Starting phenix.real_space_refine
on Fri Mar 14 02:52:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vd2_31904/03_2025/7vd2_31904_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vd2_31904/03_2025/7vd2_31904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2025/7vd2_31904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2025/7vd2_31904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2025/7vd2_31904_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2025/7vd2_31904_neut.cif"
  }
  resolution = 2.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.033
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      27      5.49       5
     S      34      5.16       5
     C    6179      2.51       5
     N    1322      2.21       5
     O    1555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9117
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "A"
      Number of atoms: 354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 354
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
    Chain: "D"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 304
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
    Chain: "F"
      Number of atoms: 354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 354
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
    Chain: "G"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 433
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "E"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 304
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
    Chain: "H"
      Number of atoms: 458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 458
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 1, 'TRANS': 54}
    Chain: "C"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 463
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "J"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 433
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2190
          Classifications: {'peptide': 286}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272}
    Chain: "I"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2190
          Classifications: {'peptide': 286}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272}
    Chain: "A"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 130
          Unusual residues: {'PC1': 2, 'UND': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "F"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {'PC1': 1, 'UND': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "G"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 227
          Unusual residues: {'PC1': 4, 'UND': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "H"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 173
          Unusual residues: {'PC1': 3, 'UND': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 119
          Unusual residues: {'PC1': 2, 'UND': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "J"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 227
          Unusual residues: {'PC1': 4, 'UND': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 314
          Unusual residues: {'PC1': 5, 'UND': 4}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
    Chain: "I"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 368
          Unusual residues: {'PC1': 6, 'UND': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 5.71, per 1000 atoms: 0.63
  Number of scatterers: 9117
  At special positions: 0
  Unit cell: (132.398, 113.845, 95.2929, 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      27     15.00
     O    1555      8.00
     N    1322      7.00
     C    6179      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 851.1 milliseconds
  

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1734

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 2 sheets defined
      37.5% alpha, 38.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 37
      removed outlier: 3.596A  pdb=" N   ARG A  33 " --> pdb=" O   ARG A  29 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE A  34 " --> pdb=" O   GLY A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 60
    Processing helix  chain 'D' and resid 14 through 48
      Proline residue:  D  42  - end of helix
    Processing helix  chain 'F' and resid 26 through 36
      removed outlier: 3.506A  pdb=" N   ARG F  33 " --> pdb=" O   ARG F  29 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE F  34 " --> pdb=" O   GLY F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 61
    Processing helix  chain 'G' and resid 5 through 39
      removed outlier: 3.914A  pdb=" N   GLN G  10 " --> pdb=" O   LYS G   6 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG G  11 " --> pdb=" O   GLU G   7 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   ILE G  28 " --> pdb=" O   ARG G  24 " (cutoff:3.500A)
      Proline residue:  G  29  - end of helix
    Processing helix  chain 'G' and resid 48 through 53
    Processing helix  chain 'E' and resid 16 through 48
      removed outlier: 3.553A  pdb=" N   MET E  20 " --> pdb=" O   MET E  16 " (cutoff:3.500A)
      Proline residue:  E  42  - end of helix
    Processing helix  chain 'H' and resid 64 through 96
      removed outlier: 3.871A  pdb=" N   ASP H  68 " --> pdb=" O   GLY H  64 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU H  69 " --> pdb=" O   ALA H  65 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 96 through 118
      removed outlier: 4.000A  pdb=" N   GLN H 115 " --> pdb=" O   GLN H 111 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLN H 116 " --> pdb=" O   GLN H 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 96
    Processing helix  chain 'C' and resid 96 through 118
    Processing helix  chain 'J' and resid 6 through 39
      removed outlier: 3.820A  pdb=" N   GLN J  10 " --> pdb=" O   LYS J   6 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN J  14 " --> pdb=" O   GLN J  10 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   ILE J  28 " --> pdb=" O   ARG J  24 " (cutoff:3.500A)
      Proline residue:  J  29  - end of helix
    Processing helix  chain 'J' and resid 48 through 53
    Processing helix  chain 'B' and resid 82 through 86
    Processing helix  chain 'B' and resid 87 through 92
    Processing helix  chain 'B' and resid 308 through 310
      No H-bonds generated for 'chain 'B' and resid 308 through 310'
    Processing helix  chain 'I' and resid 82 through 86
    Processing helix  chain 'I' and resid 87 through 93
      removed outlier: 4.054A  pdb=" N   LEU I  93 " --> pdb=" O   LYS I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 308 through 310
      No H-bonds generated for 'chain 'I' and resid 308 through 310'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 108
      removed outlier: 7.643A  pdb=" N   PHE B 147 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   GLN B 167 " --> pdb=" O   PHE B 147 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU B 160 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU B 172 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS B 175 " --> pdb=" O   ASP B 191 " (cutoff:3.500A)
      removed outlier: 14.043A  pdb=" N   VAL B 186 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
      removed outlier: 10.063A  pdb=" N   ASP B 209 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   TRP B 188 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   SER B 214 " --> pdb=" O   PRO B 208 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA B 251 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE B 323 " --> pdb=" O   ASP B 319 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 100 through 110
      removed outlier: 6.305A  pdb=" N   PHE I 113 " --> pdb=" O   LEU I 109 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LYS I 139 " --> pdb=" O   ALA I 146 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ALA I 146 " --> pdb=" O   LYS I 139 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   PHE I 147 " --> pdb=" O   GLN I 167 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   GLN I 167 " --> pdb=" O   PHE I 147 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU I 172 " --> pdb=" O   LEU I 168 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ARG I 173 " --> pdb=" O   GLY I 192 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   GLY I 192 " --> pdb=" O   ARG I 173 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LYS I 175 " --> pdb=" O   VAL I 190 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL I 190 " --> pdb=" O   LYS I 175 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA I 177 " --> pdb=" O   TRP I 188 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   TRP I 188 " --> pdb=" O   ALA I 177 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   GLN I 179 " --> pdb=" O   VAL I 186 " (cutoff:3.500A)
      removed outlier: 14.025A  pdb=" N   VAL I 186 " --> pdb=" O   ASP I 209 " (cutoff:3.500A)
      removed outlier: 10.334A  pdb=" N   ASP I 209 " --> pdb=" O   VAL I 186 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   TRP I 188 " --> pdb=" O   ASN I 207 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   SER I 214 " --> pdb=" O   PRO I 208 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA I 251 " --> pdb=" O   GLY I 232 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE I 323 " --> pdb=" O   ASP I 319 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   GLY I 100 " --> pdb=" O   PHE I 356 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   LEU I 358 " --> pdb=" O   GLY I 100 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS I 102 " --> pdb=" O   LEU I 358 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   ILE I 360 " --> pdb=" O   LYS I 102 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   THR I 104 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)

    548 hydrogen bonds defined for protein.
