Starting phenix.real_space_refine
on Fri Oct 10 21:38:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ubf_42085/10_2025/8ubf_42085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ubf_42085/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ubf_42085/10_2025/8ubf_42085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ubf_42085/10_2025/8ubf_42085.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ubf_42085/10_2025/8ubf_42085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ubf_42085/10_2025/8ubf_42085.map"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.49, per 1000 atoms: 0.27
  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: 1.03
  Conformation dependent library (CDL) restraints added in 280.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.40
  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: 1.60

  Time building geometry restraints manager: 1.27 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.600
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.570
-------------------------------------------------------------------------------
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= 0.348
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.010   0.001   ARG A  30 
 TYR   0.026   0.005   TYR A 107 
 PHE   0.040   0.005   PHE A 231 
 TRP   0.035   0.005   TRP A 309 
 HIS   0.023   0.003   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 ( 9705)
  covalent geometry    : angle       0.97915 (13604)
  hydrogen bonds       : bond        0.19722 (  552)
  hydrogen bonds       : angle       8.51678 ( 1518)

*********************** 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  : 0.326 
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: 0.7497 (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: 0.7093 (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: 0.8216 (p-90)
REVERT: A  226 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (tp30)
REVERT: A  265 ILE cc_start: 0.9212 (mt) cc_final: 0.8940 (tp)
REVERT: A  319 MET cc_start: 0.7278 (mtp) cc_final: 0.6980 (ptp)
REVERT: B    1 MET cc_start: 0.7588 (tmm) cc_final: 0.7379 (tmm)
REVERT: B    2 GLU cc_start: 0.8183 (tp30) cc_final: 0.7458 (pp20)
REVERT: B   16 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8749 (tt)
REVERT: B   22 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8692 (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: 0.8296 (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: 0.9094 (mt)
REVERT: D   69 TYR cc_start: 0.9126 (m-10) cc_final: 0.8638 (m-80)
REVERT: D   77 MET cc_start: 0.8942 (tpt) cc_final: 0.8724 (tpp)
REVERT: D   99 VAL cc_start: 0.7994 (t) cc_final: 0.7752 (t)
REVERT: D  120 VAL cc_start: 0.8318 (t) cc_final: 0.7814 (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: 0.8508 (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: 0.1448
  time to fit residues: 77.0057
Evaluate side-chains
  257 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 217
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
E  38 HIS
** 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 = 0.4200 r_free = 0.4200 target = 0.146034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.111621 restraints weight = 20443.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.114770 restraints weight = 12309.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.116784 restraints weight = 9294.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.117982 restraints weight = 7909.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.118535 restraints weight = 7197.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9705  Z= 0.173
  Angle     :  0.714  11.804  13604  Z= 0.372
  Chirality :  0.042   0.248   1589
  Planarity :  0.007   0.139   1338
  Dihedral  : 22.254 171.475   2675
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  8.29 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 19.16 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.28), residues: 868
  helix:  0.07 (0.20), residues: 660
  sheet: -1.86 (1.06), residues: 20
  loop : -3.35 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  36 
 TYR   0.028   0.002   TYR B  69 
 PHE   0.046   0.003   PHE C  80 
 TRP   0.013   0.002   TRP B 116 
 HIS   0.005   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9705)
  covalent geometry    : angle       0.71411 (13604)
  hydrogen bonds       : bond        0.05348 (  552)
  hydrogen bonds       : angle       4.52649 ( 1518)

