Starting phenix.real_space_refine
on Wed Mar 12 22:56:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xp4_33364/03_2025/7xp4_33364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xp4_33364/03_2025/7xp4_33364.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2025/7xp4_33364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2025/7xp4_33364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2025/7xp4_33364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xp4_33364/03_2025/7xp4_33364.cif"
  }
  resolution = 3.01
  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=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    5382      2.51       5
     N    1456      2.21       5
     O    1550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8437
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1964
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 981
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "R"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2440
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
  Time building chain proxies: 6.77, per 1000 atoms: 0.80
  Number of scatterers: 8437
  At special positions: 0
  Unit cell: (83.2, 101.92, 134.16, 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      49     16.00
     O    1550      8.00
     N    1456      7.00
     C    5382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 100 " - pdb=" SG  CYS N 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2008

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      45.5% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 36
    Processing helix  chain 'A' and resid 48 through 60
      removed outlier: 3.562A  pdb=" N   LEU A  59 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS A  60 " --> pdb=" O   MET A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 117 through 133
      removed outlier: 4.072A  pdb=" N   GLN A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLU A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 138
      removed outlier: 3.784A  pdb=" N   ARG A 138 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 159
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.214A  pdb=" N   TYR A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 206
    Processing helix  chain 'A' and resid 222 through 247
      removed outlier: 3.967A  pdb=" N   ASN A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.111A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.702A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.774A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 63 through 66
    Processing helix  chain 'N' and resid 88 through 92
    Processing helix  chain 'R' and resid 4 through 39
      removed outlier: 4.814A  pdb=" N   SER R  10 " --> pdb=" O   PRO R   6 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 70
    Processing helix  chain 'R' and resid 77 through 111
      removed outlier: 3.584A  pdb=" N   ILE R  82 " --> pdb=" O   ILE R  78 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE R  94 " --> pdb=" O   VAL R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 124
      removed outlier: 4.103A  pdb=" N   ARG R 124 " --> pdb=" O   HIS R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 151
      removed outlier: 3.615A  pdb=" N   VAL R 128 " --> pdb=" O   ARG R 124 " (cutoff:3.500A)
      Proline residue:  R 136  - end of helix
      removed outlier: 3.643A  pdb=" N   PHE R 139 " --> pdb=" O   GLY R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 160
    Processing helix  chain 'R' and resid 176 through 213
      removed outlier: 4.864A  pdb=" N   VAL R 186 " --> pdb=" O   LEU R 182 " (cutoff:3.500A)
      Proline residue:  R 187  - end of helix
      removed outlier: 3.933A  pdb=" N   HIS R 212 " --> pdb=" O   LYS R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 250
    Processing helix  chain 'R' and resid 257 through 283
      removed outlier: 3.934A  pdb=" N   PHE R 263 " --> pdb=" O   PRO R 259 " (cutoff:3.500A)
      Proline residue:  R 272  - end of helix
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 283 through 301
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79
      removed outlier: 4.609A  pdb=" N   VAL A  89 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   GLY A  43 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ARG A  38 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ILE A 110 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   LEU A  40 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   VAL A 112 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 8.681A  pdb=" N   ASP A 114 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ILE A 109 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   PHE A 111 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASN A 147 " --> pdb=" O   PHE A 111 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL A 113 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   HIS A 217 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A 144 " --> pdb=" O   HIS A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.779A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.762A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.377A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.506A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.722A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.278A  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: 3.571A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.110A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.541A  pdb=" N   GLN N   6 " --> pdb=" O   ALA N  24 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 12 through 13
