101
       0.174 -    0.262: 6
       0.262 -    0.349: 2
       0.349 -    0.436: 3
  Chirality restraints: 1589
  Sorted by residual:
  chirality pdb=" P     U H 118 "
            pdb=" OP1   U H 118 "
            pdb=" OP2   U H 118 "
            pdb=" O5'   U H 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.85   -0.44 2.00e-01 2.50e+01 4.75e+00
  chirality pdb=" P     U I   7 "
            pdb=" OP1   U I   7 "
            pdb=" OP2   U I   7 "
            pdb=" O5'   U I   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.83   -0.42 2.00e-01 2.50e+01 4.44e+00
  chirality pdb=" CB  ILE A 181 "
            pdb=" CA  ILE A 181 "
            pdb=" CG1 ILE A 181 "
            pdb=" CG2 ILE A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.62e+00
  ... (remaining 1586 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  90 "   -0.042 5.00e-02 4.00e+02   6.19e-02 6.14e+00
        pdb=" N   PRO C  91 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G I   4 "   -0.000 2.00e-02 2.50e+03   1.39e-02 5.79e+00
        pdb=" N9    G I   4 "   -0.038 2.00e-02 2.50e+03
        pdb=" C8    G I   4 "    0.019 2.00e-02 2.50e+03
        pdb=" N7    G I   4 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    G I   4 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    G I   4 "   -0.009 2.00e-02 2.50e+03
        pdb=" O6    G I   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G I   4 "    0.007 2.00e-02 2.50e+03
        pdb=" C2    G I   4 "    0.005 2.00e-02 2.50e+03
        pdb=" N2    G I   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    G I   4 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G I   4 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 231 "    0.024 2.00e-02 2.50e+03   1.78e-02 5.54e+00
        pdb=" CG  PHE A 231 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 231 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 231 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 231 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 231 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 231 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 2729
        2.82 -     3.34: 9149
        3.34 -     3.86: 18895
        3.86 -     4.38: 22753
        4.38 -     4.90: 32113
  Nonbonded interactions: 85639
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  31 "
            pdb=" OH  TYR B  11 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG1 THR A 106 "
            pdb=" OD2 ASP A 198 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   LYS C  90 "
            pdb=" C   PRO C  91 "
     model   vdw
     2.369 3.270
  nonbonded pdb=" NE2 HIS B  97 "
            pdb=" OP1   A H 123 "
     model   vdw
     2.419 3.120
  nonbonded pdb=" O   ALA A 108 "
            pdb=" N   ARG A 110 "
     model   vdw
     2.420 3.120
  ... (remaining 85634 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 'B' and resid 13 through 121)
  selection = (chain 'C' and resid 13 through 121)
  selection = (chain 'D' and resid 13 through 121)
  selection = (chain 'E' and resid 13 through 121)
  selection = (chain 'F' and resid 13 through 121)
}

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=0.00 max=1.00 mean=0.99
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.590
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
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      :  0.007   0.080   9705  Z= 0.459
  Angle     :  0.979  12.072  13604  Z= 0.549
  Chirality :  0.053   0.436   1589
  Planarity :  0.008   0.062   1338
  Dihedral  : 24.771 176.442   4295
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  3.23 %
    Allowed  :  9.22 %
    Favored  : 87.56 %
  Rotamer:
    Outliers : 22.69 %
    Allowed  : 12.64 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.90 (0.23), residues: 868
  helix: -1.94 (0.17), residues: 656
  sheet: -3.17 (1.11), residues: 18
  loop : -4.21 (0.35), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.005   TRP A 309 
 HIS   0.023   0.003   HIS C  38 
 PHE   0.040   0.005   PHE A 231 
 TYR   0.026   0.005   TYR A 107 
 ARG   0.010   0.001   ARG A  30 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  498 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 167
    poor density    : 331
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (ptm160)
REVERT: A   14 THR cc_start: 0.7743 (p) cc_final: 0.7498 (p)
REVERT: A   63 TYR cc_start: 0.6104 (m-80) cc_final: 0.5053 (m-80)
REVERT: A   99 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7845 (tm-30)
REVERT: A  102 LEU cc_start: 0.8435 (mt) cc_final: 0.8208 (mp)
REVERT: A  110 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7092 (ptm160)
REVERT: A  128 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8626 (ttt180)
REVERT: A  145 SER cc_start: 0.8724 (m) cc_final: 0.8502 (p)
REVERT: A  156 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8481 (m-30)
REVERT: A  158 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6661 (mttt)
REVERT: A  200 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7562 (mm)
