Starting phenix.real_space_refine
on Wed Sep 17 20:54:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i7t_52661/09_2025/9i7t_52661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i7t_52661/09_2025/9i7t_52661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i7t_52661/09_2025/9i7t_52661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i7t_52661/09_2025/9i7t_52661.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i7t_52661/09_2025/9i7t_52661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i7t_52661/09_2025/9i7t_52661.map"
  }
  resolution = 3.8
  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=   0.005 sd=   0.049
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      11      5.49       5
     S      34      5.16       5
     C    7316      2.51       5
     N    1817      2.21       5
     O    2160      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11338
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "C"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 718
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
    Chain: "E"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 326
          Classifications: {'peptide': 43}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 39}
    Chain: "G"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 298
          Classifications: {'peptide': 41}
          Link IDs: {'TRANS': 40}
    Chain: "I"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 410
          Classifications: {'peptide': 51}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46}
    Chain: "K"
      Number of atoms: 1093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1093
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 5, 'TRANS': 129}
    Chain: "A"
      Number of atoms: 2466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2466
          Classifications: {'peptide': 318}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 718
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
    Chain: "C"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 121
          Unusual residues: {'DU0': 1, 'PC1': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 24
    Chain: "G"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'DU0': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "A"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 175
          Unusual residues: {'DU0': 2, 'PC1': 2, 'PLC': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 49
    Chain: "D"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 121
          Unusual residues: {'DU0': 1, 'PC1': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 24
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 28
  Restraints were copied for chains:
    B, F, H, J, L
  Time building chain proxies: 3.01, per 1000 atoms: 0.27
  Number of scatterers: 11338
  At special positions: 0
  Unit cell: (149.823, 149.823, 108.81, 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      34     16.00
     P      11     15.00
     O    2160      8.00
     N    1817      7.00
     C    7316      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 516.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2552

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 2 sheets defined
      52.1% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 45 through 57
      removed outlier: 3.578A  pdb=" N   LEU C  53 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ARG C  54 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL C  57 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 117
      Proline residue:  C 100  - end of helix
    Processing helix  chain 'E' and resid 11 through 50
      Proline residue:  E  40  - end of helix
      removed outlier: 3.964A  pdb=" N   PHE E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 26
      removed outlier: 3.537A  pdb=" N   ASN G  22 " --> pdb=" O   THR G  18 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ALA G  23 " --> pdb=" O   GLY G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 48
    Processing helix  chain 'G' and resid 49 through 56
      removed outlier: 3.560A  pdb=" N   SER G  56 " --> pdb=" O   GLU G  52 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 23 through 57
      removed outlier: 5.490A  pdb=" N   LEU I  46 " --> pdb=" O   HIS I  42 " (cutoff:3.500A)
      Proline residue:  I  47  - end of helix
    Processing helix  chain 'I' and resid 64 through 68
      removed outlier: 3.636A  pdb=" N   LEU I  67 " --> pdb=" O   ILE I  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 23 through 36
    Processing helix  chain 'K' and resid 36 through 80
    Processing helix  chain 'K' and resid 84 through 104
    Processing helix  chain 'K' and resid 105 through 107
      No H-bonds generated for 'chain 'K' and resid 105 through 107'
    Processing helix  chain 'K' and resid 108 through 123
    Processing helix  chain 'K' and resid 125 through 137
    Processing helix  chain 'K' and resid 138 through 152
    Processing helix  chain 'A' and resid 22 through 34
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'D' and resid 29 through 34
    Processing helix  chain 'D' and resid 45 through 57
      removed outlier: 3.578A  pdb=" N   LEU D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ARG D  54 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL D  57 " --> pdb=" O   LEU D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 117
      Proline residue:  D 100  - end of helix
    Processing helix  chain 'F' and resid 11 through 50
      Proline residue:  F  40  - end of helix
      removed outlier: 3.964A  pdb=" N   PHE F  50 " --> pdb=" O   VAL F  46 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 17 through 26
      removed outlier: 3.537A  pdb=" N   ASN H  22 " --> pdb=" O   THR H  18 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ALA H  23 " --> pdb=" O   GLY H  19 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 48
    Processing helix  chain 'H' and resid 49 through 56
      removed outlier: 3.560A  pdb=" N   SER H  56 " --> pdb=" O   GLU H  52 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 23 through 57
      removed outlier: 5.490A  pdb=" N   LEU J  46 " --> pdb=" O   HIS J  42 " (cutoff:3.500A)
      Proline residue:  J  47  - end of helix
    Processing helix  chain 'J' and resid 64 through 68
      removed outlier: 3.636A  pdb=" N   LEU J  67 " --> pdb=" O   ILE J  64 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 23 through 36
    Processing helix  chain 'L' and resid 36 through 80
    Processing helix  chain 'L' and resid 84 through 104
    Processing helix  chain 'L' and resid 105 through 107
      No H-bonds generated for 'chain 'L' and resid 105 through 107'
    Processing helix  chain 'L' and resid 108 through 123
    Processing helix  chain 'L' and resid 125 through 137
    Processing helix  chain 'L' and resid 138 through 152
    Processing helix  chain 'B' and resid 22 through 34
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 332 through 337
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73
      removed outlier: 6.406A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   PHE A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ALA A 146 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 174 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY A 175 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL A 213 " --> pdb=" O   GLY A 192 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LYS A 293 " --> pdb=" O   ASP A 289 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73
      removed outlier: 6.406A  pdb=" N   PHE B  78 " --> pdb=" O   PHE B  72 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   PHE B 128 " --> pdb=" O   TRP B 124 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ALA B 146 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 174 " --> pdb=" O   PRO B 166 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY B 175 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL B 213 " --> pdb=" O   GLY B 192 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LYS B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)

    812 hydrogen bonds defined for protein.
