Starting phenix.real_space_refine
on Tue Feb  3 22:17:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ytf_73460/02_2026/9ytf_73460.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ytf_73460/02_2026/9ytf_73460.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ytf_73460/02_2026/9ytf_73460.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ytf_73460/02_2026/9ytf_73460.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ytf_73460/02_2026/9ytf_73460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ytf_73460/02_2026/9ytf_73460.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4546      2.51       5
     N    1258      2.21       5
     O    1435      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7270
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2235
          Classifications: {'peptide': 275}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 259}
    Chain: "B"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 837
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 74
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "D"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 873
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "F"
      Number of atoms: 1600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1600
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205}
    Chain: "G"
      Number of atoms: 1651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1651
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204}
  Time building chain proxies: 1.52, per 1000 atoms: 0.21
  Number of scatterers: 7270
  At special positions: 0
  Unit cell: (69.4701, 94.8322, 148.865, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1435      8.00
     N    1258      7.00
     C    4546      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 259 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 147 " - pdb=" SG  CYS F 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 135 " - pdb=" SG  CYS G 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 318.5 milliseconds
  

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 22 sheets defined
      14.1% alpha, 49.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 55
      removed outlier: 3.514A  pdb=" N   GLU A  53 " --> pdb=" O   PRO A  50 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN A  54 " --> pdb=" O   TRP A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 86
    Processing helix  chain 'A' and resid 137 through 151
    Processing helix  chain 'A' and resid 151 through 162
    Processing helix  chain 'A' and resid 162 through 180
      removed outlier: 6.165A  pdb=" N   GLU A 177 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   THR A 178 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 255
      No H-bonds generated for 'chain 'A' and resid 253 through 255'
    Processing helix  chain 'D' and resid 29 through 33
      removed outlier: 4.097A  pdb=" N   ILE D  33 " --> pdb=" O   ILE D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 92
    Processing helix  chain 'F' and resid 87 through 91
    Processing helix  chain 'F' and resid 134 through 136
      No H-bonds generated for 'chain 'F' and resid 134 through 136'
    Processing helix  chain 'F' and resid 163 through 165
      No H-bonds generated for 'chain 'F' and resid 163 through 165'
    Processing helix  chain 'F' and resid 194 through 196
      No H-bonds generated for 'chain 'F' and resid 194 through 196'
    Processing helix  chain 'G' and resid 79 through 83
      removed outlier: 3.650A  pdb=" N   PHE G  83 " --> pdb=" O   PRO G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 122 through 129
    Processing helix  chain 'G' and resid 184 through 190
      removed outlier: 3.844A  pdb=" N   HIS G 190 " --> pdb=" O   ASP G 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 6.857A  pdb=" N   GLY A  26 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA A  24 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ASP A  37 " --> pdb=" O   PHE A  22 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   PHE A  22 " --> pdb=" O   ASP A  37 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   THR A  94 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   TYR A 118 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   GLN A  96 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ASP A 116 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   MET A  98 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ARG A 114 " --> pdb=" O   MET A  98 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY A 100 " --> pdb=" O   GLY A 112 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   GLY A 112 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ASP A 102 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   ARG A 114 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   TYR A 118 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   ASP A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 193