      removed outlier: 7.160A  pdb=" N   MET N  35 " --> pdb=" O   ASP N  51 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ASP N  51 " --> pdb=" O   MET N  35 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   TRP N  37 " --> pdb=" O   VAL N  49 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1338 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.84

  Time building geometry restraints manager: 2.88 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: 2722
        1.34 -     1.46: 1493
        1.46 -     1.58: 4332
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8617
  Sorted by residual:
  bond pdb=" N   GLY B 341 "
       pdb=" CA  GLY B 341 "
    ideal  model  delta    sigma   weight residual
    1.452  1.494 -0.042 1.05e-02 9.07e+03 1.60e+01
  bond pdb=" N   SER B 342 "
       pdb=" CA  SER B 342 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.21e-02 6.83e+03 6.15e+00
  bond pdb=" N   ASN B 340 "
       pdb=" CA  ASN B 340 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.20e-02 6.94e+03 5.36e+00
  bond pdb=" CA  SER B 342 "
       pdb=" CB  SER B 342 "
    ideal  model  delta    sigma   weight residual
    1.531  1.506  0.024 1.52e-02 4.33e+03 2.52e+00
  bond pdb=" CA  GLY B 341 "
       pdb=" C   GLY B 341 "
    ideal  model  delta    sigma   weight residual
    1.519  1.532 -0.013 9.70e-03 1.06e+04 1.86e+00
  ... (remaining 8612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 11443
        1.75 -     3.49: 185
        3.49 -     5.24: 41
        5.24 -     6.99: 3
        6.99 -     8.73: 1
  Bond angle restraints: 11673
  Sorted by residual:
  angle pdb=" CA  GLY B 341 "
        pdb=" C   GLY B 341 "
        pdb=" O   GLY B 341 "
      ideal   model   delta    sigma   weight residual
     121.41  118.27    3.14 8.80e-01 1.29e+00 1.27e+01
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  128.23   -6.69 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   LYS R 167 "
        pdb=" N   LEU R 168 "
        pdb=" CA  LEU R 168 "
      ideal   model   delta    sigma   weight residual
     122.42  118.04    4.38 1.55e+00 4.16e-01 7.99e+00
  angle pdb=" C   LYS A  98 "
        pdb=" N   TRP A  99 "
        pdb=" CA  TRP A  99 "
      ideal   model   delta    sigma   weight residual
     121.14  116.33    4.81 1.75e+00 3.27e-01 7.57e+00
  angle pdb=" C   GLY A 159 "
        pdb=" N   LYS A 160 "
        pdb=" CA  LYS A 160 "
      ideal   model   delta    sigma   weight residual
     121.54  126.42   -4.88 1.91e+00 2.74e-01 6.52e+00
  ... (remaining 11668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 4678
       17.58 -    35.15: 369
       35.15 -    52.73: 60
       52.73 -    70.30: 3
       70.30 -    87.88: 4
  Dihedral angle restraints: 5114
    sinusoidal: 2015
      harmonic: 3099
  Sorted by residual:
  dihedral pdb=" CA  CYS N 108 "
           pdb=" C   CYS N 108 "
           pdb=" N   PHE N 109 "
           pdb=" CA  PHE N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLY B 185 "
           pdb=" C   GLY B 185 "
           pdb=" N   ASP B 186 "
           pdb=" CA  ASP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.63   17.37     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CB  CYS N 100 "
           pdb=" SG  CYS N 100 "
           pdb=" SG  CYS N 108 "
           pdb=" CB  CYS N 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   66.09   26.91     1      1.00e+01 1.00e-02 1.04e+01
  ... (remaining 5111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 836
       0.033 -    0.066: 323
       0.066 -    0.099: 105
       0.099 -    0.132: 54
       0.132 -    0.165: 4
  Chirality restraints: 1322
  Sorted by residual:
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CA  TRP A  99 "
            pdb=" N   TRP A  99 "
            pdb=" C   TRP A  99 "
            pdb=" CB  TRP A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CG  LEU R 168 "
            pdb=" CB  LEU R 168 "
            pdb=" CD1 LEU R 168 "
            pdb=" CD2 LEU R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 1319 not shown)

  Planarity restraints: 1475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "   -0.061 5.00e-02 4.00e+02   9.21e-02 1.36e+01