    2370 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1826
        1.32 -     1.44: 3030
        1.44 -     1.56: 6635
        1.56 -     1.68: 28
        1.68 -     1.80: 64
  Bond restraints: 11583
  Sorted by residual:
  bond pdb=" CB  PRO F   8 "
       pdb=" CG  PRO F   8 "
    ideal  model  delta    sigma   weight residual
    1.492  1.576 -0.084 5.00e-02 4.00e+02 2.80e+00
  bond pdb=" CB  PRO E   8 "
       pdb=" CG  PRO E   8 "
    ideal  model  delta    sigma   weight residual
    1.492  1.576 -0.084 5.00e-02 4.00e+02 2.80e+00
  bond pdb=" CB  PRO F  10 "
       pdb=" CG  PRO F  10 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.24e+00
  bond pdb=" CB  PRO E  10 "
       pdb=" CG  PRO E  10 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.24e+00
  bond pdb=" CB  ARG A 285 "
       pdb=" CG  ARG A 285 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 1.92e+00
  ... (remaining 11578 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 15464
        2.90 -     5.79: 225
        5.79 -     8.69: 10
        8.69 -    11.58: 0
       11.58 -    14.48: 2
  Bond angle restraints: 15701
  Sorted by residual:
  angle pdb=" N   GLY A 142 "
        pdb=" CA  GLY A 142 "
        pdb=" C   GLY A 142 "
      ideal   model   delta    sigma   weight residual
     113.18   98.70   14.48 2.37e+00 1.78e-01 3.73e+01
  angle pdb=" N   GLY B 142 "
        pdb=" CA  GLY B 142 "
        pdb=" C   GLY B 142 "
      ideal   model   delta    sigma   weight residual
     113.18   98.70   14.48 2.37e+00 1.78e-01 3.73e+01
  angle pdb=" CA  PRO F  40 "
        pdb=" N   PRO F  40 "
        pdb=" CD  PRO F  40 "
      ideal   model   delta    sigma   weight residual
     112.00  107.49    4.51 1.40e+00 5.10e-01 1.04e+01
  angle pdb=" CA  PRO E  40 "
        pdb=" N   PRO E  40 "
        pdb=" CD  PRO E  40 "
      ideal   model   delta    sigma   weight residual
     112.00  107.49    4.51 1.40e+00 5.10e-01 1.04e+01
  angle pdb=" N   ALA F  39 "
        pdb=" CA  ALA F  39 "
        pdb=" C   ALA F  39 "
      ideal   model   delta    sigma   weight residual
     113.45  117.79   -4.34 1.39e+00 5.18e-01 9.73e+00
  ... (remaining 15696 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.30: 7238
       26.30 -    52.60: 260
       52.60 -    78.90: 58
       78.90 -   105.20: 43
      105.20 -   131.51: 22
  Dihedral angle restraints: 7621
    sinusoidal: 3667
      harmonic: 3954
  Sorted by residual:
  dihedral pdb=" C3  PLC A 404 "
           pdb=" C1  PLC A 404 "
           pdb=" C2  PLC A 404 "
           pdb=" O3P PLC A 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      67.16  -64.35  131.51     1      3.00e+01 1.11e-03 1.77e+01
  dihedral pdb=" O2  PLC A 404 "
           pdb=" C1  PLC A 404 "
           pdb=" C2  PLC A 404 "
           pdb=" O3P PLC A 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     304.29  175.90  128.39     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C09 DU0 A 403 "
           pdb=" C11 DU0 A 403 "
           pdb=" O10 DU0 A 403 "
           pdb=" C12 DU0 A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
      58.49  -62.93  121.42     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 7618 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1250
       0.045 -    0.090: 338
       0.090 -    0.135: 115
       0.135 -    0.181: 18
       0.181 -    0.226: 6
  Chirality restraints: 1727
  Sorted by residual:
  chirality pdb=" CA  PRO E  40 "
            pdb=" N   PRO E  40 "
            pdb=" C   PRO E  40 "
            pdb=" CB  PRO E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  PRO F  40 "
            pdb=" N   PRO F  40 "
            pdb=" C   PRO F  40 "
            pdb=" CB  PRO F  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" C22 DU0 G 101 "
            pdb=" C21 DU0 G 101 "
            pdb=" C75 DU0 G 101 "
            pdb=" O23 DU0 G 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.67   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1724 not shown)

  Planarity restraints: 1930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  39 "   -0.074 5.00e-02 4.00e+02   1.10e-01 1.94e+01
        pdb=" N   PRO F  40 "    0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO F  40 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO F  40 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E  39 "    0.074 5.00e-02 4.00e+02   1.10e-01 1.94e+01
        pdb=" N   PRO E  40 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO E  40 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO E  40 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  11 "    0.064 5.00e-02 4.00e+02   9.58e-02 1.47e+01
        pdb=" N   PRO F  12 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO F  12 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO F  12 "    0.053 5.00e-02 4.00e+02
  ... (remaining 1927 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 964
        2.74 -     3.28: 10911
        3.28 -     3.82: 17937
        3.82 -     4.36: 20982
        4.36 -     4.90: 37569
  Nonbonded interactions: 88363
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 147 "
            pdb=" OE2 GLU B 149 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" NE2 GLN A 147 "