      removed outlier: 5.492A  pdb=" N   PHE A 241 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193
      removed outlier: 5.492A  pdb=" N   PHE A 241 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223
      removed outlier: 3.674A  pdb=" N   VAL A 261 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11
      removed outlier: 5.944A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11
      removed outlier: 5.944A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER B  55 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 9
      removed outlier: 4.190A  pdb=" N   THR D  79 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 14
      removed outlier: 6.459A  pdb=" N   GLY D  12 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   VAL D  94 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   MET D  36 " --> pdb=" O   ASP D  52 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ASP D  52 " --> pdb=" O   MET D  36 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   TRP D  38 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN D  46 " --> pdb=" O   THR D  42 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 14
      removed outlier: 6.459A  pdb=" N   GLY D  12 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.856A  pdb=" N   ILE F  34 " --> pdb=" O   GLY F  50 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLY F  50 " --> pdb=" O   ILE F  34 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   TRP F  36 " --> pdb=" O   MET F  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12
      removed outlier: 3.598A  pdb=" N   ILE F 109 " --> pdb=" O   ARG F  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 18 through 20
    Processing sheet with id=AB6, first strand: chain 'F' and resid 127 through 131
      removed outlier: 6.011A  pdb=" N   TYR F 183 " --> pdb=" O   ASP F 151 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 138 through 139
      removed outlier: 6.011A  pdb=" N   TYR F 183 " --> pdb=" O   ASP F 151 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 158 through 161
      removed outlier: 4.827A  pdb=" N   TYR F 201 " --> pdb=" O   VAL F 218 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 13
      removed outlier: 6.647A  pdb=" N   LEU G  33 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   TYR G  49 " --> pdb=" O   LEU G  33 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TRP G  35 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 13
      removed outlier: 3.552A  pdb=" N   THR G  98 " --> pdb=" O   GLN G  90 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   SER G  92 " --> pdb=" O   GLN G  96 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   GLN G  96 " --> pdb=" O   SER G  92 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 115 through 119
      removed outlier: 5.803A  pdb=" N   TYR G 174 " --> pdb=" O   ASN G 139 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 154 through 155

    378 hydrogen bonds defined for protein.
    978 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: 0.85

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2399
        1.34 -     1.46: 1660
        1.46 -     1.57: 3335
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 7439
  Sorted by residual:
  bond pdb=" N   HIS A 151 "
       pdb=" CA  HIS A 151 "
    ideal  model  delta    sigma   weight residual
    1.458  1.471 -0.013 1.35e-02 5.49e+03 9.62e-01
  bond pdb=" C   ASP A  29 "
       pdb=" O   ASP A  29 "
    ideal  model  delta    sigma   weight residual
    1.243  1.235  0.009 9.50e-03 1.11e+04 8.51e-01
  bond pdb=" CG1 ILE G  48 "
       pdb=" CD1 ILE G  48 "
    ideal  model  delta    sigma   weight residual
    1.513  1.478  0.035 3.90e-02 6.57e+02 8.01e-01
  bond pdb=" CA  ILE A 194 "
       pdb=" CB  ILE A 194 "
    ideal  model  delta    sigma   weight residual
    1.545  1.538  0.007 9.10e-03 1.21e+04 6.31e-01
  bond pdb=" C   SER A  13 "
       pdb=" N   ARG A  14 "
    ideal  model  delta    sigma   weight residual
    1.333  1.320  0.012 1.59e-02 3.96e+03 6.00e-01
  ... (remaining 7434 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 9960
        1.68 -     3.36: 122
