Starting phenix.real_space_refine
on Mon May 12 03:05:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ejc_28177/05_2025/8ejc_28177.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ejc_28177/05_2025/8ejc_28177.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ejc_28177/05_2025/8ejc_28177.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ejc_28177/05_2025/8ejc_28177.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ejc_28177/05_2025/8ejc_28177.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ejc_28177/05_2025/8ejc_28177.cif"
  }
  resolution = 3.0
  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=   0.004
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      50      5.16       5
     C    5506      2.51       5
     N    1489      2.21       5
     O    1614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8659
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1877
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2572
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "C"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 406
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "E"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 1983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1983
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 20, 'TRANS': 250}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "R"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'2YB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.54, per 1000 atoms: 0.76
  Number of scatterers: 8659
  At special positions: 0
  Unit cell: (96.3, 115.56, 129.47, 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      50     16.00
     O    1614      8.00
     N    1489      7.00
     C    5506      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      39.0% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 4.324A  pdb=" N   THR A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.918A  pdb=" N   ILE A  49 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 93
      removed outlier: 3.737A  pdb=" N   ASN A  93 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 122
    Processing helix  chain 'A' and resid 137 through 148
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 3.870A  pdb=" N   PHE A 156 " --> pdb=" O   GLU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 4.040A  pdb=" N   ARG A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 195
      removed outlier: 3.620A  pdb=" N   PHE A 189 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 235
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.915A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 7 through 28
      removed outlier: 4.306A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.137A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.582A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 37
      Proline residue:  R  21  - end of helix
      removed outlier: 4.197A  pdb=" N   LEU R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG R  37 " --> pdb=" O   HIS R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 68
      Proline residue:  R  60  - end of helix
    Processing helix  chain 'R' and resid 75 through 77
      No H-bonds generated for 'chain 'R' and resid 75 through 77'
    Processing helix  chain 'R' and resid 78 through 110
      Proline residue:  R  89  - end of helix
    Processing helix  chain 'R' and resid 110 through 117
    Processing helix  chain 'R' and resid 119 through 144
      removed outlier: 3.683A  pdb=" N   SER R 123 " --> pdb=" O   ARG R 119 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU R 144 " --> pdb=" O   LEU R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 212
      Proline residue:  R 181  - end of helix
      removed outlier: 4.919A  pdb=" N   LEU R 193 " --> pdb=" O   LEU R 189 " (cutoff:3.500A)
      Proline residue:  R 194  - end of helix
    Processing helix  chain 'R' and resid 215 through 235
    Processing helix  chain 'R' and resid 236 through 250
      removed outlier: 3.875A  pdb=" N   TYR R 240 " --> pdb=" O   CYS R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 277
      removed outlier: 3.801A  pdb=" N   LYS R 259 " --> pdb=" O   GLY R 255 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   VAL R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68
      removed outlier: 3.820A  pdb=" N   ALA A  97 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.179A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.598A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.515A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.535A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.727A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.540A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.506A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60
      removed outlier: 6.546A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149
      removed outlier: 3.893A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    456 hydrogen bonds defined for protein.