            pdb=" OE2 GLU A 149 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" O   ALA E  29 "
            pdb=" OG1 THR E  32 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ALA F  29 "
            pdb=" OG1 THR F  32 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" NH2 ARG B 301 "
            pdb=" O   ALA B 304 "
     model   vdw
     2.260 3.120
  ... (remaining 88358 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 21 through 403)
  selection = (chain 'B' and resid 21 through 403)
}
ncs_group {
  reference = (chain 'C' and (resid 28 through 118 or (resid 201 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or  \ 
name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ 
 or name C29 or name C2A or name C3 or name C31 or name C32 or name C33 or name  \ 
C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or n \ 
ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32  \ 
or name P ))))
  selection = (chain 'D' and resid 28 through 201)
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     12.070
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
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   0.084  11585  Z= 0.286
  Angle     :  0.837  14.476  15701  Z= 0.419
  Chirality :  0.048   0.226   1727
  Planarity :  0.009   0.110   1930
  Dihedral  : 17.422 131.505   5069
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.35 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.26 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.55 (0.22), residues: 1330
  helix:  1.60 (0.19), residues: 638
  sheet:  1.02 (0.25), residues: 402
  loop : -0.10 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.003   ARG L  34 
 TYR   0.014   0.002   TYR B  93 
 PHE   0.014   0.002   PHE B  72 
 TRP   0.014   0.002   TRP D  88 
 HIS   0.005   0.002   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 (11583)
  covalent geometry    : angle       0.83746 (15701)
  hydrogen bonds       : bond        0.19988 (  812)
  hydrogen bonds       : angle       7.03319 ( 2370)
  Misc. bond           : bond        0.00292 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 380
  time to evaluate  : 0.451 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LYS cc_start: 0.8784 (mttt) cc_final: 0.8426 (tmtt)
REVERT: E   28 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7309 (mmt180)
REVERT: G   24 LEU cc_start: 0.8848 (tp) cc_final: 0.8585 (tt)
REVERT: G   25 PHE cc_start: 0.8322 (m-80) cc_final: 0.8100 (t80)
REVERT: I   68 SER cc_start: 0.7940 (m) cc_final: 0.7563 (p)
REVERT: A  117 SER cc_start: 0.8954 (m) cc_final: 0.8598 (t)
REVERT: A  168 PHE cc_start: 0.7994 (t80) cc_final: 0.7629 (t80)
REVERT: A  198 GLN cc_start: 0.8793 (mt0) cc_final: 0.8546 (mt0)
REVERT: D   78 LYS cc_start: 0.8783 (mttt) cc_final: 0.8424 (tmtt)
REVERT: F   28 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7311 (mmt180)
REVERT: H   24 LEU cc_start: 0.8845 (tp) cc_final: 0.8584 (tt)
REVERT: H   25 PHE cc_start: 0.8325 (m-80) cc_final: 0.8099 (t80)
REVERT: J   68 SER cc_start: 0.7941 (m) cc_final: 0.7564 (p)
REVERT: B  117 SER cc_start: 0.8950 (m) cc_final: 0.8594 (t)
REVERT: B  168 PHE cc_start: 0.7996 (t80) cc_final: 0.7632 (t80)
REVERT: B  198 GLN cc_start: 0.8789 (mt0) cc_final: 0.8542 (mt0)
  outliers start: 2
  outliers final: 0
  residues processed: 380
  average time/residue: 0.1351
  time to fit residues: 68.5289
Evaluate side-chains
  230 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:   30.0000
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN
I  27 GLN
** K  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
A 228 GLN
D 116 GLN
J  27 GLN
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
B 228 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.166212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.130259 restraints weight = 22320.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.127342 restraints weight = 24726.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.129085 restraints weight = 20796.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.132290 restraints weight = 12207.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.132444 restraints weight = 9409.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11585  Z= 0.185
  Angle     :  0.792  12.092  15701  Z= 0.387
  Chirality :  0.046   0.232   1727
  Planarity :  0.005   0.064   1930
  Dihedral  : 14.298 113.031   2581
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.39 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.24), residues: 1330
  helix:  2.21 (0.20), residues: 654
  sheet:  1.12 (0.25), residues: 398
  loop :  0.09 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 240 
 TYR   0.021   0.002   TYR L 133 
 PHE   0.021   0.001   PHE L 116 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.009   0.002   HIS L 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11583)
  covalent geometry    : angle       0.79234 (15701)
  hydrogen bonds       : bond        0.05157 (  812)
  hydrogen bonds       : angle       5.04663 ( 2370)
  Misc. bond           : bond        0.00200 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 244
  time to evaluate  : 0.431 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LYS cc_start: 0.8707 (mttt) cc_final: 0.8391 (tmtt)