        3.36 -     5.04: 12
        5.04 -     6.71: 1
        6.71 -     8.39: 1
  Bond angle restraints: 10096
  Sorted by residual:
  angle pdb=" C   ASP A  29 "
        pdb=" CA  ASP A  29 "
        pdb=" CB  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     117.23  110.90    6.33 1.36e+00 5.41e-01 2.16e+01
  angle pdb=" CA  ASP A  29 "
        pdb=" C   ASP A  29 "
        pdb=" N   ASP A  30 "
      ideal   model   delta    sigma   weight residual
     119.98  117.32    2.66 8.50e-01 1.38e+00 9.77e+00
  angle pdb=" N   ILE A 194 "
        pdb=" CA  ILE A 194 "
        pdb=" C   ILE A 194 "
      ideal   model   delta    sigma   weight residual
     111.48  108.67    2.81 9.40e-01 1.13e+00 8.95e+00
  angle pdb=" C   LEU G  50 "
        pdb=" N   SER G  51 "
        pdb=" CA  SER G  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.15   -4.61 1.91e+00 2.74e-01 5.83e+00
  angle pdb=" CA  LEU F 185 "
        pdb=" CB  LEU F 185 "
        pdb=" CG  LEU F 185 "
      ideal   model   delta    sigma   weight residual
     116.30  124.69   -8.39 3.50e+00 8.16e-02 5.75e+00
  ... (remaining 10091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4254
       17.79 -    35.57: 164
       35.57 -    53.36: 28
       53.36 -    71.14: 8
       71.14 -    88.93: 2
  Dihedral angle restraints: 4456
    sinusoidal: 1769
      harmonic: 2687
  Sorted by residual:
  dihedral pdb=" CA  TYR A  27 "
           pdb=" C   TYR A  27 "
           pdb=" N   VAL A  28 "
           pdb=" CA  VAL A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.59   19.41     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  VAL A 150 "
           pdb=" C   VAL A 150 "
           pdb=" N   HIS A 151 "
           pdb=" CA  HIS A 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  ILE G  93 "
           pdb=" C   ILE G  93 "
           pdb=" N   ALA G  94 "
           pdb=" CA  ALA G  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.61  -17.39     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 4453 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 592
       0.026 -    0.052: 296
       0.052 -    0.078: 104
       0.078 -    0.104: 68
       0.104 -    0.130: 32
  Chirality restraints: 1092
  Sorted by residual:
  chirality pdb=" CA  ILE G  75 "
            pdb=" N   ILE G  75 "
            pdb=" C   ILE G  75 "
            pdb=" CB  ILE G  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE G  21 "
            pdb=" N   ILE G  21 "
            pdb=" C   ILE G  21 "
            pdb=" CB  ILE G  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  chirality pdb=" CA  VAL F  37 "
            pdb=" N   VAL F  37 "
            pdb=" C   VAL F  37 "
            pdb=" CB  VAL F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 1089 not shown)

  Planarity restraints: 1313
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F 155 "   -0.034 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO F 156 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO F 156 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO F 156 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B   4 "    0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO B   5 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B   5 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B   5 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 268 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 269 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 269 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 269 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1310 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 644
        2.74 -     3.28: 6450
        3.28 -     3.82: 11945
        3.82 -     4.36: 14771
        4.36 -     4.90: 25909
  Nonbonded interactions: 59719
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 232 "
            pdb=" OG  SER B  28 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   PRO A 235 "
            pdb=" OH  TYR B  10 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR A 159 "
            pdb=" O   GLU C   1 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" NH2 ARG D  68 "
            pdb=" OD2 ASP D  91 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" NZ  LYS G  39 "
            pdb=" OD1 ASP G  81 "
     model   vdw
     2.260 3.120
  ... (remaining 59714 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.790
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.310
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:6.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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      :  0.004   0.035   7447  Z= 0.185