REVERT: A  210 TRP cc_start: 0.9149 (p-90) cc_final: 0.8217 (p-90)
REVERT: A  226 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (tp30)
REVERT: A  258 ILE cc_start: 0.8718 (mp) cc_final: 0.8469 (mp)
REVERT: A  319 MET cc_start: 0.7278 (mtp) cc_final: 0.6976 (ptp)
REVERT: B    1 MET cc_start: 0.7588 (tmm) cc_final: 0.7367 (tmm)
REVERT: B    2 GLU cc_start: 0.8183 (tp30) cc_final: 0.7793 (tp30)
REVERT: B   16 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8748 (tt)
REVERT: B   22 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (ttp-170)
REVERT: B   65 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.7411 (p)
REVERT: B   80 PHE cc_start: 0.8845 (t80) cc_final: 0.8627 (t80)
REVERT: B  105 LEU cc_start: 0.8540 (mt) cc_final: 0.8305 (mp)
REVERT: B  113 LEU cc_start: 0.9138 (tp) cc_final: 0.8930 (tt)
REVERT: B  115 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9116 (p)
REVERT: D   53 VAL cc_start: 0.9239 (t) cc_final: 0.8916 (t)
REVERT: D   68 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9067 (mt)
REVERT: D   69 TYR cc_start: 0.9126 (m-10) cc_final: 0.8639 (m-80)
REVERT: D   77 MET cc_start: 0.8942 (tpt) cc_final: 0.8725 (tpp)
REVERT: D   99 VAL cc_start: 0.7994 (t) cc_final: 0.7751 (t)
REVERT: D  120 VAL cc_start: 0.8318 (t) cc_final: 0.7815 (m)
REVERT: E   43 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8096 (tm-30)
REVERT: E   56 PHE cc_start: 0.8610 (m-10) cc_final: 0.8342 (m-10)
REVERT: E  108 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9081 (tp30)
REVERT: F   21 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8509 (tm-30)
REVERT: F   22 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8906 (mtm-85)
REVERT: F   61 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (tptp)
REVERT: F   69 TYR cc_start: 0.8983 (m-80) cc_final: 0.8580 (m-80)
  outliers start: 167
  outliers final: 25
  residues processed: 422
  average time/residue: 0.3105
  time to fit residues: 163.6460
Evaluate side-chains
  255 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 215
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   82 LYS
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   10 CYS
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   64 GLN
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   63 ASN
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   22 ARG
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   32 GLN
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain F residue   61 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0980
   chunk 56 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A  92 ASN
A 297 GLN
C  92 HIS
C 121 ASN
D  32 GLN
D  89 GLN
D 103 GLN
E  32 GLN
** E  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  92 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.144585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.109428 restraints weight = 20218.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.112528 restraints weight = 12381.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.114470 restraints weight = 9428.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9705  Z= 0.257
  Angle     :  0.718  11.301  13604  Z= 0.374
  Chirality :  0.042   0.258   1589
  Planarity :  0.007   0.140   1338
  Dihedral  : 22.276 172.075   2675
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  8.29 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 18.48 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.29), residues: 868
  helix:  0.10 (0.20), residues: 654
  sheet: -1.84 (1.07), residues: 20
  loop : -3.22 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 116 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.043   0.003   PHE C  80 
 TYR   0.027   0.002   TYR B  69 
 ARG   0.007   0.001   ARG E  36 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 253
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 TYR cc_start: 0.7941 (m-80) cc_final: 0.7656 (m-80)
REVERT: A  145 SER cc_start: 0.8630 (m) cc_final: 0.8386 (p)
REVERT: A  158 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6711 (mttt)
REVERT: A  200 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7556 (mm)
REVERT: A  247 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8355 (t)
REVERT: B   16 ILE cc_start: 0.9615 (tt) cc_final: 0.9312 (tt)
REVERT: C  100 GLU cc_start: 0.6812 (tt0) cc_final: 0.6543 (tt0)
REVERT: C  108 GLU cc_start: 0.6564 (tp30) cc_final: 0.6180 (tp30)
REVERT: D   65 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.6907 (t)
REVERT: D   69 TYR cc_start: 0.8309 (m-10) cc_final: 0.8056 (m-80)
REVERT: F   69 TYR cc_start: 0.7928 (m-80) cc_final: 0.7595 (m-80)
  outliers start: 50
  outliers final: 18
  residues processed: 288
  average time/residue: 0.2739
  time to fit residues: 103.5983
Evaluate side-chains
  226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   63 ASN
Chi-restraints excluded: chain F residue   32 GLN
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue  123 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 2 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 68 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