REVERT: E   28 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7211 (mmt180)
REVERT: I   36 ILE cc_start: 0.8869 (pt) cc_final: 0.8385 (mm)
REVERT: I   68 SER cc_start: 0.8256 (m) cc_final: 0.7844 (p)
REVERT: A   25 TYR cc_start: 0.7166 (t80) cc_final: 0.6902 (t80)
REVERT: A  117 SER cc_start: 0.8849 (m) cc_final: 0.8565 (t)
REVERT: A  168 PHE cc_start: 0.7756 (t80) cc_final: 0.7312 (t80)
REVERT: D   67 HIS cc_start: 0.8659 (t70) cc_final: 0.8455 (t-90)
REVERT: D   78 LYS cc_start: 0.8698 (mttt) cc_final: 0.8387 (tmtt)
REVERT: F   28 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7209 (mmt180)
REVERT: J   36 ILE cc_start: 0.8858 (pt) cc_final: 0.8374 (mm)
REVERT: J   68 SER cc_start: 0.8254 (m) cc_final: 0.7845 (p)
REVERT: B   25 TYR cc_start: 0.7166 (t80) cc_final: 0.6904 (t80)
REVERT: B  117 SER cc_start: 0.8829 (m) cc_final: 0.8548 (t)
REVERT: B  168 PHE cc_start: 0.7759 (t80) cc_final: 0.7315 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 252
  average time/residue: 0.1202
  time to fit residues: 41.7544
Evaluate side-chains
  208 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 200
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain K residue  117 TYR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain L residue  117 TYR
Chi-restraints excluded: chain B residue  203 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 75 optimal weight:    0.0870
   chunk 54 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 97 optimal weight:   20.0000
   chunk 126 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.4164

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN
A 230 GLN
D 116 GLN
B 230 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.163765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.127348 restraints weight = 22585.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.127406 restraints weight = 26579.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.128491 restraints weight = 23687.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.129569 restraints weight = 13499.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.131346 restraints weight = 11620.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11585  Z= 0.238
  Angle     :  0.759   9.500  15701  Z= 0.376
  Chirality :  0.046   0.237   1727
  Planarity :  0.005   0.045   1930
  Dihedral  : 12.849 111.782   2581
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.09 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.97 (0.24), residues: 1330
  helix:  2.03 (0.20), residues: 662
  sheet:  0.95 (0.25), residues: 402
  loop :  0.18 (0.45), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  48 
 TYR   0.015   0.002   TYR B  25 
 PHE   0.023   0.002   PHE C  82 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.007   0.001   HIS L 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (11583)
  covalent geometry    : angle       0.75917 (15701)
  hydrogen bonds       : bond        0.04466 (  812)
  hydrogen bonds       : angle       4.83288 ( 2370)
  Misc. bond           : bond        0.00124 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.418 
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: C   78 LYS cc_start: 0.8709 (mttt) cc_final: 0.8428 (tmtt)
REVERT: E   28 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7438 (mmt180)
REVERT: I   32 LYS cc_start: 0.8951 (mttt) cc_final: 0.8737 (mttp)
REVERT: I   36 ILE cc_start: 0.8844 (pt) cc_final: 0.8538 (mm)
REVERT: K  133 TYR cc_start: 0.6527 (m-10) cc_final: 0.6055 (m-80)
REVERT: A  117 SER cc_start: 0.8779 (m) cc_final: 0.8553 (t)
REVERT: A  168 PHE cc_start: 0.7694 (t80) cc_final: 0.7250 (t80)
REVERT: D   78 LYS cc_start: 0.8713 (mttt) cc_final: 0.8420 (tmtt)
REVERT: F   28 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7442 (mmt180)
REVERT: J   32 LYS cc_start: 0.8949 (mttt) cc_final: 0.8737 (mttp)
REVERT: J   36 ILE cc_start: 0.8844 (pt) cc_final: 0.8533 (mm)
REVERT: L  133 TYR cc_start: 0.6548 (m-10) cc_final: 0.6074 (m-80)
REVERT: B  117 SER cc_start: 0.8759 (m) cc_final: 0.8540 (t)
REVERT: B  168 PHE cc_start: 0.7697 (t80) cc_final: 0.7255 (t80)
  outliers start: 20
  outliers final: 14
  residues processed: 221
  average time/residue: 0.1133
  time to fit residues: 35.1113
Evaluate side-chains
  200 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain K residue  117 TYR
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain L residue  117 TYR
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   chunk 32 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
C 116 GLN
K  65 GLN
D 116 GLN
L  65 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.164825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.128510 restraints weight = 22855.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.124469 restraints weight = 23469.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.126696 restraints weight = 19462.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.129181 restraints weight = 12119.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.129473 restraints weight = 10223.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11585  Z= 0.175
  Angle     :  0.713  12.789  15701  Z= 0.354
  Chirality :  0.043   0.201   1727
  Planarity :  0.005   0.042   1930
  Dihedral  : 12.297 108.737   2581
