Starting phenix.real_space_refine
on Sat Jul 26 22:22:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e3z_27874/07_2025/8e3z_27874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e3z_27874/07_2025/8e3z_27874.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e3z_27874/07_2025/8e3z_27874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e3z_27874/07_2025/8e3z_27874.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e3z_27874/07_2025/8e3z_27874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e3z_27874/07_2025/8e3z_27874.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      59      5.16       5
     C    5650      2.51       5
     N    1550      2.21       5
     O    1639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8898
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1819
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 217, 1807
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 6, 'TRANS': 210}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 217, 1807
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 6, 'TRANS': 210}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 1827
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2572
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 234
          Classifications: {'peptide': 28}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 27}
    Chain: "R"
      Number of atoms: 2883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2883
          Classifications: {'peptide': 372}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 14, 'TRANS': 357}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 136
          Unresolved non-hydrogen angles: 178
          Unresolved non-hydrogen dihedrals: 114
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 78
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 358 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR A 358 " occ=0.50
  Time building chain proxies: 6.35, per 1000 atoms: 0.71
  Number of scatterers: 8898
  At special positions: 0
  Unit cell: (87.15, 101.26, 166.83, 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      59     16.00
     O    1639      8.00
     N    1550      7.00
     C    5650      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  37 " - pdb=" SG  CYS R 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  50 " - pdb=" SG  CYS R  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  63 " - pdb=" SG  CYS R 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  86 " - pdb=" SG  CYS R 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 215 " - pdb=" SG  CYS R 285 " 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: 2.32
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      41.5% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 38
      removed outlier: 3.929A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.625A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.932A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.514A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.504A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.585A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.631A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 26
      removed outlier: 3.631A  pdb=" N   ILE P  26 " --> pdb=" O   TYR P  22 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 50
      removed outlier: 4.127A  pdb=" N   ILE R  43 " --> pdb=" O   TYR R  39 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU R  44 " --> pdb=" O   VAL R  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 92
      removed outlier: 3.659A  pdb=" N   PHE R  90 " --> pdb=" O   PRO R  87 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU R  92 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 167
      removed outlier: 3.523A  pdb=" N   ASP R 132 " --> pdb=" O   ALA R 128 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU R 133 " --> pdb=" O   ALA R 129 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL R 159 " --> pdb=" O   ALA R 155 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE R 167 " --> pdb=" O   ILE R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 200
    Processing helix  chain 'R' and resid 203 through 210
    Processing helix  chain 'R' and resid 212 through 246
      removed outlier: 3.593A  pdb=" N   LYS R 216 " --> pdb=" O   SER R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 253
      No H-bonds generated for 'chain 'R' and resid 251 through 253'
    Processing helix  chain 'R' and resid 254 through 280
      removed outlier: 4.561A  pdb=" N   VAL R 265 " --> pdb=" O   ILE R 261 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 293 through 324
      removed outlier: 3.950A  pdb=" N   ILE R 297 " --> pdb=" O   LEU R 293 " (cutoff:3.500A)
      Proline residue:  R 300  - end of helix
      removed outlier: 3.945A  pdb=" N   ASN R 308 " --> pdb=" O   SER R 304 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN R 321 " --> pdb=" O   ARG R 317 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LYS R 322 " --> pdb=" O   ILE R 318 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 334 through 351
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 352 through 357
      removed outlier: 3.522A  pdb=" N   PHE R 357 " --> pdb=" O   TYR R 354 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 389
      removed outlier: 4.390A  pdb=" N   GLY R 381 " --> pdb=" O   GLY R 377 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   PHE R 382 " --> pdb=" O   SER R 378 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 392 through 407
      removed outlier: 3.518A  pdb=" N   ARG R 401 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.754A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.865A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.981A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.072A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.678A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.642A  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: 3.535A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.650A  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: 3.549A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 276
      removed outlier: 3.756A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.052A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 83 through 85

    426 hydrogen bonds defined for protein.