    1563 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 3.04 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: 1294
        1.32 -     1.44: 2079
        1.44 -     1.56: 5751
        1.56 -     1.69: 54
        1.69 -     1.81: 58
  Bond restraints: 9236
  Sorted by residual:
  bond pdb=" CA  SER I 183 "
       pdb=" CB  SER I 183 "
    ideal  model  delta    sigma   weight residual
    1.532  1.486  0.046 1.74e-02 3.30e+03 7.06e+00
  bond pdb=" O13 PC1 I 402 "
       pdb=" P   PC1 I 402 "
    ideal  model  delta    sigma   weight residual
    1.652  1.601  0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" O13 PC1 H 203 "
       pdb=" P   PC1 H 203 "
    ideal  model  delta    sigma   weight residual
    1.652  1.601  0.051 2.00e-02 2.50e+03 6.41e+00
  bond pdb=" C11 PC1 A 104 "
       pdb=" O13 PC1 A 104 "
    ideal  model  delta    sigma   weight residual
    1.407  1.457 -0.050 2.00e-02 2.50e+03 6.26e+00
  bond pdb=" C11 PC1 F 102 "
       pdb=" O13 PC1 F 102 "
    ideal  model  delta    sigma   weight residual
    1.407  1.457 -0.050 2.00e-02 2.50e+03 6.23e+00
  ... (remaining 9231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 11497
        1.82 -     3.64: 521
        3.64 -     5.47: 87
        5.47 -     7.29: 15
        7.29 -     9.11: 8
  Bond angle restraints: 12128
  Sorted by residual:
  angle pdb=" C   SER I 183 "
        pdb=" N   LYS I 184 "
        pdb=" CA  LYS I 184 "
      ideal   model   delta    sigma   weight residual
     122.72  115.96    6.76 1.38e+00 5.25e-01 2.40e+01
  angle pdb=" N   GLU B  85 "
        pdb=" CA  GLU B  85 "
        pdb=" C   GLU B  85 "
      ideal   model   delta    sigma   weight residual
     112.93  108.24    4.69 1.12e+00 7.97e-01 1.75e+01
  angle pdb=" CA  GLU G  46 "
        pdb=" C   GLU G  46 "
        pdb=" N   PRO G  47 "
      ideal   model   delta    sigma   weight residual
     118.87  122.18   -3.31 9.00e-01 1.23e+00 1.35e+01
  angle pdb=" CA  CYS B  86 "
        pdb=" C   CYS B  86 "
        pdb=" O   CYS B  86 "
      ideal   model   delta    sigma   weight residual
     121.07  117.56    3.51 1.10e+00 8.26e-01 1.02e+01
  angle pdb=" CA  THR I 180 "
        pdb=" C   THR I 180 "
        pdb=" O   THR I 180 "
      ideal   model   delta    sigma   weight residual
     120.70  117.37    3.33 1.08e+00 8.57e-01 9.53e+00
  ... (remaining 12123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5008
       17.99 -    35.97: 641
       35.97 -    53.96: 214
       53.96 -    71.94: 68
       71.94 -    89.93: 20
  Dihedral angle restraints: 5951
    sinusoidal: 3250
      harmonic: 2701
  Sorted by residual:
  dihedral pdb=" CA  THR B 180 "
           pdb=" C   THR B 180 "
           pdb=" N   GLN B 181 "
           pdb=" CA  GLN B 181 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.40   23.60     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  LEU B 256 "
           pdb=" C   LEU B 256 "
           pdb=" N   ASN B 257 "
           pdb=" CA  ASN B 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.51  -16.49     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  GLN J  13 "
           pdb=" C   GLN J  13 "
           pdb=" N   GLN J  14 "
           pdb=" CA  GLN J  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.89   16.11     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 5948 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 763
       0.035 -    0.069: 293
       0.069 -    0.104: 83
       0.104 -    0.139: 37
       0.139 -    0.174: 6
  Chirality restraints: 1182
  Sorted by residual:
  chirality pdb=" CA  ASN I 258 "
            pdb=" N   ASN I 258 "
            pdb=" C   ASN I 258 "
            pdb=" CB  ASN I 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CA  GLN I 179 "
            pdb=" N   GLN I 179 "
            pdb=" C   GLN I 179 "
            pdb=" CB  GLN I 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.03e-01
  chirality pdb=" C2  PC1 B 408 "
            pdb=" C1  PC1 B 408 "
            pdb=" C3  PC1 B 408 "
            pdb=" O21 PC1 B 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 6.99e-01
  ... (remaining 1179 not shown)

  Planarity restraints: 1371
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I 180 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   THR I 180 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   THR I 180 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLN I 181 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  41 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO D  42 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO D  42 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D  42 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  85 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   GLU B  85 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLU B  85 "    0.010 2.00e-02 2.50e+03
        pdb=" N   CYS B  86 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1368 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1032
        2.74 -     3.28: 7920
        3.28 -     3.82: 13203
        3.82 -     4.36: 16799
        4.36 -     4.90: 29894
  Nonbonded interactions: 68848
  Sorted by model distance:
  nonbonded pdb=" O   LEU J  12 "
            pdb=" N   LEU J  15 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   SER G   5 "
            pdb=" N   ALA G   8 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OH  TYR E  34 "
            pdb=" O   GLY B 232 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OH  TYR D  34 "
            pdb=" O   GLY I 232 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" NZ  LYS I  91 "
            pdb=" OE2 GLU I 287 "
     model   vdw
     2.255 3.120
  ... (remaining 68843 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 25 through 67 or resid 101 through 103))
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'B' and (resid 76 through 361 or resid 401 through 402 or resid 405 throu \ 
gh 407))
  selection = (chain 'I' and (resid 76 through 361 or resid 401 through 402 or resid 405 throu \ 
gh 407))
}
ncs_group {
  reference = (chain 'C' and (resid 63 through 118 or resid 201 through 202))
  selection = (chain 'H' and (resid 63 through 118 or resid 201 through 202))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.780