D  98 GLN
D 103 GLN
E  64 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.144277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.109321 restraints weight = 20660.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112401 restraints weight = 12744.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.114387 restraints weight = 9700.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9705  Z= 0.237
  Angle     :  0.675  10.126  13604  Z= 0.346
  Chirality :  0.040   0.195   1589
  Planarity :  0.006   0.122   1338
  Dihedral  : 21.538 179.739   2597
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.69 %
    Allowed  :  7.49 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.69 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.29), residues: 868
  helix:  0.60 (0.20), residues: 649
  sheet:  0.04 (1.27), residues: 18
  loop : -2.70 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 303 
 HIS   0.007   0.001   HIS F  92 
 PHE   0.047   0.003   PHE C  80 
 TYR   0.013   0.002   TYR F  28 
 ARG   0.008   0.001   ARG A  30 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 227
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7188 (m-30) cc_final: 0.6885 (m-30)
REVERT: A  210 TRP cc_start: 0.8699 (p-90) cc_final: 0.7948 (p-90)
REVERT: B   16 ILE cc_start: 0.9613 (tt) cc_final: 0.9360 (tt)
REVERT: B   32 GLN cc_start: 0.7487 (tt0) cc_final: 0.7049 (tp-100)
REVERT: B   63 ASN cc_start: 0.7667 (p0) cc_final: 0.7048 (p0)
REVERT: B  119 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6668 (ttp-110)
REVERT: C   92 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.5918 (t-90)
REVERT: C  108 GLU cc_start: 0.6605 (tp30) cc_final: 0.6245 (tp30)
REVERT: C  117 ILE cc_start: 0.8849 (mt) cc_final: 0.8520 (mt)
REVERT: D   44 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (mtm)
REVERT: D   52 GLN cc_start: 0.7667 (tp40) cc_final: 0.7418 (tp-100)
REVERT: D   65 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7176 (t)
REVERT: D   69 TYR cc_start: 0.8270 (m-10) cc_final: 0.7983 (m-80)
REVERT: E  108 GLU cc_start: 0.7575 (tp30) cc_final: 0.7253 (tp30)
REVERT: F  113 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8914 (mm)
  outliers start: 36
  outliers final: 14
  residues processed: 251
  average time/residue: 0.2767
  time to fit residues: 90.3637
Evaluate side-chains
  215 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   95 THR
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  123 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 47 optimal weight:    0.1980
   chunk 84 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 28 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0060
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
D  98 GLN
E  38 HIS
E  64 GLN
F  98 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.145154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.110756 restraints weight = 20644.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.113825 restraints weight = 12666.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.115750 restraints weight = 9604.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9705  Z= 0.213
  Angle     :  0.660   9.536  13604  Z= 0.337
  Chirality :  0.039   0.246   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 21.200 179.406   2583
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  7.03 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.32 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.30), residues: 868
  helix:  0.66 (0.20), residues: 652
  sheet:  1.04 (1.42), residues: 18
  loop : -2.45 (0.48), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 303 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.052   0.003   PHE C  80 
 TYR   0.011   0.001   TYR F  28 
 ARG   0.008   0.001   ARG D 111 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7271 (m-30) cc_final: 0.6983 (m-30)
REVERT: A  210 TRP cc_start: 0.8688 (p-90) cc_final: 0.8181 (p-90)
REVERT: B   16 ILE cc_start: 0.9572 (tt) cc_final: 0.9352 (tt)
REVERT: C   92 HIS cc_start: 0.6558 (OUTLIER) cc_final: 0.6026 (t-90)
REVERT: C  108 GLU cc_start: 0.6484 (tp30) cc_final: 0.6209 (tp30)
REVERT: D   44 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7631 (mtm)
REVERT: D   65 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7127 (m)
REVERT: D   89 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7289 (mm-40)
REVERT: F   69 TYR cc_start: 0.7941 (m-80) cc_final: 0.7552 (m-80)
REVERT: F  108 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6203 (tm-30)
  outliers start: 25
  outliers final: 10
  residues processed: 236
  average time/residue: 0.2650
  time to fit residues: 81.8222
Evaluate side-chains
  212 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 199
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain F residue   13 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 48 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
A  57 ASN
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
D  52 GLN
D  92 HIS
D  98 GLN
E  64 GLN