    1284 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: 3.34

  Time building geometry restraints manager: 2.59 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: 2831
        1.34 -     1.46: 2186
        1.46 -     1.58: 3770
        1.58 -     1.71: 0
        1.71 -     1.83: 68
  Bond restraints: 8855
  Sorted by residual:
  bond pdb=" C27 2YB R 401 "
       pdb=" C28 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.505  1.384  0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" C1  2YB R 401 "
       pdb=" C2  2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.391  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C14 2YB R 401 "
       pdb=" C15 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.390  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C21 2YB R 401 "
       pdb=" C22 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.498  1.391  0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C16 2YB R 401 "
       pdb=" C17 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.485  1.394  0.091 2.00e-02 2.50e+03 2.05e+01
  ... (remaining 8850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 11699
        1.62 -     3.25: 281
        3.25 -     4.87: 42
        4.87 -     6.50: 14
        6.50 -     8.12: 6
  Bond angle restraints: 12042
  Sorted by residual:
  angle pdb=" CA  TRP R 131 "
        pdb=" CB  TRP R 131 "
        pdb=" CG  TRP R 131 "
      ideal   model   delta    sigma   weight residual
     113.60  119.94   -6.34 1.90e+00 2.77e-01 1.11e+01
  angle pdb=" O11 2YB R 401 "
        pdb=" S9  2YB R 401 "
        pdb=" O12 2YB R 401 "
      ideal   model   delta    sigma   weight residual
     117.70  109.58    8.12 3.00e+00 1.11e-01 7.33e+00
  angle pdb=" N   GLU A 171 "
        pdb=" CA  GLU A 171 "
        pdb=" C   GLU A 171 "
      ideal   model   delta    sigma   weight residual
     109.81  115.39   -5.58 2.21e+00 2.05e-01 6.37e+00
  angle pdb=" C22 2YB R 401 "
        pdb=" O23 2YB R 401 "
        pdb=" C24 2YB R 401 "
      ideal   model   delta    sigma   weight residual
     118.60  111.15    7.45 3.00e+00 1.11e-01 6.17e+00
  angle pdb=" C   TYR B  59 "
        pdb=" N   ALA B  60 "
        pdb=" CA  ALA B  60 "
      ideal   model   delta    sigma   weight residual
     121.85  117.88    3.97 1.77e+00 3.19e-01 5.03e+00
  ... (remaining 12037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.52: 4962
       24.52 -    49.04: 224
       49.04 -    73.56: 18
       73.56 -    98.08: 3
       98.08 -   122.60: 1
  Dihedral angle restraints: 5208
    sinusoidal: 1958
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  GLY B 141 "
           pdb=" C   GLY B 141 "
           pdb=" N   HIS B 142 "
           pdb=" CA  HIS B 142 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.09   20.91     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  GLY B 182 "
           pdb=" C   GLY B 182 "
           pdb=" N   HIS B 183 "
           pdb=" CA  HIS B 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.70   20.30     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" C8  2YB R 401 "
           pdb=" C6  2YB R 401 "
           pdb=" C7  2YB R 401 "
           pdb=" O5  2YB R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.08   57.48  122.60     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 5205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 824
       0.034 -    0.068: 367
       0.068 -    0.102: 113
       0.102 -    0.136: 48
       0.136 -    0.170: 4
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CB  THR E 172 "
            pdb=" CA  THR E 172 "
            pdb=" OG1 THR E 172 "
            pdb=" CG2 THR E 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.24e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CG  LEU R  11 "
            pdb=" CB  LEU R  11 "
            pdb=" CD1 LEU R  11 "
            pdb=" CD2 LEU R  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 238 "   -0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO R 239 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R 239 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 239 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 131 "    0.014 2.00e-02 2.50e+03   1.07e-02 2.86e+00
        pdb=" CG  TRP R 131 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 131 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 131 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 131 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 131 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 131 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 131 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 131 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 131 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO B 236 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 851
        2.74 -     3.28: 8711
        3.28 -     3.82: 14578
        3.82 -     4.36: 17216
        4.36 -     4.90: 29793
  Nonbonded interactions: 71149
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  15 "