        pdb=" N   PRO G  60 "    0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 186 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO A 187 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 187 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 187 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 218 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO R 219 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO R 219 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 219 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1472 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 849
        2.74 -     3.28: 8437
        3.28 -     3.82: 14068
        3.82 -     4.36: 15810
        4.36 -     4.90: 28449
  Nonbonded interactions: 67613
  Sorted by model distance:
  nonbonded pdb=" O   VAL N 111 "
            pdb=" OG1 THR N 112 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OG  SER R 244 "
            pdb=" O   CYS R 264 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASN R  31 "
            pdb=" NZ  LYS R 285 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   ALA A  44 "
            pdb=" OG  SER A  47 "
     model   vdw
     2.252 3.040
  ... (remaining 67608 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:             75.140
  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:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.240
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  109.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
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      :  0.003   0.042   8617  Z= 0.221
  Angle     :  0.577   8.735  11673  Z= 0.311
  Chirality :  0.043   0.165   1322
  Planarity :  0.005   0.092   1475
  Dihedral  : 12.473  87.879   3100
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.94 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.87 (0.26), residues: 1054
  helix:  2.11 (0.24), residues: 437
  sheet:  0.12 (0.34), residues: 227
  loop : -0.91 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R  66 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.023   0.001   PHE R   9 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.014   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LYS cc_start: 0.6997 (tptp) cc_final: 0.6764 (tptp)
REVERT: A   23 GLU cc_start: 0.7301 (tp30) cc_final: 0.6910 (tp30)
REVERT: A   29 ASP cc_start: 0.6665 (t0) cc_final: 0.6404 (t0)
REVERT: A   42 LEU cc_start: 0.7911 (mt) cc_final: 0.7696 (mt)
REVERT: A   74 GLU cc_start: 0.7137 (pt0) cc_final: 0.6769 (pt0)
REVERT: A  103 PHE cc_start: 0.7741 (m-10) cc_final: 0.7518 (m-80)
REVERT: A  117 ASP cc_start: 0.6723 (m-30) cc_final: 0.6262 (m-30)
REVERT: A  123 GLU cc_start: 0.6958 (pt0) cc_final: 0.5993 (pt0)
REVERT: A  241 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6303 (mt-10)
REVERT: B   25 CYS cc_start: 0.7178 (m) cc_final: 0.6676 (m)
REVERT: B  135 VAL cc_start: 0.8461 (t) cc_final: 0.8203 (p)
REVERT: B  245 SER cc_start: 0.7960 (p) cc_final: 0.7547 (p)
REVERT: G   13 ARG cc_start: 0.7198 (tmt-80) cc_final: 0.6615 (tmt-80)
REVERT: R  207 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7540 (tmtt)
REVERT: R  250 TRP cc_start: 0.7126 (p-90) cc_final: 0.6650 (p-90)
REVERT: R  262 MET cc_start: 0.6038 (ppp) cc_final: 0.5696 (ppp)
REVERT: R  284 LYS cc_start: 0.7464 (tptp) cc_final: 0.7083 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.3821
  time to fit residues: 128.5528
Evaluate side-chains
  242 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
B 155 ASN
B 220 GLN
B 266 HIS
B 340 ASN
** N  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  40 GLN
N  85 ASN
R  65 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.143107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.125132 restraints weight = 12376.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.24
r_work: 0.3510 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8617  Z= 0.259
  Angle     :  0.582   7.047  11673  Z= 0.311
  Chirality :  0.043   0.174   1322
  Planarity :  0.005   0.067   1475
  Dihedral  :  4.214  19.391   1147
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 10.40 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.98 (0.26), residues: 1054
  helix:  2.22 (0.24), residues: 450
  sheet:  0.24 (0.36), residues: 221
  loop : -1.02 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  99 
 HIS   0.004   0.001   HIS A 212 
 PHE   0.022   0.002   PHE R   9 
 TYR   0.012   0.001   TYR N  61 
 ARG   0.006   0.001   ARG B  96 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 243
  time to evaluate  : 1.109 
Fit side-chains
REVERT: A   20 LYS cc_start: 0.7654 (tptp) cc_final: 0.7423 (tptp)
REVERT: A   23 GLU cc_start: 0.8233 (tp30) cc_final: 0.7712 (tp30)
REVERT: A   29 ASP cc_start: 0.7720 (t0) cc_final: 0.7420 (t0)
REVERT: A   74 GLU cc_start: 0.7883 (pt0) cc_final: 0.7266 (pt0)
REVERT: A  117 ASP cc_start: 0.7480 (m-30) cc_final: 0.6832 (m-30)
REVERT: A  123 GLU cc_start: 0.7640 (pt0) cc_final: 0.7152 (pt0)