  Angle     :  0.504   8.392  10112  Z= 0.275
  Chirality :  0.042   0.130   1092
  Planarity :  0.004   0.051   1313
  Dihedral  : 10.125  88.926   2718
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.27), residues: 920
  helix:  2.04 (0.52), residues: 92
  sheet:  1.23 (0.25), residues: 420
  loop :  0.28 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  47 
 TYR   0.015   0.001   TYR A  99 
 PHE   0.014   0.002   PHE A 109 
 TRP   0.009   0.001   TRP A  60 
 HIS   0.003   0.001   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 7439)
  covalent geometry    : angle       0.50329 (10096)
  SS BOND              : bond        0.00338 (    8)
  SS BOND              : angle       0.67069 (   16)
  hydrogen bonds       : bond        0.17417 (  325)
  hydrogen bonds       : angle       7.77039 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8159 (mm110)
REVERT: A   98 MET cc_start: 0.8366 (tmm) cc_final: 0.8145 (tmt)
REVERT: A  106 ASP cc_start: 0.8046 (p0) cc_final: 0.7277 (p0)
REVERT: A  108 ARG cc_start: 0.7345 (ptt90) cc_final: 0.6819 (ptt90)
REVERT: A  116 ASP cc_start: 0.8533 (m-30) cc_final: 0.8277 (m-30)
REVERT: B    0 MET cc_start: 0.5503 (tpt) cc_final: 0.5017 (tpt)
REVERT: B    7 ILE cc_start: 0.8909 (mt) cc_final: 0.8707 (mp)
REVERT: B   99 MET cc_start: 0.5054 (mmm) cc_final: 0.4670 (mmm)
REVERT: D   84 MET cc_start: 0.8704 (mtm) cc_final: 0.8298 (mtp)
REVERT: F    3 GLN cc_start: 0.8211 (mt0) cc_final: 0.7963 (mt0)
REVERT: F   46 GLU cc_start: 0.8253 (tt0) cc_final: 0.7963 (tt0)
REVERT: F  190 THR cc_start: 0.8941 (p) cc_final: 0.8714 (m)
REVERT: G   82 ASP cc_start: 0.8243 (m-30) cc_final: 0.7893 (m-30)
REVERT: G  164 VAL cc_start: 0.8981 (t) cc_final: 0.8769 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.6978
  time to fit residues: 115.9384
Evaluate side-chains
  139 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0970
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
G 125 GLN
** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.108815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.097644 restraints weight = 10286.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.71
r_work: 0.3189 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7447  Z= 0.175
  Angle     :  0.527   8.051  10112  Z= 0.284
  Chirality :  0.043   0.142   1092
  Planarity :  0.005   0.050   1313
  Dihedral  :  4.494  25.770   1026
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.77 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.27), residues: 920
  helix:  2.16 (0.54), residues: 92
  sheet:  1.29 (0.24), residues: 420
  loop :  0.26 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B   3 
 TYR   0.015   0.002   TYR A  99 
 PHE   0.012   0.002   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7439)
  covalent geometry    : angle       0.52655 (10096)
  SS BOND              : bond        0.00685 (    8)
  SS BOND              : angle       0.68943 (   16)
  hydrogen bonds       : bond        0.04311 (  325)
  hydrogen bonds       : angle       5.56181 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   72 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8123 (mm-40)
REVERT: A  106 ASP cc_start: 0.8206 (p0) cc_final: 0.7457 (p0)
REVERT: A  108 ARG cc_start: 0.8012 (ptt90) cc_final: 0.7399 (ptt90)
REVERT: A  121 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8207 (mtmm)
REVERT: B    0 MET cc_start: 0.5730 (tpt) cc_final: 0.5256 (tpt)
REVERT: B    7 ILE cc_start: 0.8868 (mt) cc_final: 0.8650 (mp)
REVERT: B   99 MET cc_start: 0.4972 (mmm) cc_final: 0.4621 (mmm)
REVERT: D   84 MET cc_start: 0.8540 (mtm) cc_final: 0.8236 (mtp)
REVERT: D   86 SER cc_start: 0.8583 (m) cc_final: 0.8371 (t)
REVERT: F   81 MET cc_start: 0.8474 (tmm) cc_final: 0.7854 (tmt)
REVERT: G   82 ASP cc_start: 0.8200 (m-30) cc_final: 0.7862 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 134
  average time/residue: 0.6659
  time to fit residues: 92.7446
Evaluate side-chains
  129 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  130 THR
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  197 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0040
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  24 ASN
** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.109144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.097679 restraints weight = 9951.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.73
r_work: 0.3175 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7447  Z= 0.182