            pdb=" O   VAL B  90 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OE2 GLU A 234 "
            pdb=" NH1 ARG R 118 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER C  57 "
            pdb=" OE1 GLU C  58 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.317 3.040
  ... (remaining 71144 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:             3.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.290
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     24.930
  Find NCS groups from input model:        0.130
  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:15.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
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      :  0.006   0.121   8856  Z= 0.252
  Angle     :  0.645   8.121  12044  Z= 0.323
  Chirality :  0.044   0.170   1356
  Planarity :  0.004   0.052   1543
  Dihedral  : 13.368 122.600   3119
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.20 (0.26), residues: 1118
  helix:  2.17 (0.26), residues: 375
  sheet:  0.40 (0.32), residues: 294
  loop : -0.02 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.014   0.002   PHE B 253 
 TYR   0.017   0.002   TYR B 105 
 ARG   0.005   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13729 (  456)
  hydrogen bonds       : angle       5.74050 ( 1284)
  SS BOND              : bond        0.00644 (    1)
  SS BOND              : angle       0.69569 (    2)
  covalent geometry    : bond        0.00557 ( 8855)
  covalent geometry    : angle       0.64459 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: C   32 LYS cc_start: 0.8887 (tttm) cc_final: 0.8540 (tttm)
REVERT: E   93 MET cc_start: 0.7848 (tpt) cc_final: 0.7597 (tpt)
REVERT: E  201 ASP cc_start: 0.7962 (p0) cc_final: 0.7738 (t70)
REVERT: R  137 HIS cc_start: 0.8206 (t-90) cc_final: 0.7843 (t-90)
REVERT: R  170 CYS cc_start: 0.7786 (m) cc_final: 0.7584 (m)
REVERT: R  240 TYR cc_start: 0.8514 (t80) cc_final: 0.8231 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 1.2109
  time to fit residues: 207.7322
Evaluate side-chains
  117 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
B  16 ASN
B  36 ASN
B 220 GLN
E  77 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.110964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.082579 restraints weight = 15588.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.65
r_work: 0.2991 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8856  Z= 0.158
  Angle     :  0.588   7.438  12044  Z= 0.303
  Chirality :  0.043   0.129   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  5.358  87.375   1249
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.07 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.31 (0.25), residues: 1118
  helix:  2.27 (0.26), residues: 381
  sheet:  0.55 (0.33), residues: 282
  loop : -0.06 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.011   0.001   PHE B 234 
 TYR   0.010   0.001   TYR E 190 
 ARG   0.007   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04398 (  456)
  hydrogen bonds       : angle       4.62741 ( 1284)
  SS BOND              : bond        0.00592 (    1)
  SS BOND              : angle       0.51163 (    2)
  covalent geometry    : bond        0.00360 ( 8855)
  covalent geometry    : angle       0.58766 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7580 (mt-10)
REVERT: B   16 ASN cc_start: 0.8672 (m-40) cc_final: 0.8238 (m110)
REVERT: B   17 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: B   20 ASP cc_start: 0.8189 (m-30) cc_final: 0.7892 (m-30)
REVERT: B  175 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8334 (mp10)
REVERT: B  260 GLU cc_start: 0.8473 (tt0) cc_final: 0.8268 (tt0)
REVERT: E   93 MET cc_start: 0.8661 (tpt) cc_final: 0.8174 (tpt)
REVERT: E  201 ASP cc_start: 0.8563 (p0) cc_final: 0.7953 (t70)
REVERT: R   53 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8727 (tp)
REVERT: R  137 HIS cc_start: 0.8226 (t-90) cc_final: 0.7744 (t-90)
REVERT: R  161 ASN cc_start: 0.8374 (t0) cc_final: 0.8087 (t0)
REVERT: R  170 CYS cc_start: 0.8012 (m) cc_final: 0.7753 (m)
REVERT: R  221 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6702 (ttm170)
REVERT: R  240 TYR cc_start: 0.8716 (t80) cc_final: 0.8311 (t80)
  outliers start: 18
  outliers final: 7
  residues processed: 144
  average time/residue: 1.1371
  time to fit residues: 175.1533
Evaluate side-chains
  131 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
B  36 ASN
C  11 GLN
E  77 ASN
R  23 ASN
R  47 ASN
R 115 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.109632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081356 restraints weight = 15826.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.64
r_work: 0.2967 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8856  Z= 0.187
  Angle     :  0.589   7.585  12044  Z= 0.305
  Chirality :  0.043   0.129   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.338  75.590   1249
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 13.40 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.21 (0.25), residues: 1118