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.53 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.85 (0.24), residues: 1330
  helix:  1.95 (0.20), residues: 664
  sheet:  0.82 (0.25), residues: 400
  loop :  0.17 (0.45), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  44 
 TYR   0.018   0.001   TYR B  25 
 PHE   0.031   0.001   PHE G  25 
 TRP   0.012   0.001   TRP A 197 
 HIS   0.002   0.001   HIS K 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (11583)
  covalent geometry    : angle       0.71343 (15701)
  hydrogen bonds       : bond        0.04112 (  812)
  hydrogen bonds       : angle       4.68042 ( 2370)
  Misc. bond           : bond        0.00170 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 208
  time to evaluate  : 0.342 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LYS cc_start: 0.8736 (mttt) cc_final: 0.8375 (tmtt)
REVERT: E   28 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7409 (mmt180)
REVERT: I   28 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8346 (mp0)
REVERT: I   32 LYS cc_start: 0.9024 (mttt) cc_final: 0.8776 (mttp)
REVERT: I   36 ILE cc_start: 0.8977 (pt) cc_final: 0.8654 (mm)
REVERT: K  133 TYR cc_start: 0.6846 (m-10) cc_final: 0.6348 (m-80)
REVERT: A  117 SER cc_start: 0.8749 (m) cc_final: 0.8489 (t)
REVERT: A  168 PHE cc_start: 0.7798 (t80) cc_final: 0.7382 (t80)
REVERT: D   78 LYS cc_start: 0.8722 (mttt) cc_final: 0.8369 (tmtt)
REVERT: F   28 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7410 (mmt180)
REVERT: J   32 LYS cc_start: 0.9016 (mttt) cc_final: 0.8771 (mttp)
REVERT: J   36 ILE cc_start: 0.8975 (pt) cc_final: 0.8649 (mm)
REVERT: L  133 TYR cc_start: 0.6856 (m-10) cc_final: 0.6357 (m-80)
REVERT: B  117 SER cc_start: 0.8716 (m) cc_final: 0.8476 (t)
REVERT: B  168 PHE cc_start: 0.7806 (t80) cc_final: 0.7395 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 218
  average time/residue: 0.1128
  time to fit residues: 34.8653
Evaluate side-chains
  215 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain K residue  117 TYR
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain L residue  117 TYR
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 115 optimal weight:    0.7980
   chunk 95 optimal weight:   20.0000
   chunk 102 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** K  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.165327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.128845 restraints weight = 22646.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.126702 restraints weight = 23638.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.128521 restraints weight = 21935.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.129435 restraints weight = 12983.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.130573 restraints weight = 11448.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11585  Z= 0.149
  Angle     :  0.692  12.640  15701  Z= 0.340
  Chirality :  0.042   0.175   1727
  Planarity :  0.005   0.043   1930
  Dihedral  : 11.898 104.504   2581
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.34 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.88 (0.24), residues: 1330
  helix:  2.01 (0.20), residues: 658
  sheet:  0.83 (0.25), residues: 400
  loop :  0.13 (0.44), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  44 
 TYR   0.015   0.001   TYR B  25 
 PHE   0.023   0.001   PHE D  82 
 TRP   0.014   0.001   TRP B 197 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (11583)
  covalent geometry    : angle       0.69244 (15701)
  hydrogen bonds       : bond        0.03775 (  812)
  hydrogen bonds       : angle       4.51279 ( 2370)
  Misc. bond           : bond        0.00115 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 208
  time to evaluate  : 0.434 
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: C   56 MET cc_start: 0.7376 (ppp) cc_final: 0.7080 (ppp)
REVERT: C   78 LYS cc_start: 0.8711 (mttt) cc_final: 0.8369 (tmtt)
REVERT: E   28 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7351 (mmt180)
REVERT: I   36 ILE cc_start: 0.8965 (pt) cc_final: 0.8644 (mm)
REVERT: K  133 TYR cc_start: 0.6666 (m-10) cc_final: 0.6253 (m-80)
REVERT: A  117 SER cc_start: 0.8733 (m) cc_final: 0.8506 (t)
REVERT: A  168 PHE cc_start: 0.7766 (t80) cc_final: 0.7449 (t80)
REVERT: A  183 GLN cc_start: 0.8311 (tp40) cc_final: 0.8071 (tm-30)
REVERT: D   56 MET cc_start: 0.7374 (ppp) cc_final: 0.7079 (ppp)
REVERT: D   78 LYS cc_start: 0.8695 (mttt) cc_final: 0.8362 (tmtt)
REVERT: F   28 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7347 (mmt180)
REVERT: J   36 ILE cc_start: 0.8968 (pt) cc_final: 0.8653 (mm)
REVERT: L  133 TYR cc_start: 0.6694 (m-10) cc_final: 0.6274 (m-80)
REVERT: B  117 SER cc_start: 0.8712 (m) cc_final: 0.8500 (t)
REVERT: B  168 PHE cc_start: 0.7770 (t80) cc_final: 0.7456 (t80)
REVERT: B  183 GLN cc_start: 0.8303 (tp40) cc_final: 0.8057 (tm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 224
  average time/residue: 0.1075
  time to fit residues: 34.3116
Evaluate side-chains
  213 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain K residue  117 TYR
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain L residue  117 TYR
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 127 optimal weight:    0.6980
   chunk 24 optimal weight:    9.9990
