Starting phenix.real_space_refine
on Wed Feb 12 15:13:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p9x_20277/02_2025/6p9x_20277.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p9x_20277/02_2025/6p9x_20277.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p9x_20277/02_2025/6p9x_20277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p9x_20277/02_2025/6p9x_20277.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p9x_20277/02_2025/6p9x_20277.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p9x_20277/02_2025/6p9x_20277.cif"
  }
  resolution = 2.91
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    5198      2.51       5
     N    1435      2.21       5
     O    1495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8177
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1638
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 192, 1627
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 185}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 192, 1627
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 185}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 1648
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    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: "R"
      Number of atoms: 2267
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 270, 2256
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 7, 'TRANS': 262}
      Conformer: "B"
        Number of residues, atoms: 270, 2256
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 7, 'TRANS': 262}
          bond proxies already assigned to first conformer: 2316
    Chain: "P"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 265
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 2, 'TRANS': 30}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "R"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "P"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AARG A  38 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  38 " occ=0.50
    residue:
      pdb=" N   SER R 301 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER R 301 " occ=0.00
    residue:
      pdb=" N   THR R 302 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR R 302 " occ=0.00
    residue:
      pdb=" N   THR R 303 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR R 303 " occ=0.00
    residue:
      pdb=" N   GLY R 335 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY R 335 " occ=0.00
    residue:
      pdb=" N   GLU R 336 " occ=0.00
      ... (7 atoms not shown)
      pdb=" OE2 GLU R 336 " occ=0.00
    residue:
      pdb=" N  APHE R 362 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE R 362 " occ=0.50
  Time building chain proxies: 6.65, per 1000 atoms: 0.81
  Number of scatterers: 8177
  At special positions: 0
  Unit cell: (88.1309, 144.873, 96.5818, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1495      8.00
     N    1435      7.00
     C    5198      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, 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=2.04
    Simple disulfide: pdb=" SG  CYS R 188 " - pdb=" SG  CYS R 258 " 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: 2.10
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      41.5% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.766A  pdb=" N   GLN A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.624A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.517A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
      removed outlier: 3.503A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.517A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 22
      removed outlier: 4.217A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.856A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.697A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.685A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 144
      removed outlier: 3.820A  pdb=" N   HIS R 117 " --> pdb=" O   LYS R 113 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE R 121 " --> pdb=" O   HIS R 117 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE R 129 " --> pdb=" O   LEU R 125 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE R 141 " --> pdb=" O   ALA R 137 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LEU R 142 " --> pdb=" O   PHE R 138 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU R 144 " --> pdb=" O   LEU R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 175
    Processing helix  chain 'R' and resid 177 through 184
      removed outlier: 3.586A  pdb=" N   GLN R 182 " --> pdb=" O   PRO R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 207
      removed outlier: 3.539A  pdb=" N   VAL R 191 " --> pdb=" O   TRP R 187 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE R 203 " --> pdb=" O   HIS R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 219