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:10.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
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      :  0.011   0.051   9236  Z= 0.686
  Angle     :  0.907   9.108  12128  Z= 0.418
  Chirality :  0.044   0.174   1182
  Planarity :  0.003   0.042   1371
  Dihedral  : 18.201  89.928   4217
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  0.37 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.28), residues: 931
  helix:  2.37 (0.29), residues: 312
  sheet:  0.70 (0.26), residues: 398
  loop : -0.48 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I 188 
 HIS   0.008   0.001   HIS B 271 
 PHE   0.012   0.001   PHE G  27 
 TYR   0.008   0.001   TYR D  34 
 ARG   0.006   0.001   ARG A  33 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 211
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   19 LYS cc_start: 0.9251 (tptp) cc_final: 0.8764 (tppp)
REVERT: D   22 GLU cc_start: 0.8278 (pp20) cc_final: 0.7708 (pp20)
REVERT: G    9 LYS cc_start: 0.8581 (pttm) cc_final: 0.8375 (pttm)
REVERT: G   41 ASP cc_start: 0.8818 (m-30) cc_final: 0.8541 (m-30)
REVERT: E   19 LYS cc_start: 0.8235 (mppt) cc_final: 0.7555 (mptt)
REVERT: E   22 GLU cc_start: 0.8341 (pp20) cc_final: 0.8081 (pp20)
REVERT: H   67 PHE cc_start: 0.8848 (t80) cc_final: 0.8535 (t80)
REVERT: H  104 GLU cc_start: 0.8772 (tp30) cc_final: 0.8541 (mm-30)
REVERT: H  111 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8686 (tm-30)
REVERT: C   75 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8567 (tm-30)
REVERT: C  104 GLU cc_start: 0.8772 (tp30) cc_final: 0.8552 (mm-30)
REVERT: J   15 LEU cc_start: 0.9222 (tp) cc_final: 0.8984 (tt)
REVERT: B   76 CYS cc_start: 0.8486 (m) cc_final: 0.7972 (t)
REVERT: B  294 MET cc_start: 0.8754 (mpp) cc_final: 0.8309 (mpp)
REVERT: B  296 ASP cc_start: 0.7970 (m-30) cc_final: 0.7672 (m-30)
REVERT: I  294 MET cc_start: 0.8740 (mpp) cc_final: 0.8509 (mpp)
  outliers start: 4
  outliers final: 1
  residues processed: 212
  average time/residue: 1.6088
  time to fit residues: 360.2771
Evaluate side-chains
  182 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.1980
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.099207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.067420 restraints weight = 16547.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.52
r_work: 0.2767 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9236  Z= 0.186
  Angle     :  0.646   7.707  12128  Z= 0.322
  Chirality :  0.042   0.175   1182
  Planarity :  0.004   0.047   1371
  Dihedral  : 19.808  89.564   2441
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.18 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.29), residues: 931
  helix:  3.35 (0.28), residues: 316
  sheet:  1.22 (0.26), residues: 388
  loop : -0.22 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  27 
 HIS   0.002   0.001   HIS I 271 
 PHE   0.021   0.001   PHE C  67 
 TYR   0.010   0.001   TYR A  32 
 ARG   0.008   0.001   ARG D  29 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.8972 (t0) cc_final: 0.8575 (t0)
REVERT: D   18 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8710 (ttp80)
REVERT: D   19 LYS cc_start: 0.9206 (tptp) cc_final: 0.8600 (tppp)
REVERT: D   20 MET cc_start: 0.8431 (mtp) cc_final: 0.8128 (mtm)
REVERT: D   22 GLU cc_start: 0.8724 (pp20) cc_final: 0.8306 (pp20)
REVERT: F   37 ASP cc_start: 0.9224 (t70) cc_final: 0.9022 (t0)
REVERT: F   38 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8160 (tpp80)
REVERT: G   19 SER cc_start: 0.8970 (p) cc_final: 0.8760 (p)
REVERT: G   44 MET cc_start: 0.8435 (mpp) cc_final: 0.8186 (mpp)
REVERT: E   19 LYS cc_start: 0.8505 (mppt) cc_final: 0.8207 (mptt)
REVERT: E   22 GLU cc_start: 0.8633 (pp20) cc_final: 0.8370 (pp20)
REVERT: H   67 PHE cc_start: 0.8732 (t80) cc_final: 0.8434 (t80)
REVERT: H   72 PHE cc_start: 0.8890 (t80) cc_final: 0.8366 (t80)
REVERT: H   75 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: H   76 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8281 (mptm)
REVERT: H  107 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: H  111 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8649 (tm-30)
REVERT: H  112 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: C   75 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: C   76 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (mptm)
REVERT: C  102 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8029 (mp0)
REVERT: C  107 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: C  110 GLN cc_start: 0.8536 (pp30) cc_final: 0.8316 (pp30)
REVERT: J    9 LYS cc_start: 0.8873 (mptt) cc_final: 0.8652 (mptt)
REVERT: J   14 GLN cc_start: 0.8704 (mt0) cc_final: 0.8290 (tt0)
REVERT: J   44 MET cc_start: 0.8290 (mpp) cc_final: 0.7943 (mpp)
REVERT: J   46 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8520 (mm-30)
REVERT: B   76 CYS cc_start: 0.9015 (m) cc_final: 0.8256 (t)
REVERT: B  163 GLN cc_start: 0.8684 (mt0) cc_final: 0.8286 (mt0)
REVERT: B  240 ARG cc_start: 0.8306 (ptp-110) cc_final: 0.8086 (mtm110)
REVERT: B  294 MET cc_start: 0.9076 (mpp) cc_final: 0.8837 (mpt)
REVERT: B  296 ASP cc_start: 0.8070 (m-30) cc_final: 0.7798 (m-30)
REVERT: I   84 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: I  163 GLN cc_start: 0.8620 (mt0) cc_final: 0.8294 (mt0)
REVERT: I  240 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7894 (mtm110)
REVERT: I  293 ARG cc_start: 0.9297 (mtp85) cc_final: 0.9078 (ttm-80)
  outliers start: 18
  outliers final: 2
  residues processed: 218
  average time/residue: 1.3458
  time to fit residues: 310.6159
Evaluate side-chains
  204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 199
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain G residue    6 LYS
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain C residue  102 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 HIS
I 267 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.099357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.067627 restraints weight = 16663.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.54
r_work: 0.2780 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9236  Z= 0.176