   chunk 130 optimal weight:    0.2980
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
K  46 ASN
K  65 GLN
L  46 ASN
L  65 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.166079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.130262 restraints weight = 22914.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.126276 restraints weight = 22144.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.128546 restraints weight = 20102.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.128933 restraints weight = 12464.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.131195 restraints weight = 11165.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11585  Z= 0.136
  Angle     :  0.712  14.306  15701  Z= 0.345
  Chirality :  0.042   0.177   1727
  Planarity :  0.004   0.044   1930
  Dihedral  : 11.488 101.646   2581
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.16 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.85 (0.24), residues: 1330
  helix:  1.94 (0.20), residues: 658
  sheet:  0.92 (0.25), residues: 400
  loop :  0.08 (0.44), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  44 
 TYR   0.017   0.001   TYR B  99 
 PHE   0.026   0.001   PHE G  25 
 TRP   0.013   0.001   TRP B 197 
 HIS   0.001   0.000   HIS I  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11583)
  covalent geometry    : angle       0.71168 (15701)
  hydrogen bonds       : bond        0.03625 (  812)
  hydrogen bonds       : angle       4.46613 ( 2370)
  Misc. bond           : bond        0.00057 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.405 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 MET cc_start: 0.7417 (ppp) cc_final: 0.7185 (ppp)
REVERT: C   78 LYS cc_start: 0.8705 (mttt) cc_final: 0.8357 (tmtt)
REVERT: E   28 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7287 (mmt180)
REVERT: I   36 ILE cc_start: 0.9001 (pt) cc_final: 0.8732 (mm)
REVERT: K  133 TYR cc_start: 0.6908 (m-10) cc_final: 0.6383 (m-80)
REVERT: A  117 SER cc_start: 0.8689 (m) cc_final: 0.8459 (t)
REVERT: A  168 PHE cc_start: 0.7784 (t80) cc_final: 0.7521 (t80)
REVERT: D   56 MET cc_start: 0.7424 (ppp) cc_final: 0.7187 (ppp)
REVERT: D   78 LYS cc_start: 0.8695 (mttt) cc_final: 0.8353 (tmtt)
REVERT: F   28 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7286 (mmt180)
REVERT: J   36 ILE cc_start: 0.8983 (pt) cc_final: 0.8717 (mm)
REVERT: L  133 TYR cc_start: 0.6929 (m-10) cc_final: 0.6403 (m-80)
REVERT: B  117 SER cc_start: 0.8676 (m) cc_final: 0.8458 (t)
REVERT: B  168 PHE cc_start: 0.7796 (t80) cc_final: 0.7541 (t80)
  outliers start: 27
  outliers final: 15
  residues processed: 216
  average time/residue: 0.1039
  time to fit residues: 32.1986
Evaluate side-chains
  205 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 190
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   30 ILE
Chi-restraints excluded: chain K residue  117 TYR
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain L residue  117 TYR
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 124 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 147 GLN
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.165274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.128342 restraints weight = 22778.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.125751 restraints weight = 23170.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.127378 restraints weight = 20299.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.129447 restraints weight = 12499.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.129744 restraints weight = 10822.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11585  Z= 0.161
  Angle     :  0.738  14.944  15701  Z= 0.351
  Chirality :  0.042   0.178   1727
  Planarity :  0.004   0.044   1930
  Dihedral  : 11.415  99.232   2581
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.06 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.91 (0.24), residues: 1330
  helix:  2.02 (0.20), residues: 656
  sheet:  0.91 (0.25), residues: 400
  loop :  0.08 (0.44), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  52 
 TYR   0.016   0.001   TYR A  99 
 PHE   0.021   0.001   PHE A 157 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11583)
  covalent geometry    : angle       0.73758 (15701)
  hydrogen bonds       : bond        0.03569 (  812)
  hydrogen bonds       : angle       4.43680 ( 2370)
  Misc. bond           : bond        0.00103 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.436 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LYS cc_start: 0.8709 (mttt) cc_final: 0.8358 (tmtt)
REVERT: E   28 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7358 (mmt180)
REVERT: I   28 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8328 (pm20)
REVERT: I   36 ILE cc_start: 0.9000 (pt) cc_final: 0.8726 (mm)
REVERT: A  117 SER cc_start: 0.8765 (m) cc_final: 0.8530 (t)
REVERT: A  168 PHE cc_start: 0.7797 (t80) cc_final: 0.7591 (t80)
REVERT: D   78 LYS cc_start: 0.8696 (mttt) cc_final: 0.8352 (tmtt)
REVERT: F   28 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7352 (mmt180)
REVERT: J   36 ILE cc_start: 0.8959 (pt) cc_final: 0.8688 (mm)
REVERT: B  117 SER cc_start: 0.8744 (m) cc_final: 0.8533 (t)