  Angle     :  0.524   8.023  10112  Z= 0.278
  Chirality :  0.043   0.142   1092
  Planarity :  0.005   0.048   1313
  Dihedral  :  4.463  26.752   1026
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 10.40 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.27), residues: 920
  helix:  2.03 (0.53), residues: 92
  sheet:  1.26 (0.24), residues: 421
  loop :  0.26 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B   3 
 TYR   0.016   0.002   TYR A  99 
 PHE   0.012   0.002   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 7439)
  covalent geometry    : angle       0.52398 (10096)
  SS BOND              : bond        0.00409 (    8)
  SS BOND              : angle       0.62691 (   16)
  hydrogen bonds       : bond        0.03983 (  325)
  hydrogen bonds       : angle       5.19569 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   72 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8001 (mm-40)
REVERT: A  106 ASP cc_start: 0.8222 (p0) cc_final: 0.7515 (p0)
REVERT: A  108 ARG cc_start: 0.8040 (ptt90) cc_final: 0.7387 (ptt90)
REVERT: B    0 MET cc_start: 0.5726 (tpt) cc_final: 0.5306 (tpt)
REVERT: B    7 ILE cc_start: 0.8861 (mt) cc_final: 0.8644 (mp)
REVERT: B   99 MET cc_start: 0.4953 (mmm) cc_final: 0.4614 (mmm)
REVERT: D   86 SER cc_start: 0.8581 (m) cc_final: 0.8325 (t)
REVERT: F   81 MET cc_start: 0.8488 (tmm) cc_final: 0.7836 (tmt)
REVERT: F  150 LYS cc_start: 0.8228 (tttp) cc_final: 0.7670 (mtmt)
REVERT: G   82 ASP cc_start: 0.8232 (m-30) cc_final: 0.7847 (m-30)
  outliers start: 11
  outliers final: 7
  residues processed: 128
  average time/residue: 0.7571
  time to fit residues: 100.6890
Evaluate side-chains
  126 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain F residue  210 SER
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  197 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0980
   chunk 85 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.109212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098007 restraints weight = 10105.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.68
r_work: 0.3182 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7447  Z= 0.152
  Angle     :  0.498   7.509  10112  Z= 0.265
  Chirality :  0.042   0.138   1092
  Planarity :  0.004   0.048   1313
  Dihedral  :  4.373  27.168   1026
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.78 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.27), residues: 920
  helix:  2.07 (0.53), residues: 92
  sheet:  1.25 (0.24), residues: 422
  loop :  0.26 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  82 
 TYR   0.014   0.001   TYR A  99 
 PHE   0.012   0.001   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7439)
  covalent geometry    : angle       0.49800 (10096)
  SS BOND              : bond        0.00336 (    8)
  SS BOND              : angle       0.53536 (   16)
  hydrogen bonds       : bond        0.03653 (  325)
  hydrogen bonds       : angle       4.97268 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.8225 (p0) cc_final: 0.7508 (p0)
REVERT: A  108 ARG cc_start: 0.8042 (ptt90) cc_final: 0.7406 (ptt90)
REVERT: B    0 MET cc_start: 0.5817 (tpt) cc_final: 0.5394 (tpt)
REVERT: B   99 MET cc_start: 0.4893 (mmm) cc_final: 0.4572 (mmm)
REVERT: D   21 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8267 (ttt90)
REVERT: D   86 SER cc_start: 0.8582 (m) cc_final: 0.8334 (t)
REVERT: F   81 MET cc_start: 0.8495 (tmm) cc_final: 0.7782 (tmt)
REVERT: F   85 SER cc_start: 0.8676 (m) cc_final: 0.8394 (t)
REVERT: F  115 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8310 (tpt)
REVERT: F  150 LYS cc_start: 0.8187 (tttp) cc_final: 0.7695 (mtmt)
REVERT: G   82 ASP cc_start: 0.8206 (m-30) cc_final: 0.7844 (m-30)
REVERT: G  125 GLN cc_start: 0.8173 (tt0) cc_final: 0.7853 (tt0)
  outliers start: 19
  outliers final: 10
  residues processed: 128
  average time/residue: 0.6745
  time to fit residues: 89.8705
Evaluate side-chains
  133 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  210 SER
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  24 ASN
G   6 GLN
G 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.108999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.097895 restraints weight = 9970.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.65
r_work: 0.3178 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7447  Z= 0.177
  Angle     :  0.515   7.795  10112  Z= 0.272
  Chirality :  0.043   0.139   1092
  Planarity :  0.004   0.047   1313
  Dihedral  :  4.407  27.941   1026