*********************** 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
  310 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 260
  time to evaluate  : 0.310 
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: A   83 ASP cc_start: 0.7379 (m-30) cc_final: 0.6899 (m-30)
REVERT: A  107 TYR cc_start: 0.7956 (m-80) cc_final: 0.7424 (m-80)
REVERT: A  145 SER cc_start: 0.8630 (m) cc_final: 0.8363 (p)
REVERT: A  200 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7539 (mm)
REVERT: A  247 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8321 (t)
REVERT: B   16 ILE cc_start: 0.9604 (tt) cc_final: 0.9267 (tt)
REVERT: B   21 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7207 (tm-30)
REVERT: C  100 GLU cc_start: 0.6822 (tt0) cc_final: 0.6520 (tt0)
REVERT: C  108 GLU cc_start: 0.6484 (tp30) cc_final: 0.6131 (tp30)
REVERT: D   44 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7887 (mtm)
REVERT: D   65 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7359 (t)
REVERT: D   69 TYR cc_start: 0.8239 (m-10) cc_final: 0.8015 (m-80)
REVERT: F   69 TYR cc_start: 0.7855 (m-80) cc_final: 0.7568 (m-80)
  outliers start: 50
  outliers final: 17
  residues processed: 294
  average time/residue: 0.1261
  time to fit residues: 48.5707
Evaluate side-chains
  226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 205
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
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   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
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   95 THR
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain F residue   32 GLN
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 65 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
C  13 GLN
C  64 GLN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 103 GLN
E  32 GLN
E  38 HIS
** E  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  13 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.144694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110942 restraints weight = 20506.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.113866 restraints weight = 12748.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.115749 restraints weight = 9760.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.116900 restraints weight = 8335.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.117455 restraints weight = 7609.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.4912

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= 0.160
  Angle     :  0.672   7.495  13604  Z= 0.344
  Chirality :  0.040   0.196   1589
  Planarity :  0.006   0.119   1338
  Dihedral  : 21.502 178.841   2591
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.69 %
    Allowed  :  7.14 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.29), residues: 868
  helix:  0.58 (0.20), residues: 649
  sheet:  0.07 (1.27), residues: 18
  loop : -2.69 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  30 
 TYR   0.013   0.002   TYR A 213 
 PHE   0.049   0.003   PHE C  80 
 TRP   0.015   0.001   TRP A 303 
 HIS   0.010   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9705)
  covalent geometry    : angle       0.67173 (13604)
  hydrogen bonds       : bond        0.04882 (  552)
  hydrogen bonds       : angle       4.30444 ( 1518)

*********************** 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
  259 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 224
  time to evaluate  : 0.312 
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: 0.7306 (m-30) cc_final: 0.7083 (m-30)
REVERT: A  210 TRP cc_start: 0.8722 (p-90) cc_final: 0.7957 (p-90)
REVERT: B   16 ILE cc_start: 0.9589 (tt) cc_final: 0.9324 (tt)
REVERT: C  108 GLU cc_start: 0.6535 (tp30) cc_final: 0.6196 (tp30)
REVERT: C  117 ILE cc_start: 0.8828 (mt) cc_final: 0.8462 (mt)
REVERT: D   44 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7991 (mtp)
REVERT: D   65 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.6655 (t)
REVERT: E  108 GLU cc_start: 0.7537 (tp30) cc_final: 0.7254 (tp30)
REVERT: F   69 TYR cc_start: 0.7887 (m-80) cc_final: 0.7621 (m-80)
  outliers start: 35
  outliers final: 18
  residues processed: 249
  average time/residue: 0.1182
  time to fit residues: 39.0716
Evaluate side-chains
  215 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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   95 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   62 SER
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  123 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 8 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.144793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.110380 restraints weight = 20909.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.113482 restraints weight = 12818.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115394 restraints weight = 9767.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.116303 restraints weight = 8354.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.117122 restraints weight = 7703.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   9705  Z= 0.147
  Angle     :  0.647   9.437  13604  Z= 0.333
  Chirality :  0.038   0.194   1589
  Planarity :  0.006   0.113   1338
  Dihedral  : 21.163 179.490   2583
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.91 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 24.46 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.29), residues: 868
  helix:  0.61 (0.20), residues: 654
  sheet:  1.11 (1.45), residues: 18
  loop : -2.51 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  30 
 TYR   0.035   0.002   TYR D  69 
 PHE   0.050   0.003   PHE C  80 
 TRP   0.007   0.001   TRP A 303 
 HIS   0.003   0.001   HIS F  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9705)
  covalent geometry    : angle       0.64737 (13604)
  hydrogen bonds       : bond        0.04721 (  552)
  hydrogen bonds       : angle       4.14155 ( 1518)