REVERT: B  168 PHE cc_start: 0.7791 (t80) cc_final: 0.7560 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 214
  average time/residue: 0.1037
  time to fit residues: 31.8588
Evaluate side-chains
  201 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 82 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 117 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
I  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.165462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.128715 restraints weight = 22438.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.126142 restraints weight = 21647.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.127785 restraints weight = 20689.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.128437 restraints weight = 12469.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.130334 restraints weight = 11147.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11585  Z= 0.135
  Angle     :  0.742  15.721  15701  Z= 0.354
  Chirality :  0.042   0.172   1727
  Planarity :  0.004   0.045   1930
  Dihedral  : 11.169  95.900   2581
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.60 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.91 (0.24), residues: 1330
  helix:  1.92 (0.20), residues: 660
  sheet:  0.98 (0.26), residues: 400
  loop :  0.22 (0.44), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  52 
 TYR   0.015   0.001   TYR A  99 
 PHE   0.016   0.001   PHE G  25 
 TRP   0.013   0.001   TRP B 197 
 HIS   0.001   0.000   HIS L 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11583)
  covalent geometry    : angle       0.74195 (15701)
  hydrogen bonds       : bond        0.03490 (  812)
  hydrogen bonds       : angle       4.40348 ( 2370)
  Misc. bond           : bond        0.00043 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 0.470 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LYS cc_start: 0.8714 (mttt) cc_final: 0.8354 (tmtt)
REVERT: E   28 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7338 (mmt180)
REVERT: I   36 ILE cc_start: 0.8985 (pt) cc_final: 0.8710 (mm)
REVERT: A  117 SER cc_start: 0.8730 (m) cc_final: 0.8496 (t)
REVERT: A  143 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7313 (mm-40)
REVERT: A  168 PHE cc_start: 0.7839 (t80) cc_final: 0.7606 (t80)
REVERT: D   78 LYS cc_start: 0.8709 (mttt) cc_final: 0.8349 (tmtt)
REVERT: F   28 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7332 (mmt180)
REVERT: J   36 ILE cc_start: 0.9017 (pt) cc_final: 0.8743 (mm)
REVERT: B  117 SER cc_start: 0.8720 (m) cc_final: 0.8497 (t)
REVERT: B  143 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7315 (mm-40)
  outliers start: 21
  outliers final: 14
  residues processed: 214
  average time/residue: 0.1069
  time to fit residues: 32.8514
Evaluate side-chains
  207 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 191
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  117 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain L residue  117 TYR
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 99 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 118 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 131 optimal weight:    5.9990
   chunk 61 optimal weight:    0.2980
   chunk 81 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN
A 228 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.164176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.127874 restraints weight = 22482.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.125263 restraints weight = 24075.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.126693 restraints weight = 21680.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.129008 restraints weight = 13133.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.129244 restraints weight = 10756.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11585  Z= 0.195
  Angle     :  0.795  14.905  15701  Z= 0.386
  Chirality :  0.044   0.179   1727
  Planarity :  0.004   0.043   1930
  Dihedral  : 11.225  93.087   2581
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.86 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.77 (0.23), residues: 1330
  helix:  1.96 (0.20), residues: 656
  sheet:  0.81 (0.25), residues: 400
  loop : -0.08 (0.42), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  52 
 TYR   0.019   0.001   TYR A  99 
 PHE   0.014   0.001   PHE C  82 
 TRP   0.008   0.001   TRP A 197 
 HIS   0.002   0.001   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (11583)
  covalent geometry    : angle       0.79467 (15701)
  hydrogen bonds       : bond        0.03539 (  812)
  hydrogen bonds       : angle       4.49917 ( 2370)
  Misc. bond           : bond        0.00141 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 0.483 
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: symmetry clash
REVERT: C   78 LYS cc_start: 0.8716 (mttt) cc_final: 0.8377 (tmtt)
REVERT: E   28 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7374 (mmt180)
REVERT: I   36 ILE cc_start: 0.8982 (pt) cc_final: 0.8696 (mm)
REVERT: I   54 TYR cc_start: 0.7733 (t80) cc_final: 0.7438 (t80)
REVERT: K  133 TYR cc_start: 0.6889 (m-10) cc_final: 0.6244 (m-80)
REVERT: A  117 SER cc_start: 0.8805 (m) cc_final: 0.8599 (t)
REVERT: A  168 PHE cc_start: 0.7870 (t80) cc_final: 0.7642 (t80)