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.65 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.27), residues: 920
  helix:  1.99 (0.53), residues: 92
  sheet:  1.25 (0.24), residues: 422
  loop :  0.25 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  82 
 TYR   0.016   0.002   TYR A  99 
 PHE   0.012   0.002   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7439)
  covalent geometry    : angle       0.51499 (10096)
  SS BOND              : bond        0.00362 (    8)
  SS BOND              : angle       0.56679 (   16)
  hydrogen bonds       : bond        0.03727 (  325)
  hydrogen bonds       : angle       4.92852 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.8250 (p0) cc_final: 0.7563 (p0)
REVERT: A  108 ARG cc_start: 0.8046 (ptt90) cc_final: 0.7458 (ptt90)
REVERT: A  138 MET cc_start: 0.7514 (mmp) cc_final: 0.6831 (mpp)
REVERT: B    0 MET cc_start: 0.5871 (tpt) cc_final: 0.5457 (tpt)
REVERT: B   99 MET cc_start: 0.4883 (mmm) cc_final: 0.4576 (mmm)
REVERT: D   21 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8279 (ttt90)
REVERT: D   86 SER cc_start: 0.8571 (m) cc_final: 0.8350 (t)
REVERT: F   81 MET cc_start: 0.8478 (tmm) cc_final: 0.7819 (tmt)
REVERT: F   85 SER cc_start: 0.8657 (m) cc_final: 0.8397 (t)
REVERT: F  115 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8345 (tpt)
REVERT: F  150 LYS cc_start: 0.8172 (tttp) cc_final: 0.7693 (mtmt)
REVERT: G   82 ASP cc_start: 0.8196 (m-30) cc_final: 0.7856 (m-30)
REVERT: G  125 GLN cc_start: 0.8225 (tt0) cc_final: 0.7931 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 126
  average time/residue: 0.7482
  time to fit residues: 97.9148
Evaluate side-chains
  129 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  210 SER
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  157 SER
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
G   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.108810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.097728 restraints weight = 9950.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.65
r_work: 0.3179 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7447  Z= 0.185
  Angle     :  0.519   7.949  10112  Z= 0.273
  Chirality :  0.043   0.138   1092
  Planarity :  0.004   0.047   1313
  Dihedral  :  4.426  28.404   1026
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.28 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.27), residues: 920
  helix:  1.92 (0.53), residues: 92
  sheet:  1.23 (0.24), residues: 422
  loop :  0.25 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  82 
 TYR   0.014   0.001   TYR A  99 
 PHE   0.013   0.002   PHE A 109 
 TRP   0.008   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7439)
  covalent geometry    : angle       0.51869 (10096)
  SS BOND              : bond        0.00372 (    8)
  SS BOND              : angle       0.56758 (   16)
  hydrogen bonds       : bond        0.03716 (  325)
  hydrogen bonds       : angle       4.89939 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.8259 (p0) cc_final: 0.7513 (p0)
REVERT: A  108 ARG cc_start: 0.8071 (ptt90) cc_final: 0.7586 (ptt90)
REVERT: B    0 MET cc_start: 0.5910 (tpt) cc_final: 0.5528 (tpt)
REVERT: B   99 MET cc_start: 0.4876 (mmm) cc_final: 0.4575 (mmm)
REVERT: D   21 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8309 (ttt180)
REVERT: D   86 SER cc_start: 0.8566 (m) cc_final: 0.8354 (t)
REVERT: F   81 MET cc_start: 0.8467 (tmm) cc_final: 0.7801 (tmt)
REVERT: F   85 SER cc_start: 0.8648 (m) cc_final: 0.8395 (t)
REVERT: F  115 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8289 (tpt)
REVERT: F  150 LYS cc_start: 0.8164 (tttp) cc_final: 0.7692 (mtmt)
REVERT: G   82 ASP cc_start: 0.8191 (m-30) cc_final: 0.7855 (m-30)
REVERT: G  125 GLN cc_start: 0.8216 (tt0) cc_final: 0.7927 (tt0)
  outliers start: 18
  outliers final: 10
  residues processed: 126
  average time/residue: 0.5772
  time to fit residues: 75.7122
Evaluate side-chains
  132 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain F residue   48 MET
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  210 SER
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 262 GLN
B  24 ASN
G   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.108884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.097663 restraints weight = 9986.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.67
r_work: 0.3187 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7447  Z= 0.189
  Angle     :  0.524   7.976  10112  Z= 0.275
  Chirality :  0.043   0.138   1092
  Planarity :  0.004   0.047   1313
  Dihedral  :  4.445  28.894   1026