F  13 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.144352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.109931 restraints weight = 21006.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.113023 restraints weight = 12782.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.114969 restraints weight = 9674.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   9705  Z= 0.248
  Angle     :  0.673  10.164  13604  Z= 0.345
  Chirality :  0.039   0.191   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 21.015 178.172   2579
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.26 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.36 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.29), residues: 868
  helix:  0.63 (0.20), residues: 657
  sheet:  0.53 (1.40), residues: 20
  loop : -2.49 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 303 
 HIS   0.007   0.001   HIS D  92 
 PHE   0.038   0.003   PHE B  80 
 TYR   0.020   0.002   TYR E  20 
 ARG   0.009   0.001   ARG B  83 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 209
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7390 (m-30) cc_final: 0.7068 (m-30)
REVERT: A  210 TRP cc_start: 0.8705 (p-90) cc_final: 0.8174 (p-90)
REVERT: B   63 ASN cc_start: 0.7841 (p0) cc_final: 0.7468 (p0)
REVERT: C   92 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.6142 (t-90)
REVERT: C  108 GLU cc_start: 0.6789 (tp30) cc_final: 0.6430 (tp30)
REVERT: D   44 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7697 (mtm)
REVERT: D   64 GLN cc_start: 0.6706 (tp-100) cc_final: 0.6486 (tp-100)
REVERT: D   69 TYR cc_start: 0.8109 (m-80) cc_final: 0.7816 (m-80)
REVERT: F   69 TYR cc_start: 0.7894 (m-80) cc_final: 0.7566 (m-80)
  outliers start: 23
  outliers final: 14
  residues processed: 224
  average time/residue: 0.2736
  time to fit residues: 80.9739
Evaluate side-chains
  209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue   97 HIS
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain F residue   13 GLN
Chi-restraints excluded: chain F residue   97 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 83 optimal weight:    0.3980
   chunk 7 optimal weight:    0.5980
   chunk 90 optimal weight:    8.9990
   chunk 54 optimal weight:    0.0770
   chunk 66 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A  87 GLN
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 HIS
D  98 GLN
E  64 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.145189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.111382 restraints weight = 20753.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.114455 restraints weight = 12704.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.116301 restraints weight = 9613.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.6102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   9705  Z= 0.206
  Angle     :  0.651  10.612  13604  Z= 0.332
  Chirality :  0.038   0.185   1589
  Planarity :  0.006   0.111   1338
  Dihedral  : 20.869 176.960   2578
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.34 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.17 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.29), residues: 868
  helix:  0.67 (0.20), residues: 659
  sheet:  1.37 (1.37), residues: 18
  loop : -2.44 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 303 
 HIS   0.006   0.001   HIS A   5 
 PHE   0.050   0.002   PHE C  80 
 TYR   0.013   0.001   TYR E  26 
 ARG   0.010   0.001   ARG D 111 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7279 (m-30) cc_final: 0.7006 (m-30)
REVERT: A  135 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7545 (tp)
REVERT: A  210 TRP cc_start: 0.8676 (p-90) cc_final: 0.8169 (p-90)
REVERT: C   92 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6094 (t-90)
REVERT: C  108 GLU cc_start: 0.6670 (tp30) cc_final: 0.6344 (tp30)
REVERT: D   44 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7588 (mtm)
REVERT: D   89 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6873 (mm-40)
REVERT: E  108 GLU cc_start: 0.7837 (tp30) cc_final: 0.6870 (tp30)
REVERT: F   69 TYR cc_start: 0.7930 (m-80) cc_final: 0.7556 (m-80)
REVERT: F  108 GLU cc_start: 0.6676 (tp30) cc_final: 0.6460 (tp30)
  outliers start: 22
  outliers final: 14
  residues processed: 226
  average time/residue: 0.2472
  time to fit residues: 74.7763
Evaluate side-chains
  209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 192
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain F residue   97 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
** A  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
C  98 GLN
D  52 GLN
D  92 HIS
D  98 GLN
E  64 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.144350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.111539 restraints weight = 20696.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114672 restraints weight = 13828.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.115109 restraints weight = 9527.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.6269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   9705  Z= 0.242