    1206 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: 2.34

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1798
        1.33 -     1.45: 2254
        1.45 -     1.57: 4949
        1.57 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 9083
  Sorted by residual:
  bond pdb=" N   LYS R 365 "
       pdb=" CA  LYS R 365 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.028 9.20e-03 1.18e+04 9.59e+00
  bond pdb=" N   VAL R 235 "
       pdb=" CA  VAL R 235 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.38e+00
  bond pdb=" N   ILE R 177 "
       pdb=" CA  ILE R 177 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.08e+00
  bond pdb=" N   VAL R 368 "
       pdb=" CA  VAL R 368 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.32e+00
  bond pdb=" N   ASN G  59 "
       pdb=" CA  ASN G  59 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.042 1.58e-02 4.01e+03 6.93e+00
  ... (remaining 9078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 11924
        1.49 -     2.99: 302
        2.99 -     4.48: 56
        4.48 -     5.97: 9
        5.97 -     7.47: 3
  Bond angle restraints: 12294
  Sorted by residual:
  angle pdb=" N   ALA R 358 "
        pdb=" CA  ALA R 358 "
        pdb=" C   ALA R 358 "
      ideal   model   delta    sigma   weight residual
     113.41  105.94    7.47 1.22e+00 6.72e-01 3.75e+01
  angle pdb=" N   LEU R 233 "
        pdb=" CA  LEU R 233 "
        pdb=" C   LEU R 233 "
      ideal   model   delta    sigma   weight residual
     111.36  106.85    4.51 1.09e+00 8.42e-01 1.71e+01
  angle pdb=" C   GLU R 373 "
        pdb=" N   LEU R 374 "
        pdb=" CA  LEU R 374 "
      ideal   model   delta    sigma   weight residual
     120.58  113.54    7.04 1.71e+00 3.42e-01 1.70e+01
  angle pdb=" C   ASN G  59 "
        pdb=" N   PRO G  60 "
        pdb=" CA  PRO G  60 "
      ideal   model   delta    sigma   weight residual
     119.05  123.11   -4.06 1.11e+00 8.12e-01 1.34e+01
  angle pdb=" CA  PHE R 360 "
        pdb=" C   PHE R 360 "
        pdb=" N   PRO R 361 "
      ideal   model   delta    sigma   weight residual
     119.27  123.25   -3.98 1.13e+00 7.83e-01 1.24e+01
  ... (remaining 12289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 4918
       16.96 -    33.91: 398
       33.91 -    50.87: 55
       50.87 -    67.83: 10
       67.83 -    84.78: 15
  Dihedral angle restraints: 5396
    sinusoidal: 2107
      harmonic: 3289
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -18.29  -67.71     1      1.00e+01 1.00e-02 5.96e+01
  dihedral pdb=" CB  CYS R 215 "
           pdb=" SG  CYS R 215 "
           pdb=" SG  CYS R 285 "
           pdb=" CB  CYS R 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.73  -55.73     1      1.00e+01 1.00e-02 4.19e+01
  dihedral pdb=" CB  CYS R  37 "
           pdb=" SG  CYS R  37 "
           pdb=" SG  CYS R 208 "
           pdb=" CB  CYS R 208 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.17   52.17     1      1.00e+01 1.00e-02 3.71e+01
  ... (remaining 5393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1150
       0.058 -    0.115: 183
       0.115 -    0.173: 24
       0.173 -    0.231: 4
       0.231 -    0.288: 1
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" CA  GLU R 373 "
            pdb=" N   GLU R 373 "
            pdb=" C   GLU R 373 "
            pdb=" CB  GLU R 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  PHE R 360 "
            pdb=" N   PHE R 360 "
            pdb=" C   PHE R 360 "
            pdb=" CB  PHE R 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ILE R 177 "
            pdb=" N   ILE R 177 "
            pdb=" C   ILE R 177 "
            pdb=" CB  ILE R 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.88e-01
  ... (remaining 1359 not shown)

  Planarity restraints: 1572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 231 "    0.017 2.00e-02 2.50e+03   3.36e-02 1.13e+01
        pdb=" C   PHE R 231 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   PHE R 231 "    0.021 2.00e-02 2.50e+03
        pdb=" N   TRP R 232 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 372 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.85e+00
        pdb=" C   PHE R 372 "    0.038 2.00e-02 2.50e+03
        pdb=" O   PHE R 372 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLU R 373 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  10 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" CD  GLU B  10 "   -0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  10 "    0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  10 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1569 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1052