  helix:  2.14 (0.26), residues: 383
  sheet:  0.56 (0.33), residues: 279
  loop : -0.13 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 131 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.014   0.002   TYR E 190 
 ARG   0.007   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  456)
  hydrogen bonds       : angle       4.57099 ( 1284)
  SS BOND              : bond        0.00548 (    1)
  SS BOND              : angle       0.52279 (    2)
  covalent geometry    : bond        0.00433 ( 8855)
  covalent geometry    : angle       0.58876 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7620 (mt-10)
REVERT: B   20 ASP cc_start: 0.8216 (m-30) cc_final: 0.8001 (m-30)
REVERT: B  175 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8337 (mp10)
REVERT: B  260 GLU cc_start: 0.8569 (tt0) cc_final: 0.8361 (tt0)
REVERT: E   19 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8787 (tttm)
REVERT: E   51 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8805 (tp)
REVERT: E   93 MET cc_start: 0.8612 (tpt) cc_final: 0.8137 (tpt)
REVERT: R   23 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8703 (t0)
REVERT: R   52 ASP cc_start: 0.8788 (t70) cc_final: 0.8472 (t70)
REVERT: R   53 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8819 (tp)
REVERT: R  137 HIS cc_start: 0.8194 (t-90) cc_final: 0.7789 (t-90)
REVERT: R  161 ASN cc_start: 0.8236 (t0) cc_final: 0.7871 (t0)
REVERT: R  170 CYS cc_start: 0.8073 (m) cc_final: 0.7785 (m)
REVERT: R  221 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6726 (ttm170)
REVERT: R  240 TYR cc_start: 0.8759 (t80) cc_final: 0.8392 (t80)
  outliers start: 39
  outliers final: 17
  residues processed: 146
  average time/residue: 1.1503
  time to fit residues: 179.3219
Evaluate side-chains
  141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 110 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 99 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 66 optimal weight:    0.4980
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
A 229 GLN
B  75 GLN
C  44 HIS
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.108893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.080702 restraints weight = 15758.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.63
r_work: 0.2958 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8856  Z= 0.203
  Angle     :  0.606  10.367  12044  Z= 0.310
  Chirality :  0.043   0.134   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.378  69.039   1249
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.28 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.14 (0.26), residues: 1118
  helix:  2.08 (0.27), residues: 383
  sheet:  0.54 (0.33), residues: 278
  loop : -0.19 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 131 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.012   0.002   PHE B 180 
 TYR   0.013   0.002   TYR E 190 
 ARG   0.008   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04550 (  456)
  hydrogen bonds       : angle       4.59745 ( 1284)
  SS BOND              : bond        0.00581 (    1)
  SS BOND              : angle       0.47876 (    2)
  covalent geometry    : bond        0.00473 ( 8855)
  covalent geometry    : angle       0.60566 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.8258 (m-30) cc_final: 0.8044 (m-30)
REVERT: B  215 GLU cc_start: 0.8438 (pt0) cc_final: 0.8225 (pp20)
REVERT: B  217 MET cc_start: 0.8051 (pp-130) cc_final: 0.7835 (pp-130)
REVERT: E   19 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8780 (tttm)
REVERT: E   51 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8808 (tp)
REVERT: E  160 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8256 (ttm110)
REVERT: R   23 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8673 (t0)
REVERT: R   52 ASP cc_start: 0.8847 (t70) cc_final: 0.8499 (t70)
REVERT: R   53 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8786 (tp)
REVERT: R  137 HIS cc_start: 0.8311 (t-90) cc_final: 0.7911 (t-90)
REVERT: R  161 ASN cc_start: 0.8255 (t0) cc_final: 0.7887 (t0)
REVERT: R  170 CYS cc_start: 0.8068 (m) cc_final: 0.7763 (m)
REVERT: R  221 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6830 (ttm170)
  outliers start: 36
  outliers final: 19
  residues processed: 137
  average time/residue: 1.1496
  time to fit residues: 168.3709
Evaluate side-chains
  136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0970
   chunk 53 optimal weight:    0.0040
   chunk 59 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0030
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6002

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 229 GLN
E  77 ASN
R  23 ASN
R  47 ASN
R 115 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.113465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085394 restraints weight = 15736.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.65
r_work: 0.3033 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8856  Z= 0.105
  Angle     :  0.540   9.633  12044  Z= 0.275