REVERT: A  241 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7252 (mt-10)
REVERT: B   68 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8167 (ttt90)
REVERT: B   88 ASN cc_start: 0.8002 (m110) cc_final: 0.7719 (m-40)
REVERT: B  212 ASP cc_start: 0.7990 (t0) cc_final: 0.7729 (t0)
REVERT: B  315 VAL cc_start: 0.8246 (t) cc_final: 0.8028 (p)
REVERT: G   13 ARG cc_start: 0.7631 (tmt-80) cc_final: 0.6917 (tmt-80)
REVERT: R  112 ASN cc_start: 0.8824 (p0) cc_final: 0.8611 (p0)
REVERT: R  207 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7774 (tmtt)
REVERT: R  247 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7324 (tmm)
REVERT: R  250 TRP cc_start: 0.7574 (p-90) cc_final: 0.7213 (p-90)
REVERT: R  262 MET cc_start: 0.6746 (ppp) cc_final: 0.6223 (ppp)
REVERT: R  284 LYS cc_start: 0.8292 (tptp) cc_final: 0.7910 (tptp)
  outliers start: 11
  outliers final: 9
  residues processed: 245
  average time/residue: 0.2615
  time to fit residues: 82.1532
Evaluate side-chains
  246 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 236
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  247 MET
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 53 optimal weight:    0.4980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 101 GLN
B  88 ASN
R  86 ASN
R 148 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.143697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.125732 restraints weight = 12490.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.27
r_work: 0.3519 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8617  Z= 0.211
  Angle     :  0.543   6.711  11673  Z= 0.288
  Chirality :  0.042   0.144   1322
  Planarity :  0.004   0.057   1475
  Dihedral  :  4.137  17.531   1147
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.08 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.04 (0.26), residues: 1054
  helix:  2.32 (0.24), residues: 450
  sheet:  0.29 (0.35), residues: 218
  loop : -1.06 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.022   0.001   PHE R   9 
 TYR   0.010   0.001   TYR A 194 
 ARG   0.010   0.000   ARG B 197 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 246
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   23 GLU cc_start: 0.7843 (tp30) cc_final: 0.7340 (tp30)
REVERT: A   74 GLU cc_start: 0.7650 (pt0) cc_final: 0.7167 (pt0)
REVERT: A  117 ASP cc_start: 0.7142 (m-30) cc_final: 0.6473 (m-30)
REVERT: A  123 GLU cc_start: 0.7268 (pt0) cc_final: 0.6897 (pt0)
REVERT: A  160 LYS cc_start: 0.8195 (ptpp) cc_final: 0.7835 (mtmm)
REVERT: A  241 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6888 (mt-10)
REVERT: B   88 ASN cc_start: 0.7723 (m-40) cc_final: 0.7368 (m-40)
REVERT: B  118 ASP cc_start: 0.7345 (t70) cc_final: 0.6794 (t0)
REVERT: B  197 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7302 (mmm160)
REVERT: B  212 ASP cc_start: 0.7760 (t0) cc_final: 0.7387 (t0)
REVERT: B  315 VAL cc_start: 0.8126 (t) cc_final: 0.7911 (p)
REVERT: G   13 ARG cc_start: 0.7452 (tmt-80) cc_final: 0.6774 (tmt-80)
REVERT: N   60 SER cc_start: 0.8148 (m) cc_final: 0.7554 (p)
REVERT: R  112 ASN cc_start: 0.8754 (p0) cc_final: 0.8532 (p0)
REVERT: R  207 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7607 (tmtt)
REVERT: R  244 SER cc_start: 0.7375 (OUTLIER) cc_final: 0.7162 (p)
REVERT: R  250 TRP cc_start: 0.7275 (p-90) cc_final: 0.6905 (p-90)
REVERT: R  262 MET cc_start: 0.6637 (ppp) cc_final: 0.6183 (ppp)
REVERT: R  284 LYS cc_start: 0.8103 (tptp) cc_final: 0.7687 (tptp)
REVERT: R  287 LYS cc_start: 0.7844 (tppp) cc_final: 0.7358 (tppp)
  outliers start: 21
  outliers final: 12
  residues processed: 255
  average time/residue: 0.2594
  time to fit residues: 85.1946
Evaluate side-chains
  254 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 241
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0170
   chunk 52 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
R  31 ASN
R 224 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.143519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.125411 restraints weight = 12342.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.25
r_work: 0.3516 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8617  Z= 0.226
  Angle     :  0.551  11.428  11673  Z= 0.289
  Chirality :  0.042   0.138   1322
  Planarity :  0.004   0.051   1475
  Dihedral  :  4.151  21.065   1147
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.85 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.82 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.07 (0.26), residues: 1054
  helix:  2.34 (0.24), residues: 450
  sheet:  0.34 (0.35), residues: 218
  loop : -1.08 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.022   0.001   PHE R   9 
 TYR   0.011   0.001   TYR A 194 
 ARG   0.007   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 252
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7858 (tp30) cc_final: 0.7395 (tp30)