  Angle     :  0.686  10.101  13604  Z= 0.349
  Chirality :  0.040   0.239   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 20.806 176.909   2578
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.14 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 27.45 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.29), residues: 868
  helix:  0.56 (0.20), residues: 660
  sheet:  1.48 (1.32), residues: 18
  loop : -2.24 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 303 
 HIS   0.013   0.001   HIS A 313 
 PHE   0.046   0.002   PHE C  80 
 TYR   0.044   0.002   TYR D  69 
 ARG   0.014   0.001   ARG D 111 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7287 (m-30) cc_final: 0.7006 (m-30)
REVERT: A  135 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7704 (tp)
REVERT: A  210 TRP cc_start: 0.8588 (p-90) cc_final: 0.8104 (p-90)
REVERT: B   79 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6996 (mtt-85)
REVERT: C   92 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.6238 (t-90)
REVERT: C  108 GLU cc_start: 0.6636 (tp30) cc_final: 0.6288 (tp30)
REVERT: D   44 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7622 (mtm)
REVERT: E   14 MET cc_start: 0.6605 (mmt) cc_final: 0.6220 (tpt)
REVERT: E  108 GLU cc_start: 0.7523 (tp30) cc_final: 0.6448 (tp30)
REVERT: F   69 TYR cc_start: 0.7943 (m-80) cc_final: 0.7657 (m-80)
  outliers start: 26
  outliers final: 12
  residues processed: 219
  average time/residue: 0.2559
  time to fit residues: 74.4505
Evaluate side-chains
  201 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   30 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 89 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A  27 HIS
A  57 ASN
A  87 GLN
A  92 ASN
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
C 121 ASN
D  92 HIS
D  98 GLN
E  64 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.145752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.111536 restraints weight = 20998.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.114556 restraints weight = 12873.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.116474 restraints weight = 9792.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.6572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   9705  Z= 0.224
  Angle     :  0.681  10.919  13604  Z= 0.347
  Chirality :  0.039   0.176   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 20.724 175.750   2578
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.03 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 27.45 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.29), residues: 868
  helix:  0.56 (0.20), residues: 663
  sheet:  1.71 (1.32), residues: 18
  loop : -2.10 (0.49), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 303 
 HIS   0.010   0.001   HIS A 313 
 PHE   0.040   0.003   PHE B  80 
 TYR   0.011   0.001   TYR F  28 
 ARG   0.014   0.001   ARG D 111 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 195
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7307 (m-30) cc_final: 0.7062 (m-30)
REVERT: A  135 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7604 (tp)
REVERT: A  210 TRP cc_start: 0.8651 (p-90) cc_final: 0.8120 (p-90)
REVERT: C   92 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.6151 (t-90)
REVERT: C  108 GLU cc_start: 0.6611 (tp30) cc_final: 0.6282 (tp30)
REVERT: D   44 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7560 (mtm)
REVERT: D   52 GLN cc_start: 0.7723 (tp40) cc_final: 0.7464 (tp-100)
REVERT: D   95 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.6980 (m)
REVERT: D  108 GLU cc_start: 0.5795 (tm-30) cc_final: 0.5148 (tm-30)
REVERT: E   14 MET cc_start: 0.6753 (mmt) cc_final: 0.6128 (tpt)
REVERT: E   43 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: E  108 GLU cc_start: 0.7566 (tp30) cc_final: 0.6967 (tp30)
REVERT: F   43 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8050 (tt0)
REVERT: F   69 TYR cc_start: 0.7860 (m-80) cc_final: 0.7596 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 211
  average time/residue: 0.2437
  time to fit residues: 68.6072
Evaluate side-chains
  201 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   53 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A  27 HIS
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
D  92 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.143493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.108823 restraints weight = 20554.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.111809 restraints weight = 12754.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113640 restraints weight = 9789.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.6653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   9705  Z= 0.274
  Angle     :  0.711  11.392  13604  Z= 0.364
  Chirality :  0.041   0.264   1589
  Planarity :  0.007   0.114   1338
  Dihedral  : 20.715 176.280   2578
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.37 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 27.58 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.29), residues: 868