    Processing helix  chain 'R' and resid 227 through 236
      removed outlier: 3.909A  pdb=" N   PHE R 231 " --> pdb=" O   ARG R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 253
      removed outlier: 3.797A  pdb=" N   ILE R 242 " --> pdb=" O   VAL R 238 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 260
    Processing helix  chain 'R' and resid 269 through 302
      Proline residue:  R 275  - end of helix
      removed outlier: 3.585A  pdb=" N   ALA R 300 " --> pdb=" O   THR R 296 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER R 301 " --> pdb=" O   LYS R 297 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 319
      removed outlier: 3.545A  pdb=" N   TYR R 309 " --> pdb=" O   GLU R 305 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LYS R 314 " --> pdb=" O   ARG R 310 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 324
    Processing helix  chain 'R' and resid 325 through 330
      removed outlier: 4.548A  pdb=" N   PHE R 330 " --> pdb=" O   THR R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 354
      removed outlier: 3.527A  pdb=" N   LEU R 351 " --> pdb=" O   PHE R 347 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 354 through 364
    Processing helix  chain 'R' and resid 367 through 380
    Processing helix  chain 'P' and resid 6 through 8
      No H-bonds generated for 'chain 'P' and resid 6 through 8'
    Processing helix  chain 'P' and resid 9 through 32
      removed outlier: 3.994A  pdb=" N   ARG P  23 " --> pdb=" O   LEU P  19 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA P  24 " --> pdb=" O   GLU P  20 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN P  29 " --> pdb=" O   GLU P  25 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.978A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.215A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.519A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.933A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.633A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.309A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.396A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.523A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 3.553A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1148 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: 2.59

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2672
        1.35 -     1.47: 2098
        1.47 -     1.59: 3507
        1.59 -     1.71: 0
        1.71 -     1.84: 69
  Bond restraints: 8346
  Sorted by residual:
  bond pdb=" N   ILE B 229 "
       pdb=" CA  ILE B 229 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 1.10e-02 8.26e+03 8.43e+00
  bond pdb=" N   ILE B 273 "
       pdb=" CA  ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.15e+00
  bond pdb=" N   THR B 249 "
       pdb=" CA  THR B 249 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.18e-02 7.18e+03 6.97e+00
  bond pdb=" N   HIS B 225 "
       pdb=" CA  HIS B 225 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 6.94e+00
  bond pdb=" N   SER B 245 "
       pdb=" CA  SER B 245 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.031 1.29e-02 6.01e+03 5.96e+00
  ... (remaining 8341 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 10635
        1.08 -     2.15: 551
        2.15 -     3.23: 93
        3.23 -     4.30: 19
        4.30 -     5.38: 7
  Bond angle restraints: 11305
  Sorted by residual:
  angle pdb=" N   ASP B 246 "
        pdb=" CA  ASP B 246 "
        pdb=" C   ASP B 246 "
      ideal   model   delta    sigma   weight residual
     113.01  109.19    3.82 1.20e+00 6.94e-01 1.01e+01
  angle pdb=" N   ASP B 247 "
        pdb=" CA  ASP B 247 "
        pdb=" C   ASP B 247 "
      ideal   model   delta    sigma   weight residual
     113.01  109.31    3.70 1.20e+00 6.94e-01 9.53e+00
  angle pdb=" CA  GLY B 272 "
        pdb=" C   GLY B 272 "
        pdb=" O   GLY B 272 "
      ideal   model   delta    sigma   weight residual
     122.31  118.24    4.07 1.34e+00 5.57e-01 9.21e+00
  angle pdb=" N   VAL R 313 "
        pdb=" CA  VAL R 313 "
        pdb=" C   VAL R 313 "
      ideal   model   delta    sigma   weight residual
     111.58  108.38    3.20 1.06e+00 8.90e-01 9.13e+00
  angle pdb=" CA  ASP B 228 "
        pdb=" C   ASP B 228 "
        pdb=" O   ASP B 228 "
      ideal   model   delta    sigma   weight residual
     121.19  118.07    3.12 1.10e+00 8.26e-01 8.03e+00
  ... (remaining 11300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 4522
       17.23 -    34.47: 339
       34.47 -    51.70: 54
       51.70 -    68.93: 8
       68.93 -    86.17: 8
  Dihedral angle restraints: 4931