REVERT: A   57 ARG cc_start: 0.7730 (tpp80) cc_final: 0.7383 (tpp80)
REVERT: A   74 GLU cc_start: 0.7646 (pt0) cc_final: 0.7158 (pt0)
REVERT: A   80 ASP cc_start: 0.7277 (m-30) cc_final: 0.7028 (m-30)
REVERT: A  123 GLU cc_start: 0.7299 (pt0) cc_final: 0.6949 (pt0)
REVERT: A  129 LYS cc_start: 0.8283 (ttmm) cc_final: 0.8015 (ttmm)
REVERT: A  160 LYS cc_start: 0.8158 (ptpp) cc_final: 0.7831 (mtmm)
REVERT: A  241 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6888 (mt-10)
REVERT: B   88 ASN cc_start: 0.7748 (m-40) cc_final: 0.7528 (m-40)
REVERT: B  188 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7360 (mmm)
REVERT: B  197 ARG cc_start: 0.7828 (mmm160) cc_final: 0.7321 (mmm160)
REVERT: B  212 ASP cc_start: 0.7809 (t0) cc_final: 0.7339 (t0)
REVERT: B  256 ARG cc_start: 0.8361 (ptp-110) cc_final: 0.8128 (mtm180)
REVERT: B  315 VAL cc_start: 0.8169 (t) cc_final: 0.7960 (p)
REVERT: B  320 VAL cc_start: 0.8145 (t) cc_final: 0.7812 (p)
REVERT: N   60 SER cc_start: 0.8149 (m) cc_final: 0.7676 (p)
REVERT: R   17 PHE cc_start: 0.8030 (t80) cc_final: 0.7660 (t80)
REVERT: R  112 ASN cc_start: 0.8785 (p0) cc_final: 0.8561 (p0)
REVERT: R  207 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7615 (tmtt)
REVERT: R  250 TRP cc_start: 0.7247 (p-90) cc_final: 0.6876 (p-90)
REVERT: R  262 MET cc_start: 0.6719 (ppp) cc_final: 0.6205 (ppp)
REVERT: R  284 LYS cc_start: 0.8111 (tptp) cc_final: 0.7719 (tptp)
  outliers start: 23
  outliers final: 15
  residues processed: 260
  average time/residue: 0.2573
  time to fit residues: 86.4227
Evaluate side-chains
  256 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 240
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 90 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
B  17 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.124799 restraints weight = 12371.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.23
r_work: 0.3513 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8617  Z= 0.243
  Angle     :  0.553  11.126  11673  Z= 0.291
  Chirality :  0.042   0.142   1322
  Planarity :  0.004   0.048   1475
  Dihedral  :  4.173  19.384   1147
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.66 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.20 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.05 (0.26), residues: 1054
  helix:  2.33 (0.24), residues: 450
  sheet:  0.36 (0.35), residues: 218
  loop : -1.12 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.022   0.001   PHE R   9 
 TYR   0.011   0.001   TYR A 194 
 ARG   0.006   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 241
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8273 (tp30) cc_final: 0.7831 (tp30)
REVERT: A   74 GLU cc_start: 0.7860 (pt0) cc_final: 0.7370 (pt0)
REVERT: A   80 ASP cc_start: 0.7468 (m-30) cc_final: 0.7209 (m-30)
REVERT: A  123 GLU cc_start: 0.7599 (pt0) cc_final: 0.7244 (pt0)
REVERT: A  160 LYS cc_start: 0.8252 (ptpp) cc_final: 0.7912 (mtmm)
REVERT: A  241 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7246 (mt-10)
REVERT: B   33 ILE cc_start: 0.6760 (mt) cc_final: 0.6559 (mm)
REVERT: B   88 ASN cc_start: 0.7967 (m-40) cc_final: 0.7707 (m-40)
REVERT: B  125 ASN cc_start: 0.8420 (t0) cc_final: 0.8134 (t0)
REVERT: B  188 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7724 (mmm)
REVERT: B  197 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7462 (mmm160)
REVERT: B  212 ASP cc_start: 0.8031 (t0) cc_final: 0.7534 (t0)
REVERT: B  304 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7818 (ttm-80)
REVERT: B  315 VAL cc_start: 0.8254 (t) cc_final: 0.8028 (p)
REVERT: B  320 VAL cc_start: 0.8256 (t) cc_final: 0.7924 (p)
REVERT: N   60 SER cc_start: 0.8318 (m) cc_final: 0.7877 (p)
REVERT: N  109 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7309 (m-80)
REVERT: R  112 ASN cc_start: 0.8885 (p0) cc_final: 0.8676 (p0)
REVERT: R  207 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7880 (tmtt)
REVERT: R  247 MET cc_start: 0.7817 (ppp) cc_final: 0.7290 (ppp)
REVERT: R  250 TRP cc_start: 0.7563 (p-90) cc_final: 0.7189 (p-90)
REVERT: R  262 MET cc_start: 0.6823 (ppp) cc_final: 0.6330 (ppp)
REVERT: R  284 LYS cc_start: 0.8339 (tptp) cc_final: 0.7959 (tptp)
REVERT: R  287 LYS cc_start: 0.8042 (tppp) cc_final: 0.7659 (tppp)
  outliers start: 27
  outliers final: 18
  residues processed: 254
  average time/residue: 0.2617
  time to fit residues: 85.4127
Evaluate side-chains
  252 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 232
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 SER
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 36 optimal weight:    0.0770
   chunk 64 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0050
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 91 optimal weight:    0.0270
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.2810

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.142874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.124314 restraints weight = 12411.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.25