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.66 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.27), residues: 920
  helix:  1.86 (0.52), residues: 92
  sheet:  1.16 (0.24), residues: 425
  loop :  0.33 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   3 
 TYR   0.014   0.002   TYR A  99 
 PHE   0.013   0.002   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 7439)
  covalent geometry    : angle       0.52431 (10096)
  SS BOND              : bond        0.00379 (    8)
  SS BOND              : angle       0.58397 (   16)
  hydrogen bonds       : bond        0.03746 (  325)
  hydrogen bonds       : angle       4.89583 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8189 (mt-10)
REVERT: A  106 ASP cc_start: 0.8264 (p0) cc_final: 0.7537 (p0)
REVERT: A  108 ARG cc_start: 0.8050 (ptt90) cc_final: 0.7555 (ptt90)
REVERT: A  253 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7464 (mm-30)
REVERT: B    0 MET cc_start: 0.5860 (tpt) cc_final: 0.5486 (tpt)
REVERT: B   99 MET cc_start: 0.4920 (mmm) cc_final: 0.4599 (mmm)
REVERT: D   21 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8343 (ttt180)
REVERT: D   86 SER cc_start: 0.8558 (m) cc_final: 0.8331 (t)
REVERT: F   81 MET cc_start: 0.8467 (tmm) cc_final: 0.7834 (tmt)
REVERT: F   85 SER cc_start: 0.8650 (m) cc_final: 0.8382 (t)
REVERT: F  115 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8346 (tpt)
REVERT: F  150 LYS cc_start: 0.8164 (tttp) cc_final: 0.7697 (mtmt)
REVERT: G   82 ASP cc_start: 0.8209 (m-30) cc_final: 0.7861 (m-30)
REVERT: G  125 GLN cc_start: 0.8163 (tt0) cc_final: 0.7840 (tt0)
  outliers start: 19
  outliers final: 12
  residues processed: 129
  average time/residue: 0.6515
  time to fit residues: 87.2824
Evaluate side-chains
  131 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain F residue   48 MET
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  210 SER
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 1 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 262 GLN
G   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.098489 restraints weight = 9966.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.66
r_work: 0.3200 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7447  Z= 0.128
  Angle     :  0.503   8.790  10112  Z= 0.262
  Chirality :  0.042   0.135   1092
  Planarity :  0.004   0.047   1313
  Dihedral  :  4.315  29.070   1026
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.91 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.27), residues: 920
  helix:  1.96 (0.52), residues: 92
  sheet:  1.20 (0.24), residues: 424
  loop :  0.32 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  82 
 TYR   0.014   0.001   TYR A  99 
 PHE   0.011   0.001   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7439)
  covalent geometry    : angle       0.50282 (10096)
  SS BOND              : bond        0.00267 (    8)
  SS BOND              : angle       0.49273 (   16)
  hydrogen bonds       : bond        0.03386 (  325)
  hydrogen bonds       : angle       4.75040 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B    0 MET cc_start: 0.5918 (tpt) cc_final: 0.5549 (tpt)
REVERT: B   99 MET cc_start: 0.4852 (mmm) cc_final: 0.4538 (mmm)
REVERT: D   86 SER cc_start: 0.8560 (m) cc_final: 0.8326 (t)
REVERT: F   81 MET cc_start: 0.8491 (tmm) cc_final: 0.7804 (tmt)
REVERT: F   85 SER cc_start: 0.8652 (m) cc_final: 0.8384 (t)
REVERT: F  115 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8291 (tpt)
REVERT: G   82 ASP cc_start: 0.8185 (m-30) cc_final: 0.7837 (m-30)
REVERT: G  125 GLN cc_start: 0.8123 (tt0) cc_final: 0.7805 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 126
  average time/residue: 0.6648
  time to fit residues: 87.1605
Evaluate side-chains
  125 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0010
   chunk 21 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 262 GLN
B  24 ASN
G   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.109837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098405 restraints weight = 9911.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.72
r_work: 0.3187 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7447  Z= 0.127
  Angle     :  0.494   7.173  10112  Z= 0.259
  Chirality :  0.041   0.135   1092
  Planarity :  0.004   0.048   1313
  Dihedral  :  4.245  29.093   1026
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.79 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.27), residues: 920
  helix:  2.00 (0.53), residues: 92
  sheet:  1.28 (0.25), residues: 415