  Chirality :  0.040   0.137   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.886  58.510   1249
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.72 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.35 (0.26), residues: 1118
  helix:  2.26 (0.26), residues: 384
  sheet:  0.78 (0.34), residues: 267
  loop : -0.14 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 131 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.009   0.001   TYR A 204 
 ARG   0.006   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  456)
  hydrogen bonds       : angle       4.24628 ( 1284)
  SS BOND              : bond        0.00540 (    1)
  SS BOND              : angle       0.31393 (    2)
  covalent geometry    : bond        0.00229 ( 8855)
  covalent geometry    : angle       0.54034 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7706 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8286 (m-30) cc_final: 0.8006 (m-30)
REVERT: B  215 GLU cc_start: 0.8518 (pt0) cc_final: 0.8114 (pp20)
REVERT: B  217 MET cc_start: 0.7974 (pp-130) cc_final: 0.7620 (pp-130)
REVERT: E   51 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8751 (tp)
REVERT: R   53 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8774 (tp)
REVERT: R  137 HIS cc_start: 0.8087 (t-90) cc_final: 0.7723 (t-90)
REVERT: R  161 ASN cc_start: 0.8247 (t0) cc_final: 0.7875 (t0)
REVERT: R  170 CYS cc_start: 0.7713 (m) cc_final: 0.7469 (m)
REVERT: R  240 TYR cc_start: 0.8705 (t80) cc_final: 0.8291 (t80)
  outliers start: 28
  outliers final: 5
  residues processed: 139
  average time/residue: 1.2211
  time to fit residues: 181.7305
Evaluate side-chains
  126 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 85 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
B  75 GLN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.113641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.085433 restraints weight = 15547.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.65
r_work: 0.3038 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8856  Z= 0.111
  Angle     :  0.552   8.857  12044  Z= 0.279
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.052   1543
  Dihedral  :  4.780  65.752   1249
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.16 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.48 (0.26), residues: 1118
  helix:  2.37 (0.27), residues: 380
  sheet:  0.83 (0.33), residues: 283
  loop : -0.07 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 131 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.013   0.001   TYR A 204 
 ARG   0.008   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  456)
  hydrogen bonds       : angle       4.17687 ( 1284)
  SS BOND              : bond        0.00481 (    1)
  SS BOND              : angle       0.34949 (    2)
  covalent geometry    : bond        0.00247 ( 8855)
  covalent geometry    : angle       0.55156 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7777 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8194 (m-30) cc_final: 0.7873 (m-30)
REVERT: B  254 ASP cc_start: 0.8690 (t0) cc_final: 0.8469 (t0)
REVERT: E   51 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8753 (tp)
REVERT: E  109 ASP cc_start: 0.8714 (p0) cc_final: 0.8399 (p0)
REVERT: E  160 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8212 (ttm110)
REVERT: R   53 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8751 (tp)
REVERT: R  137 HIS cc_start: 0.8079 (t-90) cc_final: 0.7737 (t-90)
REVERT: R  161 ASN cc_start: 0.8236 (t0) cc_final: 0.7880 (t0)
REVERT: R  240 TYR cc_start: 0.8705 (t80) cc_final: 0.8346 (t80)
  outliers start: 26
  outliers final: 7
  residues processed: 145
  average time/residue: 1.1436
  time to fit residues: 177.2459
Evaluate side-chains
  132 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 99 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 95 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
E  77 ASN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.113291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.085199 restraints weight = 15757.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.65
r_work: 0.3034 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8856  Z= 0.119
  Angle     :  0.564   8.575  12044  Z= 0.285
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.806  69.578   1249
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.71 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.43 (0.26), residues: 1118
  helix:  2.33 (0.26), residues: 380
  sheet:  0.79 (0.33), residues: 279
  loop : -0.08 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.012   0.001   TYR A 204 
 ARG   0.014   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03645 (  456)
  hydrogen bonds       : angle       4.16294 ( 1284)
  SS BOND              : bond        0.00482 (    1)
  SS BOND              : angle       0.37711 (    2)
  covalent geometry    : bond        0.00272 ( 8855)