r_work: 0.3548 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
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      :  0.002   0.025   8617  Z= 0.151
  Angle     :  0.536  13.639  11673  Z= 0.277
  Chirality :  0.040   0.131   1322
  Planarity :  0.004   0.047   1475
  Dihedral  :  3.965  18.324   1147
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.66 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.96 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.15 (0.26), residues: 1054
  helix:  2.46 (0.24), residues: 450
  sheet:  0.31 (0.35), residues: 220
  loop : -1.08 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  99 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.024   0.001   PHE R   9 
 TYR   0.007   0.001   TYR A 194 
 ARG   0.008   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 231
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8239 (tp30) cc_final: 0.7846 (tp30)
REVERT: A   29 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7725 (m-30)
REVERT: A   55 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6902 (tt0)
REVERT: A   74 GLU cc_start: 0.7835 (pt0) cc_final: 0.7324 (pt0)
REVERT: A   80 ASP cc_start: 0.7492 (m-30) cc_final: 0.7285 (m-30)
REVERT: A  123 GLU cc_start: 0.7554 (pt0) cc_final: 0.7201 (pt0)
REVERT: A  241 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7238 (mt-10)
REVERT: B   19 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7656 (ttp80)
REVERT: B   88 ASN cc_start: 0.7932 (m-40) cc_final: 0.7641 (m-40)
REVERT: B  125 ASN cc_start: 0.8482 (t0) cc_final: 0.8190 (t0)
REVERT: B  188 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7710 (mmm)
REVERT: B  197 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7600 (mmm160)
REVERT: B  212 ASP cc_start: 0.8027 (t0) cc_final: 0.7536 (t0)
REVERT: B  315 VAL cc_start: 0.8223 (t) cc_final: 0.8017 (p)
REVERT: N   60 SER cc_start: 0.8321 (m) cc_final: 0.7944 (p)
REVERT: R  112 ASN cc_start: 0.8845 (p0) cc_final: 0.8630 (p0)
REVERT: R  207 LYS cc_start: 0.8304 (tmtt) cc_final: 0.7865 (tmtt)
REVERT: R  247 MET cc_start: 0.7824 (ppp) cc_final: 0.7298 (ppp)
REVERT: R  262 MET cc_start: 0.6757 (ppp) cc_final: 0.6316 (ppp)
REVERT: R  284 LYS cc_start: 0.8278 (tptp) cc_final: 0.7907 (tptp)
REVERT: R  287 LYS cc_start: 0.8043 (tppp) cc_final: 0.7667 (tppp)
  outliers start: 23
  outliers final: 13
  residues processed: 240
  average time/residue: 0.2548
  time to fit residues: 79.1395
Evaluate side-chains
  236 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 220
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain R residue   63 VAL
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue   92 ASN
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0370
   chunk 65 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.143824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.125705 restraints weight = 12442.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.26
r_work: 0.3519 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8617  Z= 0.221
  Angle     :  0.556  13.284  11673  Z= 0.287
  Chirality :  0.041   0.162   1322
  Planarity :  0.004   0.046   1475
  Dihedral  :  4.043  17.721   1147
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 20.15 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.17 (0.26), residues: 1054
  helix:  2.50 (0.24), residues: 449
  sheet:  0.38 (0.36), residues: 218
  loop : -1.10 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  99 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.023   0.001   PHE R   9 
 TYR   0.011   0.001   TYR A 194 
 ARG   0.008   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 217
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7885 (tp30) cc_final: 0.7483 (tp30)
REVERT: A   55 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6812 (tt0)
REVERT: A   74 GLU cc_start: 0.7619 (pt0) cc_final: 0.7149 (pt0)
REVERT: A   80 ASP cc_start: 0.7344 (m-30) cc_final: 0.7082 (m-30)
REVERT: A  123 GLU cc_start: 0.7319 (pt0) cc_final: 0.6972 (pt0)
REVERT: A  198 ASP cc_start: 0.7672 (t0) cc_final: 0.7272 (m-30)
REVERT: A  241 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6857 (mt-10)
REVERT: B   88 ASN cc_start: 0.7689 (m-40) cc_final: 0.7436 (m-40)
REVERT: B  125 ASN cc_start: 0.8317 (t0) cc_final: 0.8022 (t0)
REVERT: B  188 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7439 (mmm)
REVERT: B  197 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7409 (mmm160)
REVERT: B  212 ASP cc_start: 0.7826 (t0) cc_final: 0.7222 (t0)
REVERT: B  320 VAL cc_start: 0.8094 (t) cc_final: 0.7748 (p)
REVERT: N   60 SER cc_start: 0.8145 (m) cc_final: 0.7768 (p)
REVERT: N  109 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7152 (m-80)
REVERT: R   17 PHE cc_start: 0.8046 (t80) cc_final: 0.7710 (t80)
REVERT: R  112 ASN cc_start: 0.8784 (p0) cc_final: 0.8522 (p0)
REVERT: R  207 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7609 (tmtt)