REVERT: D   78 LYS cc_start: 0.8704 (mttt) cc_final: 0.8371 (tmtt)
REVERT: F   28 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7366 (mmt180)
REVERT: J   36 ILE cc_start: 0.8956 (pt) cc_final: 0.8673 (mm)
REVERT: J   54 TYR cc_start: 0.7737 (t80) cc_final: 0.7439 (t80)
REVERT: L  133 TYR cc_start: 0.6926 (m-10) cc_final: 0.6273 (m-80)
  outliers start: 16
  outliers final: 14
  residues processed: 205
  average time/residue: 0.1172
  time to fit residues: 33.8989
Evaluate side-chains
  199 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 185
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 127 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 228 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.165043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.129025 restraints weight = 22700.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.124211 restraints weight = 23846.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.126229 restraints weight = 20377.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.128577 restraints weight = 12721.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.128836 restraints weight = 10795.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11585  Z= 0.169
  Angle     :  0.816  16.247  15701  Z= 0.398
  Chirality :  0.044   0.309   1727
  Planarity :  0.004   0.044   1930
  Dihedral  : 10.958  90.295   2581
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.58 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.78 (0.24), residues: 1330
  helix:  1.93 (0.20), residues: 660
  sheet:  0.81 (0.25), residues: 400
  loop :  0.03 (0.43), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  44 
 TYR   0.018   0.001   TYR A  99 
 PHE   0.013   0.001   PHE H  25 
 TRP   0.010   0.001   TRP A 197 
 HIS   0.001   0.000   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11583)
  covalent geometry    : angle       0.81612 (15701)
  hydrogen bonds       : bond        0.03484 (  812)
  hydrogen bonds       : angle       4.54688 ( 2370)
  Misc. bond           : bond        0.00099 (    2)

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

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

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2660 Ramachandran restraints generated.
    1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 0.444 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   78 LYS cc_start: 0.8715 (mttt) cc_final: 0.8355 (tmtt)
REVERT: E   27 GLN cc_start: 0.8093 (mt0) cc_final: 0.7727 (mp10)
REVERT: E   28 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7277 (mmt180)
REVERT: I   36 ILE cc_start: 0.9009 (pt) cc_final: 0.8735 (mm)
REVERT: I   54 TYR cc_start: 0.7675 (t80) cc_final: 0.7396 (t80)
REVERT: K  133 TYR cc_start: 0.7036 (m-10) cc_final: 0.6360 (m-80)
REVERT: A  117 SER cc_start: 0.8777 (m) cc_final: 0.8558 (t)
REVERT: D   78 LYS cc_start: 0.8712 (mttt) cc_final: 0.8345 (tmtt)
REVERT: F   27 GLN cc_start: 0.8073 (mt0) cc_final: 0.7721 (mp10)
REVERT: F   28 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7271 (mmt180)
REVERT: J   32 LYS cc_start: 0.9050 (mttt) cc_final: 0.8795 (ptpp)
REVERT: J   36 ILE cc_start: 0.9022 (pt) cc_final: 0.8758 (mm)
REVERT: J   54 TYR cc_start: 0.7676 (t80) cc_final: 0.7397 (t80)
REVERT: L  133 TYR cc_start: 0.7062 (m-10) cc_final: 0.6381 (m-80)
  outliers start: 17
  outliers final: 16
  residues processed: 208
  average time/residue: 0.1115
  time to fit residues: 33.0076
Evaluate side-chains
  204 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  224 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 112 optimal weight:    0.5980
   chunk 71 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 130 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.165972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.130392 restraints weight = 22579.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.126104 restraints weight = 25171.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.128356 restraints weight = 20560.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.130837 restraints weight = 12355.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.131107 restraints weight = 10288.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.5679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11585  Z= 0.145
  Angle     :  0.811  15.798  15701  Z= 0.394
  Chirality :  0.043   0.255   1727
  Planarity :  0.004   0.045   1930
  Dihedral  : 10.560  86.030   2581
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.68 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  1.78 (0.23), residues: 1330
  helix:  1.90 (0.20), residues: 660
  sheet:  0.86 (0.25), residues: 398
  loop :  0.03 (0.42), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  48 
 TYR   0.019   0.001   TYR B  99 
 PHE   0.014   0.001   PHE C  82 
 TRP   0.013   0.001   TRP B 197 
 HIS   0.001   0.000   HIS I  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11583)
  covalent geometry    : angle       0.81108 (15701)
  hydrogen bonds       : bond        0.03473 (  812)
  hydrogen bonds       : angle       4.49982 ( 2370)
  Misc. bond           : bond        0.00043 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2249.77 seconds
wall clock time: 39 minutes 34.45 seconds (2374.45 seconds total)