        2.76 -     3.29: 8654
        3.29 -     3.83: 15204
        3.83 -     4.36: 17461
        4.36 -     4.90: 30499
  Nonbonded interactions: 72870
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG1 THR A 364 "
            pdb=" OD1 ASN A 371 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASN A 278 "
            pdb=" NH1 ARG N 105 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.301 3.120
  ... (remaining 72865 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=0.50 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.460
  Find NCS groups from input model:        0.100
  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:10.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
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   9090  Z= 0.199
  Angle     :  0.588   7.466  12308  Z= 0.388
  Chirality :  0.044   0.288   1362
  Planarity :  0.003   0.040   1572
  Dihedral  : 12.804  84.782   3251
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.32 %
    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 (0.25), residues: 1115
  helix:  1.80 (0.25), residues: 419
  sheet:  0.85 (0.36), residues: 192
  loop : -0.57 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 335 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.009   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12557 (  426)
  hydrogen bonds       : angle       5.34864 ( 1206)
  SS BOND              : bond        0.00146 (    7)
  SS BOND              : angle       0.66106 (   14)
  covalent geometry    : bond        0.00290 ( 9083)
  covalent geometry    : angle       0.58767 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.7673 (m-30) cc_final: 0.7270 (m-30)
REVERT: B  267 ASP cc_start: 0.8619 (m-30) cc_final: 0.8385 (m-30)
REVERT: P    3 ASP cc_start: 0.8032 (m-30) cc_final: 0.7580 (m-30)
REVERT: P   11 THR cc_start: 0.8235 (t) cc_final: 0.7966 (p)
REVERT: R   38 ASP cc_start: 0.6912 (p0) cc_final: 0.6358 (OUTLIER)
REVERT: R   42 MET cc_start: 0.8096 (mpp) cc_final: 0.6788 (ppp)
REVERT: R   44 GLU cc_start: 0.6976 (pm20) cc_final: 0.6616 (pm20)
REVERT: R  134 GLN cc_start: 0.8222 (pt0) cc_final: 0.7960 (pt0)
REVERT: R  251 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6961 (mm-30)
REVERT: R  252 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6302 (tpm170)
REVERT: R  261 ILE cc_start: 0.8141 (tt) cc_final: 0.7842 (tp)
REVERT: R  398 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6713 (tm-30)
REVERT: R  406 TRP cc_start: 0.6473 (t-100) cc_final: 0.6036 (t60)
  outliers start: 1
  outliers final: 1
  residues processed: 224
  average time/residue: 1.3193
  time to fit residues: 313.8054
Evaluate side-chains
  140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B  16 ASN
B  44 GLN
B 125 ASN
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
N  53 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.156244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.110852 restraints weight = 16796.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.72
r_work: 0.3281 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9090  Z= 0.186
  Angle     :  0.590   6.253  12308  Z= 0.315
  Chirality :  0.044   0.170   1362
  Planarity :  0.004   0.044   1572
  Dihedral  :  4.840  81.572   1235
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.26 %
    Favored  : 85.29 %
  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 (0.25), residues: 1115
  helix:  2.24 (0.25), residues: 424
  sheet:  0.61 (0.34), residues: 213
  loop : -0.69 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 232 
 HIS   0.013   0.002   HIS A 357 
 PHE   0.016   0.002   PHE N 108 
 TYR   0.024   0.002   TYR R 146 
 ARG   0.011   0.001   ARG A 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04135 (  426)
  hydrogen bonds       : angle       4.31090 ( 1206)
  SS BOND              : bond        0.00143 (    7)
  SS BOND              : angle       1.71283 (   14)
  covalent geometry    : bond        0.00423 ( 9083)
  covalent geometry    : angle       0.58774 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7456 (tp30) cc_final: 0.7170 (tp30)
REVERT: A  232 ARG cc_start: 0.8789 (ttp-110) cc_final: 0.8466 (ptp-170)
REVERT: A  311 TYR cc_start: 0.6890 (m-80) cc_final: 0.6378 (m-80)
REVERT: A  343 ASP cc_start: 0.8092 (m-30) cc_final: 0.7800 (m-30)