  Angle     :  0.601   8.311  12128  Z= 0.297
  Chirality :  0.041   0.187   1182
  Planarity :  0.003   0.042   1371
  Dihedral  : 19.120  89.351   2441
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.92 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.29), residues: 931
  helix:  3.22 (0.28), residues: 316
  sheet:  1.40 (0.26), residues: 388
  loop : -0.24 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  27 
 HIS   0.004   0.001   HIS I 271 
 PHE   0.013   0.001   PHE B 356 
 TYR   0.007   0.001   TYR H  78 
 ARG   0.004   0.000   ARG G  38 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9006 (t0) cc_final: 0.8514 (t0)
REVERT: D   15 GLU cc_start: 0.9030 (pm20) cc_final: 0.8269 (pm20)
REVERT: D   18 ARG cc_start: 0.8924 (ttp80) cc_final: 0.8439 (ttp80)
REVERT: D   19 LYS cc_start: 0.9202 (tptp) cc_final: 0.8508 (tppp)
REVERT: D   20 MET cc_start: 0.8412 (mtp) cc_final: 0.8185 (mtm)
REVERT: D   22 GLU cc_start: 0.8727 (pp20) cc_final: 0.8261 (pp20)
REVERT: F   38 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8214 (tpp80)
REVERT: F   40 ASP cc_start: 0.8360 (t0) cc_final: 0.8122 (t0)
REVERT: G   15 LEU cc_start: 0.9154 (tt) cc_final: 0.8750 (tt)
REVERT: G   44 MET cc_start: 0.8492 (mpp) cc_final: 0.8194 (mpp)
REVERT: E   19 LYS cc_start: 0.8552 (mppt) cc_final: 0.8006 (mptp)
REVERT: E   29 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8682 (ttp80)
REVERT: H   67 PHE cc_start: 0.8714 (t80) cc_final: 0.8412 (t80)
REVERT: H   75 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: H  104 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8390 (tp30)
REVERT: H  107 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: H  111 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8695 (tm-30)
REVERT: H  112 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: C   75 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: C   76 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8223 (mptm)
REVERT: C  102 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8089 (mp0)
REVERT: C  104 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8361 (tp30)
REVERT: C  107 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: J   14 GLN cc_start: 0.8736 (mt0) cc_final: 0.8465 (tt0)
REVERT: J   44 MET cc_start: 0.8424 (mpp) cc_final: 0.8200 (mpp)
REVERT: J   46 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8613 (mm-30)
REVERT: B   76 CYS cc_start: 0.9008 (m) cc_final: 0.8285 (t)
REVERT: B   96 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9092 (pp)
REVERT: B  163 GLN cc_start: 0.8640 (mt0) cc_final: 0.8309 (mt0)
REVERT: B  195 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8625 (mtm-85)
REVERT: B  294 MET cc_start: 0.9193 (mpp) cc_final: 0.8876 (mmm)
REVERT: B  296 ASP cc_start: 0.8130 (m-30) cc_final: 0.7782 (m-30)
REVERT: I   96 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9092 (pp)
REVERT: I  240 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7976 (mtm110)
  outliers start: 25
  outliers final: 8
  residues processed: 214
  average time/residue: 1.4246
  time to fit residues: 323.0820
Evaluate side-chains
  211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 198
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain G residue    6 LYS
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  195 ARG
Chi-restraints excluded: chain I residue   96 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.098649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.066736 restraints weight = 16607.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.51
r_work: 0.2763 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9236  Z= 0.252
  Angle     :  0.615   8.334  12128  Z= 0.303
  Chirality :  0.041   0.192   1182
  Planarity :  0.004   0.042   1371
  Dihedral  : 18.813  85.003   2439
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.16 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.28), residues: 931
  helix:  3.18 (0.28), residues: 316
  sheet:  1.48 (0.26), residues: 388
  loop : -0.27 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  27 
 HIS   0.004   0.001   HIS I 271 
 PHE   0.022   0.001   PHE C  67 
 TYR   0.007   0.001   TYR D  34 
 ARG   0.008   0.001   ARG I 293 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9073 (t0) cc_final: 0.8559 (t0)
REVERT: D   18 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8596 (ttp80)
REVERT: D   19 LYS cc_start: 0.9190 (tptp) cc_final: 0.8490 (tppp)
REVERT: D   20 MET cc_start: 0.8492 (mtp) cc_final: 0.8180 (mtm)
REVERT: D   22 GLU cc_start: 0.8693 (pp20) cc_final: 0.8199 (pp20)
REVERT: D   38 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8866 (mp)
REVERT: F   38 ARG cc_start: 0.8554 (ttm170) cc_final: 0.8293 (tpp80)
REVERT: G   44 MET cc_start: 0.8558 (mpp) cc_final: 0.8214 (mpp)
REVERT: E   22 GLU cc_start: 0.8338 (pp20) cc_final: 0.8099 (pp20)
REVERT: E   29 ARG cc_start: 0.8911 (ttp-110) cc_final: 0.8695 (ttp80)
REVERT: E   38 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8834 (mp)
REVERT: H   67 PHE cc_start: 0.8742 (t80) cc_final: 0.8426 (t80)
REVERT: H   75 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: H  104 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8414 (tp30)
REVERT: H  107 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: H  111 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8640 (tm-30)
REVERT: C   75 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: C  102 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8049 (mp0)
REVERT: C  104 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8380 (tp30)
REVERT: C  107 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: J    9 LYS cc_start: 0.8823 (mptt) cc_final: 0.8582 (mptt)
REVERT: J   14 GLN cc_start: 0.8846 (mt0) cc_final: 0.8512 (tt0)
REVERT: J   44 MET cc_start: 0.8513 (mpp) cc_final: 0.8261 (mpp)
REVERT: J   46 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8647 (mm-30)
REVERT: B   76 CYS cc_start: 0.9016 (m) cc_final: 0.8303 (t)
REVERT: B   96 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9110 (pp)
REVERT: B  163 GLN cc_start: 0.8682 (mt0) cc_final: 0.8382 (mt0)
REVERT: B  195 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8617 (mtm-85)
REVERT: B  293 ARG cc_start: 0.9253 (ttm110) cc_final: 0.9034 (mtp-110)