REVERT: R  262 MET cc_start: 0.6646 (ppp) cc_final: 0.6219 (ppp)
REVERT: R  284 LYS cc_start: 0.8112 (tptp) cc_final: 0.7700 (tptp)
REVERT: R  287 LYS cc_start: 0.7816 (tppp) cc_final: 0.7468 (tppp)
  outliers start: 19
  outliers final: 11
  residues processed: 227
  average time/residue: 0.2579
  time to fit residues: 74.7571
Evaluate side-chains
  229 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 215
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   62 LEU
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 101 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.142788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.124627 restraints weight = 12491.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.25
r_work: 0.3505 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8617  Z= 0.282
  Angle     :  0.597  13.969  11673  Z= 0.306
  Chirality :  0.043   0.145   1322
  Planarity :  0.004   0.045   1475
  Dihedral  :  4.181  18.378   1147
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.56 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.59 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.05 (0.26), residues: 1054
  helix:  2.34 (0.24), residues: 450
  sheet:  0.36 (0.35), residues: 220
  loop : -1.14 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  99 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.023   0.002   PHE R   9 
 TYR   0.013   0.001   TYR N  61 
 ARG   0.005   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 231
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8304 (tp30) cc_final: 0.7899 (tp30)
REVERT: A   55 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6928 (tt0)
REVERT: A   74 GLU cc_start: 0.7832 (pt0) cc_final: 0.7328 (pt0)
REVERT: A  123 GLU cc_start: 0.7628 (pt0) cc_final: 0.7274 (pt0)
REVERT: A  129 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7871 (ttmm)
REVERT: A  198 ASP cc_start: 0.7956 (t0) cc_final: 0.7594 (m-30)
REVERT: A  241 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7229 (mt-10)
REVERT: B  125 ASN cc_start: 0.8440 (t0) cc_final: 0.8144 (t0)
REVERT: B  188 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7757 (mmm)
REVERT: B  197 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7573 (mmm160)
REVERT: B  212 ASP cc_start: 0.8061 (t0) cc_final: 0.7506 (t0)
REVERT: B  320 VAL cc_start: 0.8281 (t) cc_final: 0.7959 (p)
REVERT: N   60 SER cc_start: 0.8307 (m) cc_final: 0.7968 (p)
REVERT: N  109 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7272 (m-80)
REVERT: R  112 ASN cc_start: 0.8870 (p0) cc_final: 0.8651 (p0)
REVERT: R  207 LYS cc_start: 0.8328 (tmtt) cc_final: 0.7871 (tmtt)
REVERT: R  262 MET cc_start: 0.6826 (ppp) cc_final: 0.6369 (ppp)
REVERT: R  284 LYS cc_start: 0.8354 (tptp) cc_final: 0.7971 (tptp)
REVERT: R  287 LYS cc_start: 0.8055 (tppp) cc_final: 0.7752 (tppp)
  outliers start: 21
  outliers final: 15
  residues processed: 241
  average time/residue: 0.2752
  time to fit residues: 84.5940
Evaluate side-chains
  246 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 228
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.2980
   chunk 69 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 23 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.144338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.126230 restraints weight = 12535.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.26
r_work: 0.3523 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8617  Z= 0.207
  Angle     :  0.582  14.127  11673  Z= 0.298
  Chirality :  0.041   0.145   1322
  Planarity :  0.004   0.045   1475
  Dihedral  :  4.137  17.801   1147
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.34 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.11 (0.26), residues: 1054
  helix:  2.40 (0.24), residues: 450
  sheet:  0.37 (0.35), residues: 218
  loop : -1.09 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.023   0.001   PHE R   9 
 TYR   0.009   0.001   TYR N  61 
 ARG   0.004   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8245 (tp30) cc_final: 0.7847 (tp30)
REVERT: A   29 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7693 (m-30)
REVERT: A   55 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6933 (tt0)
REVERT: A   74 GLU cc_start: 0.7859 (pt0) cc_final: 0.7324 (pt0)
REVERT: A  123 GLU cc_start: 0.7614 (pt0) cc_final: 0.7254 (pt0)
REVERT: A  160 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7983 (mtmm)
REVERT: A  198 ASP cc_start: 0.7849 (t0) cc_final: 0.7455 (m-30)
REVERT: A  241 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7213 (mt-10)
REVERT: B  125 ASN cc_start: 0.8414 (t0) cc_final: 0.8108 (t0)
REVERT: B  188 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7770 (mmm)
REVERT: B  197 ARG cc_start: 0.8109 (mmm160) cc_final: 0.7579 (mmm160)
REVERT: B  212 ASP cc_start: 0.8050 (t0) cc_final: 0.7476 (t0)
REVERT: B  320 VAL cc_start: 0.8230 (t) cc_final: 0.7879 (p)
REVERT: N   60 SER cc_start: 0.8309 (m) cc_final: 0.7957 (p)