  helix:  0.45 (0.20), residues: 664
  sheet:  1.22 (1.34), residues: 20
  loop : -2.14 (0.49), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 303 
 HIS   0.011   0.001   HIS A 313 
 PHE   0.042   0.003   PHE B  80 
 TYR   0.024   0.002   TYR E  20 
 ARG   0.018   0.001   ARG D 111 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7454 (m-30) cc_final: 0.7166 (m-30)
REVERT: A  135 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7718 (tp)
REVERT: A  210 TRP cc_start: 0.8695 (p-90) cc_final: 0.8136 (p-90)
REVERT: B   32 GLN cc_start: 0.7379 (tt0) cc_final: 0.7126 (tt0)
REVERT: C   92 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.6123 (t-90)
REVERT: C  108 GLU cc_start: 0.6651 (tp30) cc_final: 0.6284 (tp30)
REVERT: D   44 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7634 (mtm)
REVERT: D   52 GLN cc_start: 0.7916 (tp40) cc_final: 0.7669 (tp-100)
REVERT: D   99 VAL cc_start: 0.8285 (t) cc_final: 0.8066 (t)
REVERT: E   14 MET cc_start: 0.6525 (mmt) cc_final: 0.6234 (tpt)
REVERT: E   56 PHE cc_start: 0.7695 (m-80) cc_final: 0.7475 (m-10)
REVERT: E  108 GLU cc_start: 0.7568 (tp30) cc_final: 0.7307 (tp30)
REVERT: F   69 TYR cc_start: 0.7926 (m-80) cc_final: 0.7648 (m-80)
REVERT: F  108 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6539 (tp30)
  outliers start: 19
  outliers final: 14
  residues processed: 201
  average time/residue: 0.2378
  time to fit residues: 64.2847
Evaluate side-chains
  201 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain F residue   32 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A  87 GLN
C  64 GLN
D  13 GLN
D  92 HIS
D  98 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.144372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.109819 restraints weight = 20779.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.112866 restraints weight = 12889.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.114756 restraints weight = 9854.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.6811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   9705  Z= 0.248
  Angle     :  0.713  11.575  13604  Z= 0.365
  Chirality :  0.040   0.265   1589
  Planarity :  0.007   0.115   1338
  Dihedral  : 20.680 175.828   2578
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.26 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 27.04 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.29), residues: 868
  helix:  0.48 (0.20), residues: 664
  sheet:  2.39 (1.38), residues: 18
  loop : -2.15 (0.49), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 303 
 HIS   0.014   0.001   HIS A  27 
 PHE   0.044   0.003   PHE C  80 
 TYR   0.012   0.002   TYR F  28 
 ARG   0.016   0.001   ARG D 111 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7345 (m-30) cc_final: 0.7078 (m-30)
REVERT: A  135 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7704 (tp)
REVERT: A  210 TRP cc_start: 0.8694 (p-90) cc_final: 0.8128 (p-90)
REVERT: B   79 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.7076 (mtt180)
REVERT: C   92 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.6154 (t-90)
REVERT: C  108 GLU cc_start: 0.6533 (tp30) cc_final: 0.6206 (tp30)
REVERT: D   44 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7595 (mtm)
REVERT: D   52 GLN cc_start: 0.7902 (tp40) cc_final: 0.7635 (tp-100)
REVERT: E   14 MET cc_start: 0.6689 (mmt) cc_final: 0.6114 (tpt)
REVERT: F   69 TYR cc_start: 0.7902 (m-80) cc_final: 0.7625 (m-80)
REVERT: F  108 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6602 (tp30)
  outliers start: 19
  outliers final: 13
  residues processed: 206
  average time/residue: 0.2419
  time to fit residues: 66.8271
Evaluate side-chains
  202 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain F residue   32 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  27 HIS
C  64 GLN
D  92 HIS
D  98 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.143699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.109298 restraints weight = 20643.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.112301 restraints weight = 12810.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.114188 restraints weight = 9796.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.6948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   9705  Z= 0.251
  Angle     :  0.723  11.582  13604  Z= 0.372
  Chirality :  0.040   0.224   1589
  Planarity :  0.006   0.113   1338
  Dihedral  : 20.656 175.292   2578
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.37 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 27.85 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.29), residues: 868
  helix:  0.44 (0.20), residues: 665
  sheet:  2.60 (1.40), residues: 18
  loop : -2.09 (0.50), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 303 
 HIS   0.007   0.001   HIS A 313 
 PHE   0.043   0.003   PHE C  80 
 TYR   0.025   0.002   TYR E  20 
 ARG   0.016   0.001   ARG B  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3276.14 seconds
wall clock time: 59 minutes 56.68 seconds (3596.68 seconds total)