REVERT: B  294 MET cc_start: 0.9207 (mpp) cc_final: 0.8805 (mmt)
REVERT: B  296 ASP cc_start: 0.8203 (m-30) cc_final: 0.7894 (m-30)
REVERT: I   88 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8485 (tpp80)
REVERT: I   96 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9110 (pp)
REVERT: I  163 GLN cc_start: 0.8608 (mt0) cc_final: 0.8173 (tt0)
REVERT: I  293 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.9015 (ttm110)
REVERT: I  294 MET cc_start: 0.9358 (mmm) cc_final: 0.9133 (mpp)
  outliers start: 28
  outliers final: 7
  residues processed: 207
  average time/residue: 1.2877
  time to fit residues: 282.6394
Evaluate side-chains
  208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 195
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  195 ARG
Chi-restraints excluded: chain I residue   96 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
H 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.099913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.068236 restraints weight = 16491.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.51
r_work: 0.2800 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9236  Z= 0.165
  Angle     :  0.612   9.401  12128  Z= 0.296
  Chirality :  0.040   0.186   1182
  Planarity :  0.004   0.043   1371
  Dihedral  : 18.428  86.535   2439
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.66 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.28), residues: 931
  helix:  3.17 (0.29), residues: 317
  sheet:  1.58 (0.26), residues: 388
  loop : -0.15 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  27 
 HIS   0.003   0.001   HIS I 271 
 PHE   0.012   0.001   PHE B 356 
 TYR   0.008   0.001   TYR H  78 
 ARG   0.009   0.001   ARG I 240 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 207
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9123 (t0) cc_final: 0.8660 (t0)
REVERT: D   15 GLU cc_start: 0.8982 (pm20) cc_final: 0.8484 (pm20)
REVERT: D   16 MET cc_start: 0.9296 (mmm) cc_final: 0.8994 (mpt)
REVERT: D   19 LYS cc_start: 0.9192 (tptp) cc_final: 0.8736 (tppp)
REVERT: D   20 MET cc_start: 0.8410 (mtp) cc_final: 0.8203 (mtm)
REVERT: D   22 GLU cc_start: 0.8695 (pp20) cc_final: 0.8240 (pp20)
REVERT: D   23 ASP cc_start: 0.8952 (m-30) cc_final: 0.8592 (m-30)
REVERT: F   38 ARG cc_start: 0.8497 (ttm170) cc_final: 0.8105 (tpp80)
REVERT: F   40 ASP cc_start: 0.8489 (t0) cc_final: 0.8009 (t0)
REVERT: G   44 MET cc_start: 0.8592 (mpp) cc_final: 0.8211 (mpp)
REVERT: E   18 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8466 (ttp80)
REVERT: E   22 GLU cc_start: 0.8432 (pp20) cc_final: 0.8224 (pp20)
REVERT: E   38 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8837 (mp)
REVERT: H   67 PHE cc_start: 0.8740 (t80) cc_final: 0.8428 (t80)
REVERT: H   75 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: H  104 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8394 (tp30)
REVERT: H  107 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: H  111 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8354 (tm-30)
REVERT: H  112 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8678 (pp30)
REVERT: H  115 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8549 (mm-40)
REVERT: C   75 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: C  102 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8051 (mp0)
REVERT: C  104 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8385 (tp30)
REVERT: C  107 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: C  111 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8880 (pp30)
REVERT: C  115 GLN cc_start: 0.9521 (tm-30) cc_final: 0.9276 (pp30)
REVERT: J    9 LYS cc_start: 0.8742 (mptt) cc_final: 0.8493 (mptt)
REVERT: J   44 MET cc_start: 0.8568 (mpp) cc_final: 0.8316 (mpp)
REVERT: J   46 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8739 (mm-30)
REVERT: B   76 CYS cc_start: 0.9020 (m) cc_final: 0.8307 (t)
REVERT: B  163 GLN cc_start: 0.8624 (mt0) cc_final: 0.8403 (mt0)
REVERT: B  195 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8629 (mtm-85)
REVERT: B  293 ARG cc_start: 0.9247 (ttm110) cc_final: 0.8996 (mtp-110)
REVERT: B  294 MET cc_start: 0.9193 (mpp) cc_final: 0.8780 (mmt)
REVERT: B  296 ASP cc_start: 0.8200 (m-30) cc_final: 0.7848 (m-30)
REVERT: I   88 ARG cc_start: 0.8739 (ttm110) cc_final: 0.8534 (tpp80)
REVERT: I  163 GLN cc_start: 0.8531 (mt0) cc_final: 0.8161 (tt0)
REVERT: I  293 ARG cc_start: 0.9281 (mtp-110) cc_final: 0.9038 (mtp-110)
REVERT: I  294 MET cc_start: 0.9369 (mmm) cc_final: 0.9001 (mpm)
  outliers start: 18
  outliers final: 7
  residues processed: 213
  average time/residue: 1.5193
  time to fit residues: 343.1022
Evaluate side-chains
  206 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 195
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue  195 ARG
Chi-restraints excluded: chain I residue  180 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    0.1980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 267 GLN
I 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.100132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.068661 restraints weight = 16542.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.50
r_work: 0.2804 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9236  Z= 0.165
  Angle     :  0.619   8.776  12128  Z= 0.301
  Chirality :  0.040   0.187   1182
  Planarity :  0.004   0.052   1371
  Dihedral  : 18.081  88.284   2439
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.02 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.28), residues: 931
  helix:  3.27 (0.29), residues: 317
  sheet:  1.65 (0.26), residues: 388
  loop : -0.08 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  27 
 HIS   0.003   0.001   HIS I 220 
 PHE   0.024   0.001   PHE C  67 
 TYR   0.007   0.001   TYR H  78 
 ARG   0.016   0.001   ARG B 240 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9099 (t0) cc_final: 0.8711 (t0)
REVERT: A   38 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8159 (mtm180)
REVERT: D   15 GLU cc_start: 0.9011 (pm20) cc_final: 0.8395 (pm20)
REVERT: D   16 MET cc_start: 0.9265 (mmm) cc_final: 0.8995 (mpt)
REVERT: D   19 LYS cc_start: 0.9244 (tptp) cc_final: 0.8767 (tppp)