  covalent geometry    : angle       0.56372 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7752 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8210 (m-30) cc_final: 0.7867 (m-30)
REVERT: E   51 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8738 (tp)
REVERT: E  109 ASP cc_start: 0.8706 (p0) cc_final: 0.8395 (p0)
REVERT: E  160 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8198 (ttm110)
REVERT: R   23 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8626 (t0)
REVERT: R   52 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8391 (t70)
REVERT: R  137 HIS cc_start: 0.8028 (t-90) cc_final: 0.7728 (t-90)
REVERT: R  161 ASN cc_start: 0.8259 (t0) cc_final: 0.7888 (t0)
REVERT: R  170 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6953 (m)
  outliers start: 25
  outliers final: 11
  residues processed: 138
  average time/residue: 1.1175
  time to fit residues: 165.3347
Evaluate side-chains
  136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   52 ASP
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  220 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 103 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
E  77 ASN
** R  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 115 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.114173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.086114 restraints weight = 15801.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.67
r_work: 0.3050 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8856  Z= 0.109
  Angle     :  0.565   9.361  12044  Z= 0.283
  Chirality :  0.040   0.138   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.740  71.540   1249
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.59 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 (0.26), residues: 1118
  helix:  2.34 (0.26), residues: 380
  sheet:  0.84 (0.33), residues: 279
  loop : -0.05 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 131 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.010   0.001   TYR A 204 
 ARG   0.011   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03493 (  456)
  hydrogen bonds       : angle       4.10925 ( 1284)
  SS BOND              : bond        0.00481 (    1)
  SS BOND              : angle       0.32729 (    2)
  covalent geometry    : bond        0.00243 ( 8855)
  covalent geometry    : angle       0.56468 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7698 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8190 (m-30) cc_final: 0.7846 (m-30)
REVERT: B  254 ASP cc_start: 0.8723 (t0) cc_final: 0.8400 (t0)
REVERT: E   51 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8765 (tp)
REVERT: E  109 ASP cc_start: 0.8751 (p0) cc_final: 0.8433 (p0)
REVERT: E  160 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8147 (ttm110)
REVERT: E  220 GLU cc_start: 0.7566 (mp0) cc_final: 0.7079 (mp0)
REVERT: R   36 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7092 (mm)
REVERT: R  137 HIS cc_start: 0.8016 (t-90) cc_final: 0.7709 (t-90)
REVERT: R  161 ASN cc_start: 0.8283 (t0) cc_final: 0.7924 (t0)
REVERT: R  170 CYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6924 (m)
  outliers start: 22
  outliers final: 13
  residues processed: 141
  average time/residue: 1.1172
  time to fit residues: 168.6344
Evaluate side-chains
  137 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   52 ASP
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  220 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
B 110 ASN
R   6 GLN
R  23 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.112075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.083933 restraints weight = 15740.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.64
r_work: 0.3010 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8856  Z= 0.144
  Angle     :  0.596   8.495  12044  Z= 0.303
  Chirality :  0.042   0.135   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  4.942  73.788   1249
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.59 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.33 (0.26), residues: 1118
  helix:  2.20 (0.26), residues: 380
  sheet:  0.78 (0.32), residues: 285
  loop : -0.13 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 131 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.010   0.001   PHE B 151 
 TYR   0.011   0.001   TYR R 202 
 ARG   0.011   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  456)
  hydrogen bonds       : angle       4.23808 ( 1284)
  SS BOND              : bond        0.00461 (    1)
  SS BOND              : angle       0.41961 (    2)
  covalent geometry    : bond        0.00337 ( 8855)
  covalent geometry    : angle       0.59625 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7699 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8221 (m-30) cc_final: 0.7878 (m-30)
REVERT: B  254 ASP cc_start: 0.8797 (t0) cc_final: 0.8481 (t0)
REVERT: E   51 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8751 (tp)
REVERT: E   93 MET cc_start: 0.8652 (tpt) cc_final: 0.8451 (tpt)
REVERT: E  160 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8185 (ttm110)