    sinusoidal: 1970
      harmonic: 2961
  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    0.17  -86.17     1      1.00e+01 1.00e-02 8.96e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.54  -29.46     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  HIS B 142 "
           pdb=" C   HIS B 142 "
           pdb=" N   THR B 143 "
           pdb=" CA  THR B 143 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.84   21.16     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 4928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 888
       0.040 -    0.079: 266
       0.079 -    0.119: 79
       0.119 -    0.159: 10
       0.159 -    0.198: 3
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.81e-01
  chirality pdb=" CA  ASP B 228 "
            pdb=" N   ASP B 228 "
            pdb=" C   ASP B 228 "
            pdb=" CB  ASP B 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CA  ILE B 229 "
            pdb=" N   ILE B 229 "
            pdb=" C   ILE B 229 "
            pdb=" CB  ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 1243 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 238 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO R 239 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO R 239 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 239 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B 236 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.011 2.00e-02 2.50e+03   1.03e-02 2.12e+00
        pdb=" CG  TYR B  59 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 955
        2.75 -     3.29: 7757
        3.29 -     3.82: 13342
        3.82 -     4.36: 17688
        4.36 -     4.90: 29567
  Nonbonded interactions: 69309
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   SER R 349 "
            pdb=" OG  SER R 353 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASP R 224 "
            pdb=" NH1 ARG R 227 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OE2 GLU R 352 "
            pdb=" O   HOH R 501 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.263 3.040
  ... (remaining 69304 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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.010
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8346  Z= 0.225
  Angle     :  0.568   5.379  11305  Z= 0.360
  Chirality :  0.042   0.198   1246
  Planarity :  0.003   0.041   1443
  Dihedral  : 12.458  79.634   3008
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.48 %
    Favored  : 98.29 %
  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: -3.97 (0.22), residues: 1001
  helix: -3.96 (0.14), residues: 390
  sheet: -1.21 (0.33), residues: 219
  loop : -1.72 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.015   0.001   PHE N 108 
 TYR   0.025   0.001   TYR B  59 
 ARG   0.002   0.000   ARG N 118 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A  209 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6481 (mt-10)
REVERT: A  220 HIS cc_start: 0.7940 (t-170) cc_final: 0.7686 (t70)
REVERT: A  280 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8360 (ptpt)
REVERT: A  283 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7089 (mtt-85)
REVERT: A  339 TYR cc_start: 0.8360 (m-80) cc_final: 0.7784 (m-80)
REVERT: A  344 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7943 (mm-30)
REVERT: B   23 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7860 (tppt)
REVERT: B   46 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7071 (mmm-85)
REVERT: B   76 ASP cc_start: 0.8810 (p0) cc_final: 0.8440 (p0)
REVERT: B  138 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7607 (mt-10)
REVERT: B  245 SER cc_start: 0.9034 (t) cc_final: 0.8735 (t)
REVERT: B  246 ASP cc_start: 0.8221 (m-30) cc_final: 0.7968 (m-30)
REVERT: B  312 ASP cc_start: 0.7919 (m-30) cc_final: 0.7714 (m-30)
REVERT: G   20 LYS cc_start: 0.8080 (mttm) cc_final: 0.7704 (mtmm)
REVERT: G   32 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8228 (tptm)
REVERT: N    5 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7492 (mm110)
REVERT: N   34 MET cc_start: 0.8941 (mmm) cc_final: 0.8444 (mmm)
REVERT: N   83 MET cc_start: 0.9050 (mtp) cc_final: 0.8422 (mtp)
REVERT: R  225 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7292 (mtp180)
REVERT: R  234 ILE cc_start: 0.8596 (mt) cc_final: 0.8385 (mm)
REVERT: R  333 ASN cc_start: 0.7704 (t0) cc_final: 0.7434 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 153
  average time/residue: 1.4711
  time to fit residues: 236.7602
Evaluate side-chains
  116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 218 ASN
A 264 ASN
A 279 ASN
A 377 ASN
B  75 GLN
B 110 ASN
B 119 ASN
B 142 HIS
B 155 ASN
R 127 HIS
R 166 ASN
R 173 GLN
R 182 GLN