REVERT: D   22 GLU cc_start: 0.8681 (pp20) cc_final: 0.8320 (pp20)
REVERT: D   23 ASP cc_start: 0.9016 (m-30) cc_final: 0.8673 (m-30)
REVERT: D   38 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8853 (mp)
REVERT: F   38 ARG cc_start: 0.8463 (ttm170) cc_final: 0.8119 (tpp80)
REVERT: F   40 ASP cc_start: 0.8396 (t0) cc_final: 0.7959 (t0)
REVERT: G   13 GLN cc_start: 0.8435 (mt0) cc_final: 0.8146 (mt0)
REVERT: G   44 MET cc_start: 0.8619 (mpp) cc_final: 0.8233 (mpp)
REVERT: E   18 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8368 (ptm-80)
REVERT: E   22 GLU cc_start: 0.8490 (pp20) cc_final: 0.8151 (pp20)
REVERT: E   38 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8824 (mp)
REVERT: H   67 PHE cc_start: 0.8728 (t80) cc_final: 0.8415 (t80)
REVERT: H   75 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: H  104 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8264 (tp30)
REVERT: H  107 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: H  111 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: H  115 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8676 (mm-40)
REVERT: C   75 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: C  102 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8028 (mp0)
REVERT: C  104 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8368 (tp30)
REVERT: C  107 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: C  111 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8835 (pp30)
REVERT: C  115 GLN cc_start: 0.9483 (tm-30) cc_final: 0.9242 (pp30)
REVERT: J    9 LYS cc_start: 0.8713 (mptt) cc_final: 0.8390 (mptt)
REVERT: J   13 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7939 (pm20)
REVERT: J   44 MET cc_start: 0.8583 (mpp) cc_final: 0.8305 (mpp)
REVERT: J   46 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8671 (mm-30)
REVERT: B   76 CYS cc_start: 0.9015 (m) cc_final: 0.8308 (t)
REVERT: B  195 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8610 (mtm-85)
REVERT: B  293 ARG cc_start: 0.9253 (ttm110) cc_final: 0.9031 (mtp-110)
REVERT: B  294 MET cc_start: 0.9179 (mpp) cc_final: 0.8861 (mmt)
REVERT: I  163 GLN cc_start: 0.8489 (mt0) cc_final: 0.8141 (tt0)
REVERT: I  293 ARG cc_start: 0.9291 (mtp-110) cc_final: 0.9032 (mtp-110)
REVERT: I  294 MET cc_start: 0.9350 (mmm) cc_final: 0.8964 (mpm)
  outliers start: 20
  outliers final: 8
  residues processed: 212
  average time/residue: 1.4463
  time to fit residues: 325.2379
Evaluate side-chains
  211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 198
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain J residue   13 GLN
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue  195 ARG
Chi-restraints excluded: chain I residue  180 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 27 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.099382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.067017 restraints weight = 16714.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.55
r_work: 0.2766 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9236  Z= 0.233
  Angle     :  0.632   9.078  12128  Z= 0.307
  Chirality :  0.040   0.191   1182
  Planarity :  0.004   0.045   1371
  Dihedral  : 17.950  89.579   2439
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.02 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.28), residues: 931
  helix:  3.29 (0.29), residues: 317
  sheet:  1.64 (0.26), residues: 388
  loop : -0.04 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  27 
 HIS   0.004   0.001   HIS I 220 
 PHE   0.013   0.001   PHE B 356 
 TYR   0.009   0.001   TYR D  34 
 ARG   0.015   0.001   ARG D  18 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9091 (t0) cc_final: 0.8757 (t0)
REVERT: D   15 GLU cc_start: 0.9009 (pm20) cc_final: 0.8440 (pm20)
REVERT: D   22 GLU cc_start: 0.8707 (pp20) cc_final: 0.8405 (pp20)
REVERT: D   23 ASP cc_start: 0.9012 (m-30) cc_final: 0.8621 (m-30)
REVERT: D   38 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8813 (mp)
REVERT: F   38 ARG cc_start: 0.8489 (ttm170) cc_final: 0.8110 (tpp80)
REVERT: F   40 ASP cc_start: 0.8417 (t0) cc_final: 0.7946 (t0)
REVERT: G   13 GLN cc_start: 0.8384 (mt0) cc_final: 0.8116 (mt0)
REVERT: G   44 MET cc_start: 0.8655 (mpp) cc_final: 0.8262 (mpp)
REVERT: E   22 GLU cc_start: 0.8516 (pp20) cc_final: 0.8301 (pp20)
REVERT: E   38 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8812 (mp)
REVERT: H   67 PHE cc_start: 0.8732 (t80) cc_final: 0.8419 (t80)
REVERT: H   75 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8147 (tm-30)
REVERT: H  104 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8295 (tp30)
REVERT: H  107 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: H  111 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8680 (tm-30)
REVERT: H  112 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8673 (pp30)
REVERT: C   75 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8239 (tm-30)
REVERT: C  102 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8008 (mp0)
REVERT: C  104 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8404 (tp30)
REVERT: C  107 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: C  115 GLN cc_start: 0.9439 (tm-30) cc_final: 0.9227 (pp30)
REVERT: J    9 LYS cc_start: 0.8801 (mptt) cc_final: 0.8388 (mptt)
REVERT: J   13 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7898 (pm20)
REVERT: J   44 MET cc_start: 0.8573 (mpp) cc_final: 0.8279 (mpp)
REVERT: J   46 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8712 (mm-30)
REVERT: B   76 CYS cc_start: 0.9065 (m) cc_final: 0.8332 (t)
REVERT: B  163 GLN cc_start: 0.8620 (mt0) cc_final: 0.8252 (tt0)
REVERT: B  195 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8587 (mtm-85)
REVERT: B  293 ARG cc_start: 0.9269 (ttm110) cc_final: 0.9035 (mtp-110)
REVERT: B  294 MET cc_start: 0.9113 (mpp) cc_final: 0.8867 (mmt)
REVERT: I  163 GLN cc_start: 0.8556 (mt0) cc_final: 0.8162 (tt0)
REVERT: I  293 ARG cc_start: 0.9320 (mtp-110) cc_final: 0.9090 (ttm110)
  outliers start: 25
  outliers final: 9
  residues processed: 209
  average time/residue: 1.8073
  time to fit residues: 400.0316
Evaluate side-chains
  210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 195
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   13 GLN