*********************** 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
  241 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 TRP cc_start: 0.8681 (p-90) cc_final: 0.8166 (p-90)
REVERT: B   16 ILE cc_start: 0.9583 (tt) cc_final: 0.9351 (tt)
REVERT: B   63 ASN cc_start: 0.7754 (p0) cc_final: 0.7237 (p0)
REVERT: B  119 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6700 (ttp-110)
REVERT: C  108 GLU cc_start: 0.6471 (tp30) cc_final: 0.6212 (tp30)
REVERT: C  117 ILE cc_start: 0.8839 (mt) cc_final: 0.8622 (mt)
REVERT: D   44 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (mtp)
REVERT: E   43 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8040 (tm-30)
REVERT: F   69 TYR cc_start: 0.7920 (m-80) cc_final: 0.7482 (m-80)
REVERT: F  108 GLU cc_start: 0.6935 (tp30) cc_final: 0.6297 (tm-30)
  outliers start: 27
  outliers final: 12
  residues processed: 231
  average time/residue: 0.1192
  time to fit residues: 36.4531
Evaluate side-chains
  208 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 194
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
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 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   44 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain F residue  123 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 89 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 91 optimal weight:   10.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
C  64 GLN
D  52 GLN
D  92 HIS
D  98 GLN
E  64 GLN
F  13 GLN
F  98 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.144025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.108903 restraints weight = 20555.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.111956 restraints weight = 12677.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113554 restraints weight = 9645.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.114787 restraints weight = 8356.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.115390 restraints weight = 7633.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.5807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   9705  Z= 0.162
  Angle     :  0.661   8.567  13604  Z= 0.342
  Chirality :  0.038   0.191   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 21.008 177.734   2578
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.83 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.63 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.29), residues: 868
  helix:  0.54 (0.20), residues: 654
  sheet:  0.49 (1.42), residues: 20
  loop : -2.37 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  83 
 TYR   0.020   0.002   TYR E  20 
 PHE   0.033   0.003   PHE C  80 
 TRP   0.008   0.001   TRP A 303 
 HIS   0.003   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9705)
  covalent geometry    : angle       0.66081 (13604)
  hydrogen bonds       : bond        0.04835 (  552)
  hydrogen bonds       : angle       4.19731 ( 1518)

*********************** 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
  231 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 TRP cc_start: 0.8726 (p-90) cc_final: 0.8185 (p-90)
REVERT: B   16 ILE cc_start: 0.9583 (tt) cc_final: 0.9382 (tt)
REVERT: B   63 ASN cc_start: 0.7714 (p0) cc_final: 0.7501 (p0)
REVERT: B   79 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7122 (mtt-85)
REVERT: B  119 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6678 (ttp-110)
REVERT: D   43 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7116 (tt0)
REVERT: E   14 MET cc_start: 0.6587 (mmt) cc_final: 0.6277 (tpt)
REVERT: F   69 TYR cc_start: 0.7876 (m-80) cc_final: 0.7642 (m-80)
REVERT: F  108 GLU cc_start: 0.6835 (tp30) cc_final: 0.6255 (tm-30)
  outliers start: 23
  outliers final: 16
  residues processed: 223
  average time/residue: 0.1153
  time to fit residues: 34.4879
Evaluate side-chains
  208 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 191
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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   44 MET
Chi-restraints excluded: chain B residue   95 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   62 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue   97 HIS
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   13 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 2 optimal weight:    0.4980
   chunk 89 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
C  98 GLN
D  52 GLN
D  98 GLN
D 103 GLN
** E  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  64 GLN
F  98 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.142885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.108122 restraints weight = 20541.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.111045 restraints weight = 12884.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.112905 restraints weight = 9823.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.114060 restraints weight = 8412.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.114565 restraints weight = 7692.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.6007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   9705  Z= 0.180
  Angle     :  0.684  10.149  13604  Z= 0.349
  Chirality :  0.039   0.190   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 20.953 178.003   2578
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.68 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 27.04 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.29), residues: 868
  helix:  0.57 (0.20), residues: 656
  sheet:  0.50 (1.40), residues: 20
  loop : -2.43 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 111 
 TYR   0.048   0.002   TYR D  69 
 PHE   0.033   0.002   PHE C  80 
 TRP   0.019   0.001   TRP A 303 
 HIS   0.012   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9705)
  covalent geometry    : angle       0.68364 (13604)
  hydrogen bonds       : bond        0.04786 (  552)
  hydrogen bonds       : angle       4.27760 ( 1518)