  loop :  0.31 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.013   0.001   TYR A  99 
 PHE   0.012   0.001   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7439)
  covalent geometry    : angle       0.49431 (10096)
  SS BOND              : bond        0.00254 (    8)
  SS BOND              : angle       0.48116 (   16)
  hydrogen bonds       : bond        0.03320 (  325)
  hydrogen bonds       : angle       4.66253 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B    0 MET cc_start: 0.5905 (tpt) cc_final: 0.5526 (tpt)
REVERT: D   86 SER cc_start: 0.8568 (m) cc_final: 0.8304 (t)
REVERT: F   81 MET cc_start: 0.8507 (tmm) cc_final: 0.7818 (tmt)
REVERT: F   85 SER cc_start: 0.8664 (m) cc_final: 0.8380 (t)
REVERT: F  115 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8307 (tpt)
REVERT: G   82 ASP cc_start: 0.8222 (m-30) cc_final: 0.7849 (m-30)
REVERT: G  125 GLN cc_start: 0.8101 (tt0) cc_final: 0.7783 (tt0)
  outliers start: 11
  outliers final: 9
  residues processed: 121
  average time/residue: 0.6713
  time to fit residues: 84.4703
Evaluate side-chains
  123 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0980
   chunk 43 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 262 GLN
G   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.108689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097258 restraints weight = 10017.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.73
r_work: 0.3170 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7447  Z= 0.220
  Angle     :  0.537   7.928  10112  Z= 0.280
  Chirality :  0.043   0.143   1092
  Planarity :  0.004   0.048   1313
  Dihedral  :  4.387  29.182   1026
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.66 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.27), residues: 920
  helix:  1.72 (0.52), residues: 92
  sheet:  1.21 (0.25), residues: 425
  loop :  0.29 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B   3 
 TYR   0.014   0.002   TYR G  91 
 PHE   0.012   0.002   PHE A 109 
 TRP   0.008   0.002   TRP A 244 
 HIS   0.007   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 7439)
  covalent geometry    : angle       0.53641 (10096)
  SS BOND              : bond        0.00409 (    8)
  SS BOND              : angle       0.72781 (   16)
  hydrogen bonds       : bond        0.03727 (  325)
  hydrogen bonds       : angle       4.80188 (  978)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.276 
Fit side-chains
REVERT: B    0 MET cc_start: 0.5918 (tpt) cc_final: 0.5546 (tpt)
REVERT: D   86 SER cc_start: 0.8567 (m) cc_final: 0.8306 (t)
REVERT: F   81 MET cc_start: 0.8483 (tmm) cc_final: 0.7852 (tmt)
REVERT: F   85 SER cc_start: 0.8676 (m) cc_final: 0.8387 (t)
REVERT: F  115 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8401 (tpt)
REVERT: G   82 ASP cc_start: 0.8240 (m-30) cc_final: 0.7891 (m-30)
  outliers start: 13
  outliers final: 11
  residues processed: 122
  average time/residue: 0.6841
  time to fit residues: 86.6919
Evaluate side-chains
  127 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain F residue   38 ARG
Chi-restraints excluded: chain F residue  115 MET
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  195 SER
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  197 VAL
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
G   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.108735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.097515 restraints weight = 10004.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.67
r_work: 0.3176 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7447  Z= 0.191
  Angle     :  0.527   7.899  10112  Z= 0.276
  Chirality :  0.043   0.141   1092
  Planarity :  0.004   0.047   1313
  Dihedral  :  4.403  29.424   1026
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.91 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.27), residues: 920
  helix:  1.65 (0.52), residues: 92
  sheet:  1.18 (0.24), residues: 425
  loop :  0.26 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   3 
 TYR   0.013   0.002   TYR A  99 
 PHE   0.012   0.002   PHE A 109 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.008   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 7439)
  covalent geometry    : angle       0.52664 (10096)
  SS BOND              : bond        0.00388 (    8)
  SS BOND              : angle       0.73237 (   16)
  hydrogen bonds       : bond        0.03673 (  325)
  hydrogen bonds       : angle       4.80945 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2649.97 seconds
wall clock time: 45 minutes 50.80 seconds (2750.80 seconds total)