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue  195 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    0.4980
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0470
   chunk 87 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.100042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.068164 restraints weight = 16813.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.58
r_work: 0.2791 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9236  Z= 0.178
  Angle     :  0.648   9.313  12128  Z= 0.317
  Chirality :  0.040   0.186   1182
  Planarity :  0.004   0.058   1371
  Dihedral  : 17.637  87.950   2439
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.14 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.29), residues: 931
  helix:  3.31 (0.29), residues: 317
  sheet:  1.67 (0.26), residues: 388
  loop :  0.07 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I 259 
 HIS   0.003   0.001   HIS I 220 
 PHE   0.026   0.001   PHE C  67 
 TYR   0.007   0.001   TYR H  78 
 ARG   0.016   0.001   ARG D  18 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9116 (t0) cc_final: 0.8809 (t0)
REVERT: A   38 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8199 (mtm180)
REVERT: D   19 LYS cc_start: 0.9160 (tptp) cc_final: 0.8540 (tppp)
REVERT: D   22 GLU cc_start: 0.8666 (pp20) cc_final: 0.8271 (pp20)
REVERT: D   23 ASP cc_start: 0.9004 (m-30) cc_final: 0.8610 (m-30)
REVERT: D   38 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8820 (mp)
REVERT: D   48 LEU cc_start: 0.8936 (tt) cc_final: 0.8736 (mp)
REVERT: F   38 ARG cc_start: 0.8501 (ttm170) cc_final: 0.8162 (tpp80)
REVERT: F   40 ASP cc_start: 0.8403 (t0) cc_final: 0.7963 (t0)
REVERT: G   13 GLN cc_start: 0.8409 (mt0) cc_final: 0.8144 (mt0)
REVERT: G   44 MET cc_start: 0.8666 (mpp) cc_final: 0.8259 (mpp)
REVERT: E   19 LYS cc_start: 0.8607 (mppt) cc_final: 0.8240 (tppp)
REVERT: E   22 GLU cc_start: 0.8545 (pp20) cc_final: 0.7982 (pp20)
REVERT: E   38 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8758 (mp)
REVERT: H   67 PHE cc_start: 0.8750 (t80) cc_final: 0.8436 (t80)
REVERT: H   72 PHE cc_start: 0.8817 (t80) cc_final: 0.8558 (t80)
REVERT: H   75 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8155 (tm-30)
REVERT: H  104 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8218 (tp30)
REVERT: H  107 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: H  111 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8678 (tm-30)
REVERT: H  112 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8627 (pp30)
REVERT: C   75 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: C  102 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7997 (mp0)
REVERT: C  104 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8438 (tp30)
REVERT: C  107 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8042 (tm-30)
REVERT: C  115 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9173 (pp30)
REVERT: J   44 MET cc_start: 0.8597 (mpp) cc_final: 0.8314 (mpp)
REVERT: J   46 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8689 (mm-30)
REVERT: B   76 CYS cc_start: 0.9052 (m) cc_final: 0.8331 (t)
REVERT: B  163 GLN cc_start: 0.8589 (mt0) cc_final: 0.8235 (tt0)
REVERT: B  195 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8631 (mtm-85)
REVERT: B  293 ARG cc_start: 0.9258 (ttm110) cc_final: 0.9031 (mtp-110)
REVERT: B  294 MET cc_start: 0.9139 (mpp) cc_final: 0.8870 (mmt)
REVERT: I   88 ARG cc_start: 0.8748 (tpp80) cc_final: 0.8434 (tpp80)
REVERT: I  163 GLN cc_start: 0.8544 (mt0) cc_final: 0.8190 (tt0)
REVERT: I  293 ARG cc_start: 0.9304 (mtp-110) cc_final: 0.9074 (ttm110)
  outliers start: 22
  outliers final: 6
  residues processed: 215
  average time/residue: 1.2797
  time to fit residues: 292.2727
Evaluate side-chains
  214 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 203
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue  195 ARG
Chi-restraints excluded: chain I residue  180 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0170
   chunk 47 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.4026

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.099138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.067337 restraints weight = 16478.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 2.52
r_work: 0.2771 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9236  Z= 0.248
  Angle     :  0.688   9.600  12128  Z= 0.339
  Chirality :  0.041   0.190   1182
  Planarity :  0.005   0.071   1371
  Dihedral  : 17.608  88.184   2439
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.89 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.29), residues: 931
  helix:  3.31 (0.29), residues: 317
  sheet:  1.68 (0.26), residues: 388
  loop :  0.04 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I 188 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.016   0.001   PHE H 101 
 TYR   0.009   0.001   TYR E  34 
 ARG   0.019   0.001   ARG I 240 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9120 (t0) cc_final: 0.8825 (t0)
REVERT: D   19 LYS cc_start: 0.9168 (tptp) cc_final: 0.8439 (tppp)
REVERT: D   22 GLU cc_start: 0.8670 (pp20) cc_final: 0.8264 (pp20)
REVERT: D   23 ASP cc_start: 0.8995 (m-30) cc_final: 0.8569 (m-30)
REVERT: D   38 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8876 (mp)
REVERT: F   38 ARG cc_start: 0.8510 (ttm170) cc_final: 0.8166 (tpp80)
REVERT: F   40 ASP cc_start: 0.8393 (t0) cc_final: 0.7945 (t0)
REVERT: G   13 GLN cc_start: 0.8417 (mt0) cc_final: 0.8142 (mt0)
REVERT: G   44 MET cc_start: 0.8668 (mpp) cc_final: 0.8298 (mpp)
REVERT: E   19 LYS cc_start: 0.8609 (mppt) cc_final: 0.8285 (tppp)
REVERT: E   22 GLU cc_start: 0.8582 (pp20) cc_final: 0.8117 (pp20)
REVERT: E   38 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8788 (mp)
REVERT: H   67 PHE cc_start: 0.8756 (t80) cc_final: 0.8438 (t80)
REVERT: H   75 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: H  104 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8236 (tp30)
REVERT: H  107 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: H  111 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: H  112 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8635 (pp30)
REVERT: C   75 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: C  102 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7962 (mp0)