REVERT: B  267 ASP cc_start: 0.8935 (m-30) cc_final: 0.8731 (m-30)
REVERT: N   76 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8403 (mtmm)
REVERT: N   77 ASN cc_start: 0.8815 (m-40) cc_final: 0.8583 (m-40)
REVERT: P    3 ASP cc_start: 0.8582 (m-30) cc_final: 0.8148 (m-30)
REVERT: P   11 THR cc_start: 0.8683 (t) cc_final: 0.8358 (p)
REVERT: R   42 MET cc_start: 0.8243 (mpp) cc_final: 0.6860 (ppp)
REVERT: R  252 ARG cc_start: 0.7562 (tpt170) cc_final: 0.6585 (tpm170)
REVERT: R  254 TYR cc_start: 0.7306 (m-80) cc_final: 0.6632 (m-80)
REVERT: R  261 ILE cc_start: 0.8515 (tt) cc_final: 0.8274 (tp)
  outliers start: 23
  outliers final: 11
  residues processed: 173
  average time/residue: 1.5095
  time to fit residues: 276.5359
Evaluate side-chains
  153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 106 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 102 optimal weight:    0.0770
   chunk 107 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  53 GLN
R 223 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.152660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.107024 restraints weight = 25781.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 3.25
r_work: 0.3227 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9090  Z= 0.185
  Angle     :  0.566   6.164  12308  Z= 0.303
  Chirality :  0.043   0.152   1362
  Planarity :  0.004   0.040   1572
  Dihedral  :  4.892  80.268   1235
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 14.61 %
    Favored  : 81.98 %
  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:  0.86 (0.25), residues: 1115
  helix:  2.20 (0.25), residues: 421
  sheet:  0.42 (0.34), residues: 200
  loop : -0.81 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 232 
 HIS   0.011   0.002   HIS B  62 
 PHE   0.017   0.002   PHE N 108 
 TYR   0.022   0.002   TYR R 146 
 ARG   0.009   0.001   ARG A 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  426)
  hydrogen bonds       : angle       4.30196 ( 1206)
  SS BOND              : bond        0.00264 (    7)
  SS BOND              : angle       1.57783 (   14)
  covalent geometry    : bond        0.00434 ( 9083)
  covalent geometry    : angle       0.56429 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7568 (tp30) cc_final: 0.7267 (tp30)
REVERT: A  311 TYR cc_start: 0.7005 (m-80) cc_final: 0.6416 (m-80)
REVERT: A  343 ASP cc_start: 0.8097 (m-30) cc_final: 0.7808 (m-30)
REVERT: B   10 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8249 (pt0)
REVERT: B  267 ASP cc_start: 0.9001 (m-30) cc_final: 0.8790 (m-30)
REVERT: G   17 GLU cc_start: 0.7794 (tt0) cc_final: 0.7507 (tm-30)
REVERT: G   42 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7340 (mm-30)
REVERT: N   12 VAL cc_start: 0.8402 (m) cc_final: 0.8122 (p)
REVERT: N   77 ASN cc_start: 0.8805 (m-40) cc_final: 0.8599 (m-40)
REVERT: P    3 ASP cc_start: 0.8640 (m-30) cc_final: 0.8298 (m-30)
REVERT: P   12 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7793 (mtt-85)
REVERT: R   42 MET cc_start: 0.8119 (mpp) cc_final: 0.6679 (ppp)
REVERT: R  134 GLN cc_start: 0.8453 (pt0) cc_final: 0.8114 (pm20)
REVERT: R  252 ARG cc_start: 0.7709 (tpt170) cc_final: 0.6721 (tpm170)
REVERT: R  254 TYR cc_start: 0.7170 (m-80) cc_final: 0.6913 (m-80)
REVERT: R  261 ILE cc_start: 0.8671 (tt) cc_final: 0.8433 (tp)
REVERT: R  344 LEU cc_start: 0.8378 (tp) cc_final: 0.8138 (mm)
  outliers start: 32
  outliers final: 17
  residues processed: 175
  average time/residue: 1.3892
  time to fit residues: 257.2305
Evaluate side-chains
  157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  341 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 268 ASN
R 223 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.152879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106446 restraints weight = 23605.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 3.18
r_work: 0.3201 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9090  Z= 0.135
  Angle     :  0.519   6.096  12308  Z= 0.280
  Chirality :  0.042   0.167   1362
  Planarity :  0.004   0.059   1572
  Dihedral  :  4.789  80.914   1235
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.80 %
    Favored  : 79.74 %
  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:  1.03 (0.25), residues: 1115
  helix:  2.43 (0.25), residues: 415
  sheet:  0.49 (0.34), residues: 198
  loop : -0.77 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 256 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.018   0.001   TYR R 146 