REVERT: N  109 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7293 (m-80)
REVERT: R   17 PHE cc_start: 0.8121 (t80) cc_final: 0.7791 (t80)
REVERT: R  109 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7594 (mmmm)
REVERT: R  112 ASN cc_start: 0.8851 (p0) cc_final: 0.8636 (p0)
REVERT: R  207 LYS cc_start: 0.8295 (tmtt) cc_final: 0.7833 (tmtt)
REVERT: R  262 MET cc_start: 0.6760 (ppp) cc_final: 0.6329 (ppp)
REVERT: R  284 LYS cc_start: 0.8331 (tptp) cc_final: 0.7971 (tptp)
REVERT: R  287 LYS cc_start: 0.8055 (tppp) cc_final: 0.7745 (tppp)
  outliers start: 20
  outliers final: 13
  residues processed: 234
  average time/residue: 0.2746
  time to fit residues: 81.4808
Evaluate side-chains
  241 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 224
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 61 optimal weight:    0.3980
   chunk 98 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 101 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.144529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126240 restraints weight = 12495.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.25
r_work: 0.3515 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8617  Z= 0.217
  Angle     :  0.585  14.613  11673  Z= 0.299
  Chirality :  0.042   0.144   1322
  Planarity :  0.004   0.057   1475
  Dihedral  :  4.155  18.020   1147
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.56 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 22.10 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.09 (0.26), residues: 1054
  helix:  2.36 (0.24), residues: 452
  sheet:  0.39 (0.35), residues: 220
  loop : -1.12 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  99 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.024   0.001   PHE R   9 
 TYR   0.010   0.001   TYR A 194 
 ARG   0.007   0.000   ARG B  19 

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 219
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8270 (tp30) cc_final: 0.7876 (tp30)
REVERT: A   29 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (m-30)
REVERT: A   55 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6937 (tt0)
REVERT: A   74 GLU cc_start: 0.7822 (pt0) cc_final: 0.7323 (pt0)
REVERT: A   87 PHE cc_start: 0.7852 (p90) cc_final: 0.7511 (p90)
REVERT: A  103 PHE cc_start: 0.8003 (m-80) cc_final: 0.7751 (t80)
REVERT: A  123 GLU cc_start: 0.7599 (pt0) cc_final: 0.7256 (pt0)
REVERT: A  198 ASP cc_start: 0.7967 (t0) cc_final: 0.7601 (m-30)
REVERT: A  241 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7252 (mt-10)
REVERT: B   23 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8507 (tmtt)
REVERT: B  125 ASN cc_start: 0.8430 (t0) cc_final: 0.8124 (t0)
REVERT: B  150 ARG cc_start: 0.8637 (mmt-90) cc_final: 0.8421 (mpt180)
REVERT: B  188 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7738 (mmm)
REVERT: B  197 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7595 (mmm160)
REVERT: B  212 ASP cc_start: 0.8051 (t0) cc_final: 0.7494 (t0)
REVERT: N   60 SER cc_start: 0.8293 (m) cc_final: 0.7969 (p)
REVERT: N  109 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7311 (m-80)
REVERT: R   17 PHE cc_start: 0.8161 (t80) cc_final: 0.7808 (t80)
REVERT: R  109 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7672 (mmmm)
REVERT: R  112 ASN cc_start: 0.8869 (p0) cc_final: 0.8648 (p0)
REVERT: R  149 MET cc_start: 0.7453 (mmp) cc_final: 0.7054 (mmm)
REVERT: R  207 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7877 (tmtt)
REVERT: R  262 MET cc_start: 0.6779 (ppp) cc_final: 0.6348 (ppp)
REVERT: R  284 LYS cc_start: 0.8365 (tptp) cc_final: 0.8018 (tptp)
REVERT: R  287 LYS cc_start: 0.8112 (tppp) cc_final: 0.7843 (tppp)
  outliers start: 18
  outliers final: 13
  residues processed: 230
  average time/residue: 0.3160
  time to fit residues: 93.4346
Evaluate side-chains
  235 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 218
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  126 THR
Chi-restraints excluded: chain R residue   78 ILE
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120809 restraints weight = 12548.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.30
r_work: 0.3497 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8617  Z= 0.274
  Angle     :  0.604  14.386  11673  Z= 0.310
  Chirality :  0.043   0.145   1322
  Planarity :  0.004   0.064   1475
  Dihedral  :  4.266  18.743   1147
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.21 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.01 (0.26), residues: 1054
  helix:  2.29 (0.24), residues: 451
  sheet:  0.40 (0.35), residues: 221
  loop : -1.19 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  99 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.023   0.002   PHE R   9 
 TYR   0.012   0.001   TYR N  61 
 ARG   0.008   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5618.98 seconds
wall clock time: 98 minutes 16.04 seconds (5896.04 seconds total)