REVERT: C  104 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8256 (tp30)
REVERT: C  107 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: J   44 MET cc_start: 0.8594 (mpp) cc_final: 0.8299 (mpp)
REVERT: J   46 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8696 (mm-30)
REVERT: B   76 CYS cc_start: 0.9059 (m) cc_final: 0.8319 (t)
REVERT: B  163 GLN cc_start: 0.8613 (mt0) cc_final: 0.8248 (tt0)
REVERT: B  195 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8605 (mtm-85)
REVERT: B  293 ARG cc_start: 0.9269 (ttm110) cc_final: 0.8833 (mtp-110)
REVERT: B  294 MET cc_start: 0.9128 (mpp) cc_final: 0.8672 (mpt)
REVERT: I  163 GLN cc_start: 0.8563 (mt0) cc_final: 0.8179 (tt0)
REVERT: I  293 ARG cc_start: 0.9310 (mtp-110) cc_final: 0.9079 (ttm110)
  outliers start: 17
  outliers final: 7
  residues processed: 211
  average time/residue: 1.2695
  time to fit residues: 284.0014
Evaluate side-chains
  212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 200
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue  195 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0020
   chunk 84 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.100548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.068378 restraints weight = 16732.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.60
r_work: 0.2797 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9236  Z= 0.183
  Angle     :  0.686   9.617  12128  Z= 0.338
  Chirality :  0.041   0.186   1182
  Planarity :  0.005   0.078   1371
  Dihedral  : 17.325  88.502   2439
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 23.26 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.29), residues: 931
  helix:  3.31 (0.29), residues: 314
  sheet:  1.76 (0.26), residues: 386
  loop : -0.01 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 259 
 HIS   0.003   0.001   HIS B 220 
 PHE   0.028   0.001   PHE C  67 
 TYR   0.007   0.001   TYR H  78 
 ARG   0.020   0.001   ARG D  18 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 209
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.9116 (t0) cc_final: 0.8846 (t0)
REVERT: A   38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8138 (mtm180)
REVERT: D   18 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8402 (ttp80)
REVERT: D   19 LYS cc_start: 0.9158 (tptp) cc_final: 0.8383 (tppp)
REVERT: D   22 GLU cc_start: 0.8671 (pp20) cc_final: 0.8167 (pp20)
REVERT: D   23 ASP cc_start: 0.8991 (m-30) cc_final: 0.8526 (m-30)
REVERT: D   38 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8856 (mp)
REVERT: F   38 ARG cc_start: 0.8474 (ttm170) cc_final: 0.8134 (tpp80)
REVERT: F   40 ASP cc_start: 0.8317 (t0) cc_final: 0.7881 (t0)
REVERT: G   13 GLN cc_start: 0.8417 (mt0) cc_final: 0.8134 (mt0)
REVERT: G   44 MET cc_start: 0.8686 (mpp) cc_final: 0.8334 (mpp)
REVERT: E   19 LYS cc_start: 0.8591 (mppt) cc_final: 0.8266 (tppp)
REVERT: E   22 GLU cc_start: 0.8589 (pp20) cc_final: 0.8145 (pp20)
REVERT: E   38 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8803 (mp)
REVERT: H   67 PHE cc_start: 0.8751 (t80) cc_final: 0.8441 (t80)
REVERT: H   72 PHE cc_start: 0.8820 (t80) cc_final: 0.8573 (t80)
REVERT: H   75 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8133 (tm-30)
REVERT: H  104 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8303 (tp30)
REVERT: H  107 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: H  111 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8747 (tm-30)
REVERT: H  112 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8617 (pp30)
REVERT: C   75 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: C  104 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8282 (tp30)
REVERT: C  107 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: C  112 GLN cc_start: 0.9267 (tt0) cc_final: 0.8920 (tm-30)
REVERT: J   44 MET cc_start: 0.8614 (mpp) cc_final: 0.8315 (mpp)
REVERT: J   46 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8687 (mm-30)
REVERT: B   76 CYS cc_start: 0.9016 (m) cc_final: 0.8315 (t)
REVERT: B  163 GLN cc_start: 0.8560 (mt0) cc_final: 0.8225 (tt0)
REVERT: B  293 ARG cc_start: 0.9267 (ttm110) cc_final: 0.8833 (mtp-110)
REVERT: B  294 MET cc_start: 0.9134 (mpp) cc_final: 0.8679 (mpt)
REVERT: I   84 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8658 (tm-30)
REVERT: I   88 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8399 (tpp80)
REVERT: I  163 GLN cc_start: 0.8539 (mt0) cc_final: 0.8194 (tt0)
REVERT: I  293 ARG cc_start: 0.9309 (mtp-110) cc_final: 0.9065 (ttm110)
  outliers start: 15
  outliers final: 7
  residues processed: 214
  average time/residue: 1.3361
  time to fit residues: 302.8687
Evaluate side-chains
  215 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 205
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain E residue   25 ILE
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain H residue   69 LEU
Chi-restraints excluded: chain H residue  112 GLN
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain J residue   13 GLN
Chi-restraints excluded: chain B residue   86 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 11 optimal weight:    0.3980
   chunk 55 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 75 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.100120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068340 restraints weight = 16572.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.57
r_work: 0.2802 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9236  Z= 0.193
  Angle     :  0.688   9.472  12128  Z= 0.338
  Chirality :  0.041   0.186   1182
  Planarity :  0.005   0.072   1371
  Dihedral  : 17.087  89.496   2439
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 23.13 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.29), residues: 931
  helix:  3.36 (0.29), residues: 315
  sheet:  1.75 (0.26), residues: 388
  loop :  0.02 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I 259 
 HIS   0.003   0.001   HIS I 220 
 PHE   0.012   0.001   PHE H 101 
 TYR   0.009   0.001   TYR E  34 
 ARG   0.018   0.001   ARG D  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8555.73 seconds
wall clock time: 151 minutes 0.67 seconds (9060.67 seconds total)