 ARG   0.007   0.001   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  426)
  hydrogen bonds       : angle       4.17894 ( 1206)
  SS BOND              : bond        0.00220 (    7)
  SS BOND              : angle       1.42208 (   14)
  covalent geometry    : bond        0.00313 ( 9083)
  covalent geometry    : angle       0.51689 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7475 (tp30) cc_final: 0.7243 (tp30)
REVERT: A   58 LYS cc_start: 0.8395 (mttp) cc_final: 0.7744 (mmtm)
REVERT: A  311 TYR cc_start: 0.6967 (m-80) cc_final: 0.6371 (m-80)
REVERT: A  343 ASP cc_start: 0.8099 (m-30) cc_final: 0.7785 (m-30)
REVERT: G   17 GLU cc_start: 0.7788 (tt0) cc_final: 0.7466 (tm-30)
REVERT: G   42 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7350 (mm-30)
REVERT: P    3 ASP cc_start: 0.8566 (m-30) cc_final: 0.8193 (m-30)
REVERT: R   42 MET cc_start: 0.8158 (mpp) cc_final: 0.6780 (ppp)
REVERT: R  134 GLN cc_start: 0.8443 (pt0) cc_final: 0.8125 (pm20)
REVERT: R  158 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7382 (mm)
REVERT: R  252 ARG cc_start: 0.7738 (tpt170) cc_final: 0.6651 (tpm170)
REVERT: R  261 ILE cc_start: 0.8622 (tt) cc_final: 0.8400 (tp)
REVERT: R  344 LEU cc_start: 0.8402 (tp) cc_final: 0.8155 (mm)
REVERT: R  365 LYS cc_start: 0.8160 (pmmt) cc_final: 0.7102 (tppt)
  outliers start: 23
  outliers final: 14
  residues processed: 160
  average time/residue: 1.3571
  time to fit residues: 230.1324
Evaluate side-chains
  157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  341 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0970
   chunk 34 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
R 223 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.152893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.105871 restraints weight = 20122.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 3.01
r_work: 0.3203 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9090  Z= 0.141
  Angle     :  0.516   6.082  12308  Z= 0.278
  Chirality :  0.042   0.149   1362
  Planarity :  0.004   0.051   1572
  Dihedral  :  4.785  80.924   1235
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.02 %
    Favored  : 79.53 %
  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:  0.92 (0.25), residues: 1115
  helix:  2.31 (0.25), residues: 421
  sheet:  0.44 (0.34), residues: 199
  loop : -0.84 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP R 256 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.020   0.002   TYR P  22 
 ARG   0.007   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03698 (  426)
  hydrogen bonds       : angle       4.15778 ( 1206)
  SS BOND              : bond        0.00201 (    7)
  SS BOND              : angle       1.37334 (   14)
  covalent geometry    : bond        0.00330 ( 9083)
  covalent geometry    : angle       0.51429 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7422 (tp30) cc_final: 0.7214 (tp30)
REVERT: A   58 LYS cc_start: 0.8402 (mttp) cc_final: 0.7756 (mmtm)
REVERT: A  311 TYR cc_start: 0.6994 (m-80) cc_final: 0.6395 (m-80)
REVERT: G   17 GLU cc_start: 0.7793 (tt0) cc_final: 0.7473 (tm-30)
REVERT: G   42 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7321 (mm-30)
REVERT: R   42 MET cc_start: 0.8107 (mpp) cc_final: 0.6662 (ppp)
REVERT: R   44 GLU cc_start: 0.6629 (pm20) cc_final: 0.6042 (pm20)
REVERT: R  134 GLN cc_start: 0.8422 (pt0) cc_final: 0.8103 (pm20)
REVERT: R  158 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7354 (mm)
REVERT: R  252 ARG cc_start: 0.7672 (tpt170) cc_final: 0.6596 (tpm170)
REVERT: R  261 ILE cc_start: 0.8629 (tt) cc_final: 0.8409 (tp)
REVERT: R  344 LEU cc_start: 0.8465 (tp) cc_final: 0.8179 (mm)
REVERT: R  357 PHE cc_start: 0.8082 (m-10) cc_final: 0.7860 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 161
  average time/residue: 1.4067
  time to fit residues: 239.9330
Evaluate side-chains
  159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  341 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0070
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
R 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.153955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106074 restraints weight = 23775.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 3.29
r_work: 0.3202 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9090  Z= 0.121
  Angle     :  0.498   5.907  12308  Z= 0.268
  Chirality :  0.041   0.161   1362
  Planarity :  0.004   0.041   1572
  Dihedral  :  4.721  80.920   1235