*********************** 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
  225 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7659 (tp)
REVERT: A  210 TRP cc_start: 0.8754 (p-90) cc_final: 0.8187 (p-90)
REVERT: B   63 ASN cc_start: 0.7811 (p0) cc_final: 0.7349 (p0)
REVERT: B   79 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7079 (mtt-85)
REVERT: C  108 GLU cc_start: 0.6839 (tp30) cc_final: 0.6547 (tp30)
REVERT: D   43 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7071 (tt0)
REVERT: E   14 MET cc_start: 0.6548 (mmt) cc_final: 0.6250 (tpt)
REVERT: E  108 GLU cc_start: 0.7716 (tp30) cc_final: 0.6649 (tp30)
REVERT: F   69 TYR cc_start: 0.7889 (m-80) cc_final: 0.7526 (m-80)
REVERT: F  108 GLU cc_start: 0.6922 (tp30) cc_final: 0.6364 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 218
  average time/residue: 0.1139
  time to fit residues: 33.5062
Evaluate side-chains
  210 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  275 SER
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   95 THR
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   92 HIS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  103 GLN
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  123 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
D  52 GLN
D  98 GLN
E  38 HIS
E  64 GLN
F  98 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.143888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.109496 restraints weight = 20725.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.112558 restraints weight = 12719.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114415 restraints weight = 9683.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115312 restraints weight = 8292.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.116123 restraints weight = 7656.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.6225

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= 0.158
  Angle     :  0.679  10.307  13604  Z= 0.345
  Chirality :  0.039   0.184   1589
  Planarity :  0.006   0.112   1338
  Dihedral  : 20.845 177.071   2578
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.57 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 26.77 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.29), residues: 868
  helix:  0.63 (0.20), residues: 656
  sheet:  1.32 (1.39), residues: 18
  loop : -2.37 (0.47), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  83 
 TYR   0.024   0.002   TYR E  20 
 PHE   0.046   0.003   PHE B  80 
 TRP   0.022   0.001   TRP A 303 
 HIS   0.010   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9705)
  covalent geometry    : angle       0.67864 (13604)
  hydrogen bonds       : bond        0.04785 (  552)
  hydrogen bonds       : angle       4.26779 ( 1518)

*********************** 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
  223 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7368 (m-30) cc_final: 0.7082 (m-30)
REVERT: A  135 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7642 (tp)
REVERT: A  210 TRP cc_start: 0.8735 (p-90) cc_final: 0.8184 (p-90)
REVERT: C  108 GLU cc_start: 0.6712 (tp30) cc_final: 0.6412 (tp30)
REVERT: E   14 MET cc_start: 0.6620 (mmt) cc_final: 0.6038 (tpt)
REVERT: E  108 GLU cc_start: 0.7506 (tp30) cc_final: 0.6644 (tp30)
REVERT: F  108 GLU cc_start: 0.6890 (tp30) cc_final: 0.6341 (tm-30)
  outliers start: 28
  outliers final: 20
  residues processed: 215
  average time/residue: 0.1113
  time to fit residues: 32.5191
Evaluate side-chains
  207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  275 SER
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 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   95 THR
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   92 HIS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue   97 HIS
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  123 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 87 optimal weight:   20.0000
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 29 optimal weight:    8.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
D  32 GLN
D  98 GLN
E  64 GLN
F  98 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.144964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.110485 restraints weight = 20536.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113500 restraints weight = 12781.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.115409 restraints weight = 9755.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.115810 restraints weight = 8367.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.116749 restraints weight = 7913.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.6504