REVERT: R   23 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8614 (t0)
REVERT: R   52 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8373 (t70)
REVERT: R  161 ASN cc_start: 0.8278 (t0) cc_final: 0.7848 (t0)
REVERT: R  170 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7071 (m)
REVERT: R  190 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8967 (mp)
  outliers start: 23
  outliers final: 12
  residues processed: 142
  average time/residue: 1.1343
  time to fit residues: 172.4619
Evaluate side-chains
  138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   52 ASP
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  232 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0470
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0980
   chunk 32 optimal weight:    0.0370
   chunk 96 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
E  77 ASN
R   6 GLN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.115583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087643 restraints weight = 15633.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.66
r_work: 0.3074 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8856  Z= 0.107
  Angle     :  0.881  43.189  12044  Z= 0.405
  Chirality :  0.041   0.139   1356
  Planarity :  0.004   0.052   1543
  Dihedral  :  4.758  75.318   1249
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 22.37 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.46 (0.26), residues: 1118
  helix:  2.28 (0.27), residues: 374
  sheet:  0.89 (0.33), residues: 283
  loop : -0.03 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R 131 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.013   0.001   TYR A 204 
 ARG   0.010   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  456)
  hydrogen bonds       : angle       4.12701 ( 1284)
  SS BOND              : bond        0.00502 (    1)
  SS BOND              : angle       0.28433 (    2)
  covalent geometry    : bond        0.00233 ( 8855)
  covalent geometry    : angle       0.88135 (12042)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7699 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8219 (m-30) cc_final: 0.7896 (m-30)
REVERT: B  215 GLU cc_start: 0.8552 (pt0) cc_final: 0.8337 (pp20)
REVERT: E   51 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8736 (tp)
REVERT: E   93 MET cc_start: 0.8575 (tpt) cc_final: 0.8295 (tpt)
REVERT: E  160 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8165 (ttm110)
REVERT: E  192 MET cc_start: 0.7548 (tpt) cc_final: 0.7344 (tpt)
REVERT: E  193 SER cc_start: 0.8826 (p) cc_final: 0.8380 (m)
REVERT: R   23 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8699 (t0)
REVERT: R   52 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8381 (t70)
REVERT: R   53 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8746 (tp)
REVERT: R  137 HIS cc_start: 0.7923 (t70) cc_final: 0.7525 (t-90)
REVERT: R  161 ASN cc_start: 0.8245 (t0) cc_final: 0.7852 (t0)
REVERT: R  170 CYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6929 (m)
REVERT: R  240 TYR cc_start: 0.8559 (t80) cc_final: 0.8348 (t80)
  outliers start: 17
  outliers final: 9
  residues processed: 140
  average time/residue: 1.0982
  time to fit residues: 164.9000
Evaluate side-chains
  140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   52 ASP
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  232 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0370
   chunk 77 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0040
   chunk 78 optimal weight:    0.9980
   chunk 69 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 85 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5270

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

Flipped N/Q/H residues before XYZ refinement:
R   6 GLN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.115445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.087601 restraints weight = 15620.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.65
r_work: 0.3075 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8856  Z= 0.111
  Angle     :  0.596  10.474  12044  Z= 0.299
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.761  77.758   1249
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 22.48 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 (0.26), residues: 1118
  helix:  2.34 (0.26), residues: 374
  sheet:  0.86 (0.33), residues: 284
  loop : -0.04 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 131 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.009   0.001   PHE A  66 
 TYR   0.032   0.001   TYR E  95 
 ARG   0.010   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  456)
  hydrogen bonds       : angle       4.10692 ( 1284)
  SS BOND              : bond        0.00467 (    1)
  SS BOND              : angle       0.33532 (    2)
  covalent geometry    : bond        0.00247 ( 8855)
  covalent geometry    : angle       0.59610 (12042)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6870.07 seconds
wall clock time: 119 minutes 18.17 seconds (7158.17 seconds total)