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.87 %
    Favored  : 78.36 %
  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 (0.25), residues: 1115
  helix:  2.50 (0.25), residues: 415
  sheet:  0.51 (0.34), residues: 198
  loop : -0.77 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP R 256 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 146 
 ARG   0.006   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03514 (  426)
  hydrogen bonds       : angle       4.07915 ( 1206)
  SS BOND              : bond        0.00188 (    7)
  SS BOND              : angle       1.30336 (   14)
  covalent geometry    : bond        0.00278 ( 9083)
  covalent geometry    : angle       0.49616 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 1.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8378 (mttp) cc_final: 0.7740 (mmtm)
REVERT: A  229 ASP cc_start: 0.8327 (p0) cc_final: 0.8123 (p0)
REVERT: A  311 TYR cc_start: 0.7004 (m-80) cc_final: 0.6400 (m-80)
REVERT: A  343 ASP cc_start: 0.8230 (m-30) cc_final: 0.7934 (m-30)
REVERT: G   17 GLU cc_start: 0.7806 (tt0) cc_final: 0.7484 (tm-30)
REVERT: G   42 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7313 (mm-30)
REVERT: R   42 MET cc_start: 0.8147 (mpp) cc_final: 0.6712 (ppp)
REVERT: R  158 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7336 (mm)
REVERT: R  252 ARG cc_start: 0.7656 (tpt170) cc_final: 0.6442 (tpm170)
REVERT: R  261 ILE cc_start: 0.8607 (tt) cc_final: 0.8396 (tp)
REVERT: R  344 LEU cc_start: 0.8470 (tp) cc_final: 0.8186 (mm)
REVERT: R  357 PHE cc_start: 0.8128 (m-10) cc_final: 0.7913 (m-80)
REVERT: R  365 LYS cc_start: 0.8209 (pmmt) cc_final: 0.7173 (tppt)
REVERT: R  367 GLU cc_start: 0.6567 (mp0) cc_final: 0.5149 (mm-30)
REVERT: R  398 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6213 (tm-30)
  outliers start: 26
  outliers final: 15
  residues processed: 168
  average time/residue: 2.0847
  time to fit residues: 373.3641
Evaluate side-chains
  153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  341 ARG
Chi-restraints excluded: chain R residue  398 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.153570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.104947 restraints weight = 27127.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 3.49
r_work: 0.3179 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9090  Z= 0.137
  Angle     :  0.528   6.891  12308  Z= 0.283
  Chirality :  0.041   0.149   1362
  Planarity :  0.004   0.042   1572
  Dihedral  :  4.818  81.172   1235
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.72 %
    Favored  : 77.61 %
  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:  1.06 (0.25), residues: 1115
  helix:  2.49 (0.25), residues: 415
  sheet:  0.48 (0.34), residues: 198
  loop : -0.77 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP R 256 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.021   0.001   TYR P  22 
 ARG   0.007   0.001   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  426)
  hydrogen bonds       : angle       4.08099 ( 1206)
  SS BOND              : bond        0.00196 (    7)
  SS BOND              : angle       1.69970 (   14)
  covalent geometry    : bond        0.00322 ( 9083)
  covalent geometry    : angle       0.52468 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8397 (mttp) cc_final: 0.7747 (mmtm)
REVERT: A  311 TYR cc_start: 0.7018 (m-80) cc_final: 0.6413 (m-80)
REVERT: A  343 ASP cc_start: 0.8259 (m-30) cc_final: 0.7975 (m-30)
REVERT: A  380 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7234 (ttp80)
REVERT: B   44 GLN cc_start: 0.8575 (mm110) cc_final: 0.8138 (mp10)
REVERT: G   17 GLU cc_start: 0.7817 (tt0) cc_final: 0.7478 (tm-30)
REVERT: G   42 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7346 (mm-30)
REVERT: R   42 MET cc_start: 0.8174 (mpp) cc_final: 0.6716 (ppp)
REVERT: R   44 GLU cc_start: 0.7095 (pm20) cc_final: 0.6733 (pm20)
REVERT: R  158 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7330 (mm)
REVERT: R  252 ARG cc_start: 0.7526 (tpt170) cc_final: 0.6307 (tpm170)
REVERT: R  261 ILE cc_start: 0.8601 (tt) cc_final: 0.8391 (tp)
REVERT: R  344 LEU cc_start: 0.8478 (tp) cc_final: 0.8197 (mm)
REVERT: R  357 PHE cc_start: 0.8177 (m-10) cc_final: 0.7947 (m-80)
REVERT: R  367 GLU cc_start: 0.6604 (mp0) cc_final: 0.5169 (mm-30)
REVERT: R  398 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6179 (tm-30)
  outliers start: 25
  outliers final: 17
  residues processed: 159
  average time/residue: 1.5104