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= 0.148
  Angle     :  0.685  11.492  13604  Z= 0.348
  Chirality :  0.039   0.176   1589
  Planarity :  0.006   0.113   1338
  Dihedral  : 20.719 175.505   2578
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.91 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.04 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.29), residues: 868
  helix:  0.57 (0.20), residues: 659
  sheet:  1.59 (1.33), residues: 18
  loop : -2.35 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 111 
 TYR   0.014   0.001   TYR F  69 
 PHE   0.041   0.002   PHE B  80 
 TRP   0.025   0.001   TRP A 303 
 HIS   0.011   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9705)
  covalent geometry    : angle       0.68458 (13604)
  hydrogen bonds       : bond        0.04714 (  552)
  hydrogen bonds       : angle       4.31135 ( 1518)

*********************** 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: 22
    poor density    : 196
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7324 (m-30) cc_final: 0.7050 (m-30)
REVERT: A  135 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7720 (tp)
REVERT: A  210 TRP cc_start: 0.8683 (p-90) cc_final: 0.8137 (p-90)
REVERT: B    2 GLU cc_start: 0.7003 (pp20) cc_final: 0.6761 (pp20)
REVERT: B   32 GLN cc_start: 0.7342 (tt0) cc_final: 0.7123 (tt0)
REVERT: B   79 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.7056 (mtt-85)
REVERT: C  108 GLU cc_start: 0.6585 (tp30) cc_final: 0.6267 (tp30)
REVERT: E   14 MET cc_start: 0.6452 (mmt) cc_final: 0.6010 (tpt)
REVERT: E  108 GLU cc_start: 0.7479 (tp30) cc_final: 0.6464 (tp30)
REVERT: F   43 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8031 (tt0)
REVERT: F  108 GLU cc_start: 0.6934 (tp30) cc_final: 0.6439 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 213
  average time/residue: 0.1136
  time to fit residues: 32.6531
Evaluate side-chains
  201 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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  244 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   95 THR
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   92 HIS
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 F residue  123 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    0.3980
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   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  57 ASN
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
D  52 GLN
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 = 0.4177 r_free = 0.4177 target = 0.144213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.109815 restraints weight = 20560.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.112750 restraints weight = 12884.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114523 restraints weight = 9882.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.115439 restraints weight = 8505.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.116200 restraints weight = 7841.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.6654

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= 0.164
  Angle     :  0.725  13.200  13604  Z= 0.369
  Chirality :  0.040   0.222   1589
  Planarity :  0.006   0.114   1338
  Dihedral  : 20.648 174.521   2578
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.57 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.90 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.29), residues: 868
  helix:  0.48 (0.20), residues: 662
  sheet:  1.91 (1.36), residues: 18
  loop : -2.19 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E 111 
 TYR   0.033   0.002   TYR F  69 
 PHE   0.042   0.002   PHE B  80 
 TRP   0.028   0.001   TRP A 303 
 HIS   0.009   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9705)
  covalent geometry    : angle       0.72493 (13604)
  hydrogen bonds       : bond        0.04764 (  552)
  hydrogen bonds       : angle       4.42601 ( 1518)