  time to fit residues: 254.1246
Evaluate side-chains
  155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  341 ARG
Chi-restraints excluded: chain R residue  398 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 93 optimal weight:    0.6980
   chunk 102 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.153776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.106977 restraints weight = 30359.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 3.58
r_work: 0.3223 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9090  Z= 0.127
  Angle     :  0.511   5.876  12308  Z= 0.276
  Chirality :  0.041   0.152   1362
  Planarity :  0.004   0.042   1572
  Dihedral  :  4.766  82.032   1235
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.94 %
    Favored  : 77.72 %
  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 (0.25), residues: 1115
  helix:  2.52 (0.25), residues: 415
  sheet:  0.55 (0.35), residues: 199
  loop : -0.78 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP R 256 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 146 
 ARG   0.007   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  426)
  hydrogen bonds       : angle       4.04430 ( 1206)
  SS BOND              : bond        0.00188 (    7)
  SS BOND              : angle       1.42967 (   14)
  covalent geometry    : bond        0.00292 ( 9083)
  covalent geometry    : angle       0.50855 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8398 (mttp) cc_final: 0.7729 (mmtm)
REVERT: A  343 ASP cc_start: 0.8284 (m-30) cc_final: 0.7937 (m-30)
REVERT: A  380 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7203 (ttp80)
REVERT: G   17 GLU cc_start: 0.7823 (tt0) cc_final: 0.7481 (tm-30)
REVERT: G   42 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7336 (mm-30)
REVERT: P   12 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7936 (mtt-85)
REVERT: R   42 MET cc_start: 0.8175 (mpp) cc_final: 0.6641 (ppp)
REVERT: R   44 GLU cc_start: 0.7094 (pm20) cc_final: 0.6617 (pm20)
REVERT: R  261 ILE cc_start: 0.8593 (tt) cc_final: 0.8384 (tp)
REVERT: R  344 LEU cc_start: 0.8445 (tp) cc_final: 0.8168 (mm)
REVERT: R  357 PHE cc_start: 0.8186 (m-10) cc_final: 0.7933 (m-80)
REVERT: R  367 GLU cc_start: 0.6473 (mp0) cc_final: 0.4945 (mm-30)
REVERT: R  398 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6295 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 159
  average time/residue: 1.3831
  time to fit residues: 232.8160
Evaluate side-chains
  156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  341 ARG
Chi-restraints excluded: chain R residue  398 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
N  84 ASN
R 223 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.153659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.107843 restraints weight = 23349.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.16
r_work: 0.3246 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9090  Z= 0.126
  Angle     :  0.518   6.945  12308  Z= 0.279
  Chirality :  0.041   0.147   1362
  Planarity :  0.004   0.042   1572
  Dihedral  :  4.745  81.061   1235
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 20.68 %
    Favored  : 77.19 %
  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 (0.25), residues: 1115
  helix:  2.54 (0.25), residues: 415
  sheet:  0.52 (0.35), residues: 199
  loop : -0.78 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP R 256 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.023   0.001   TYR P  22 
 ARG   0.007   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  426)
  hydrogen bonds       : angle       3.99871 ( 1206)
  SS BOND              : bond        0.00187 (    7)
  SS BOND              : angle       1.19438 (   14)
  covalent geometry    : bond        0.00292 ( 9083)
  covalent geometry    : angle       0.51655 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8347 (mttp) cc_final: 0.7705 (mmtm)
REVERT: A  343 ASP cc_start: 0.8277 (m-30) cc_final: 0.7963 (m-30)
REVERT: A  380 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7175 (ttp80)
REVERT: B   44 GLN cc_start: 0.8550 (mm110) cc_final: 0.7720 (mm-40)
REVERT: G   17 GLU cc_start: 0.7824 (tt0) cc_final: 0.7490 (tm-30)
REVERT: G   42 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7337 (mm-30)
REVERT: P   12 ARG cc_start: 0.8131 (mtt90) cc_final: 0.7888 (mtt-85)
REVERT: R   42 MET cc_start: 0.8219 (mpp) cc_final: 0.6667 (ppp)
REVERT: R  344 LEU cc_start: 0.8447 (tp) cc_final: 0.8185 (mm)
REVERT: R  357 PHE cc_start: 0.8176 (m-10) cc_final: 0.7930 (m-80)
REVERT: R  367 GLU cc_start: 0.6462 (mp0) cc_final: 0.4986 (mm-30)
REVERT: R  398 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6308 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 154
  average time/residue: 1.3981
  time to fit residues: 227.6745
Evaluate side-chains
  152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  341 ARG
Chi-restraints excluded: chain R residue  398 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0670
   chunk 17 optimal weight:    0.0270
   chunk 32 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0770
   chunk 35 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.2734

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
R 223 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.157250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.111195 restraints weight = 16391.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.78
r_work: 0.3291 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9090  Z= 0.099
  Angle     :  0.501   7.293  12308  Z= 0.270
  Chirality :  0.041   0.158   1362
  Planarity :  0.003   0.041   1572
  Dihedral  :  4.576  80.016   1235
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 22.17 %
    Favored  : 76.65 %
  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 (0.25), residues: 1115
  helix:  2.60 (0.25), residues: 415
  sheet:  0.51 (0.34), residues: 204
  loop : -0.72 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP R 256 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.030   0.001   TYR R 254 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03135 (  426)
  hydrogen bonds       : angle       3.86506 ( 1206)
  SS BOND              : bond        0.00153 (    7)
  SS BOND              : angle       1.08586 (   14)
  covalent geometry    : bond        0.00218 ( 9083)
  covalent geometry    : angle       0.50036 (12294)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8380 (mttp) cc_final: 0.7732 (mmtm)
REVERT: A  343 ASP cc_start: 0.8221 (m-30) cc_final: 0.7889 (m-30)
REVERT: B   44 GLN cc_start: 0.8504 (mm110) cc_final: 0.8211 (mp10)
REVERT: G   17 GLU cc_start: 0.7815 (tt0) cc_final: 0.7486 (tm-30)
REVERT: G   42 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7305 (mm-30)
REVERT: N   96 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7948 (p)
REVERT: R   42 MET cc_start: 0.8212 (mpp) cc_final: 0.6638 (ppp)
REVERT: R  281 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7107 (mp0)
REVERT: R  344 LEU cc_start: 0.8431 (tp) cc_final: 0.8164 (mm)
REVERT: R  357 PHE cc_start: 0.8150 (m-10) cc_final: 0.7906 (m-80)
REVERT: R  367 GLU cc_start: 0.6380 (mp0) cc_final: 0.4852 (mm-30)
REVERT: R  398 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6446 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 152
  average time/residue: 1.3665
  time to fit residues: 219.8803
Evaluate side-chains
  147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  183 ILE
Chi-restraints excluded: chain R residue  290 ASN
Chi-restraints excluded: chain R residue  341 ARG
Chi-restraints excluded: chain R residue  398 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
N  84 ASN
R 223 GLN
R 380 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.154976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.107840 restraints weight = 19534.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.01
r_work: 0.3235 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9090  Z= 0.121
  Angle     :  0.519   7.428  12308  Z= 0.279
  Chirality :  0.041   0.153   1362
  Planarity :  0.004   0.043   1572
  Dihedral  :  4.664  79.444   1235
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.32 %
    Favored  : 76.76 %
  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:  1.18 (0.25), residues: 1115
  helix:  2.56 (0.25), residues: 416
  sheet:  0.59 (0.34), residues: 202
  loop : -0.70 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP R 256 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.023   0.001   TYR P  22 
 ARG   0.007   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  426)
  hydrogen bonds       : angle       3.93735 ( 1206)
  SS BOND              : bond        0.00166 (    7)
  SS BOND              : angle       1.09510 (   14)
  covalent geometry    : bond        0.00278 ( 9083)
  covalent geometry    : angle       0.51803 (12294)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8986.17 seconds
wall clock time: 156 minutes 16.12 seconds (9376.12 seconds total)