*********************** 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
  211 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7398 (m-30) cc_final: 0.7099 (m-30)
REVERT: A  135 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7697 (tp)
REVERT: A  210 TRP cc_start: 0.8708 (p-90) cc_final: 0.8137 (p-90)
REVERT: B   79 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.7053 (mtt-85)
REVERT: C  108 GLU cc_start: 0.6671 (tp30) cc_final: 0.6363 (tp30)
REVERT: E   14 MET cc_start: 0.6522 (mmt) cc_final: 0.6069 (tpt)
REVERT: E   43 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: E  108 GLU cc_start: 0.7521 (tp30) cc_final: 0.7279 (tp30)
REVERT: F   69 TYR cc_start: 0.7761 (m-80) cc_final: 0.7466 (m-80)
REVERT: F  108 GLU cc_start: 0.6928 (tp30) cc_final: 0.6378 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 204
  average time/residue: 0.1156
  time to fit residues: 31.7479
Evaluate side-chains
  202 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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  244 LEU
Chi-restraints excluded: chain A residue  261 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   95 THR
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   92 HIS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   30 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  52 GLN
D  98 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.144047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.109424 restraints weight = 20707.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.112321 restraints weight = 13035.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114195 restraints weight = 9972.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115352 restraints weight = 8529.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.115567 restraints weight = 7813.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.6764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   9705  Z= 0.175
  Angle     :  0.733  11.859  13604  Z= 0.375
  Chirality :  0.041   0.205   1589
  Planarity :  0.006   0.111   1338
  Dihedral  : 20.644 175.383   2578
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.80 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.90 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.29), residues: 868
  helix:  0.45 (0.20), residues: 663
  sheet:  2.06 (1.36), residues: 18
  loop : -2.21 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  83 
 TYR   0.017   0.002   TYR F  69 
 PHE   0.040   0.003   PHE B  80 
 TRP   0.030   0.002   TRP A 303 
 HIS   0.009   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9705)
  covalent geometry    : angle       0.73332 (13604)
  hydrogen bonds       : bond        0.04808 (  552)
  hydrogen bonds       : angle       4.46583 ( 1518)

********************** 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
  219 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7406 (m-30) cc_final: 0.7099 (m-30)
REVERT: A  135 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7745 (tp)
REVERT: A  210 TRP cc_start: 0.8732 (p-90) cc_final: 0.8162 (p-90)
REVERT: B   37 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8069 (ttpp)
REVERT: B   79 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.7083 (mtt-85)
REVERT: C  108 GLU cc_start: 0.6687 (tp30) cc_final: 0.6358 (tp30)
REVERT: E   14 MET cc_start: 0.6491 (mmt) cc_final: 0.6040 (tpt)
REVERT: E  108 GLU cc_start: 0.7456 (tp30) cc_final: 0.6922 (tp30)
REVERT: F   61 LYS cc_start: 0.7885 (mptt) cc_final: 0.7564 (tptp)
REVERT: F   69 TYR cc_start: 0.7711 (m-80) cc_final: 0.7380 (m-80)
REVERT: F  108 GLU cc_start: 0.6832 (tp30) cc_final: 0.6258 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 211
  average time/residue: 0.1154
  time to fit residues: 32.6130
Evaluate side-chains
  209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 189
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  244 LEU
Chi-restraints excluded: chain A residue  261 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   95 THR
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue   92 HIS
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 E residue   53 VAL
Chi-restraints excluded: chain F residue  123 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   chunk 46 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 GLN
** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  52 GLN
D  98 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.143730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.109469 restraints weight = 20745.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.112366 restraints weight = 13009.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114133 restraints weight = 9979.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.115207 restraints weight = 8624.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.115723 restraints weight = 7927.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.6912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   9705  Z= 0.173
  Angle     :  0.745  11.808  13604  Z= 0.381
  Chirality :  0.041   0.195   1589
  Planarity :  0.006   0.113   1338
  Dihedral  : 20.636 174.643   2578
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.45 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 27.04 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.29), residues: 868
  helix:  0.41 (0.20), residues: 661
  sheet:  2.23 (1.35), residues: 18
  loop : -2.20 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG E 111 
 TYR   0.025   0.002   TYR E  20 
 PHE   0.038   0.003   PHE B  80 
 TRP   0.028   0.002   TRP A 303 
 HIS   0.012   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9705)
  covalent geometry    : angle       0.74549 (13604)
  hydrogen bonds       : bond        0.04819 (  552)
  hydrogen bonds       : angle       4.49369 ( 1518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1879.20 seconds
wall clock time: 33 minutes 18.68 seconds (1998.68 seconds total)