R 379 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.129724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.097069 restraints weight = 26425.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 4.00
r_work: 0.2697 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8346  Z= 0.406
  Angle     :  0.672  18.036  11305  Z= 0.351
  Chirality :  0.048   0.162   1246
  Planarity :  0.005   0.047   1443
  Dihedral  :  5.004  30.017   1119
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  8.77 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.24), residues: 1001
  helix: -1.56 (0.23), residues: 398
  sheet: -0.66 (0.34), residues: 222
  loop : -1.35 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N  47 
 HIS   0.013   0.002   HIS A 357 
 PHE   0.025   0.002   PHE N 108 
 TYR   0.014   0.002   TYR B 105 
 ARG   0.011   0.001   ARG R 310 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7392 (tt0) cc_final: 0.7104 (tt0)
REVERT: A   25 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7729 (tttp)
REVERT: A  280 LYS cc_start: 0.8877 (ptmt) cc_final: 0.8669 (ptpt)
REVERT: A  284 ASP cc_start: 0.8791 (m-30) cc_final: 0.8536 (m-30)
REVERT: A  389 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7345 (mtp180)
REVERT: B   13 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7370 (tt0)
REVERT: B   23 LYS cc_start: 0.8292 (ttpp) cc_final: 0.7974 (tppt)
REVERT: B   46 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7326 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9133 (p0) cc_final: 0.8817 (p0)
REVERT: B  134 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6984 (mmp80)
REVERT: B  153 ASP cc_start: 0.8828 (m-30) cc_final: 0.8502 (m-30)
REVERT: B  214 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7729 (mmp80)
REVERT: B  217 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8671 (pmt)
REVERT: B  262 MET cc_start: 0.9192 (ttm) cc_final: 0.8941 (tpp)
REVERT: G   20 LYS cc_start: 0.8010 (mttm) cc_final: 0.7657 (mtmm)
REVERT: G   32 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8492 (tptm)
REVERT: N    5 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7583 (mm110)
REVERT: N   19 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8247 (ttt180)
REVERT: N   34 MET cc_start: 0.9229 (mmm) cc_final: 0.8663 (mmm)
REVERT: N   52 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8410 (p)
REVERT: N   76 LYS cc_start: 0.8712 (ptpt) cc_final: 0.8491 (ptpt)
REVERT: N   80 TYR cc_start: 0.9044 (m-80) cc_final: 0.8761 (m-80)
REVERT: N   83 MET cc_start: 0.9205 (mtp) cc_final: 0.8754 (mtp)
REVERT: N   89 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7239 (pm20)
REVERT: N  113 THR cc_start: 0.5666 (OUTLIER) cc_final: 0.5466 (p)
REVERT: R  206 MET cc_start: 0.8900 (mtm) cc_final: 0.8524 (mtm)
REVERT: R  333 ASN cc_start: 0.7979 (t0) cc_final: 0.7608 (t0)
REVERT: P   21 MET cc_start: 0.7615 (ttm) cc_final: 0.7271 (ttp)
  outliers start: 21
  outliers final: 7
  residues processed: 140
  average time/residue: 1.5301
  time to fit residues: 225.0769
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B 142 HIS
B 155 ASN
R 182 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.130831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.098320 restraints weight = 17217.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.43
r_work: 0.2778 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8346  Z= 0.312
  Angle     :  0.604  17.340  11305  Z= 0.313
  Chirality :  0.045   0.151   1246
  Planarity :  0.005   0.048   1443
  Dihedral  :  4.875  28.935   1119
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.73 %
    Favored  : 85.99 %
  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: -1.12 (0.25), residues: 1001
  helix: -0.45 (0.25), residues: 400
  sheet: -0.48 (0.34), residues: 223
  loop : -1.01 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.012   0.002   TYR A 339 
 ARG   0.010   0.001   ARG R 310 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7379 (tt0) cc_final: 0.7127 (tt0)
REVERT: A   20 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7307 (mtm110)
REVERT: A   25 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7851 (tttp)
REVERT: A  264 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7147 (p0)
REVERT: A  389 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.7405 (mtp180)
REVERT: B   23 LYS cc_start: 0.8295 (ttpp) cc_final: 0.8027 (tppt)
REVERT: B   46 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7390 (mmm-85)
REVERT: B   76 ASP cc_start: 0.9055 (p0) cc_final: 0.8691 (p0)
REVERT: B  134 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7025 (mmp80)
REVERT: B  214 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7715 (mmp80)
REVERT: B  217 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8650 (pmt)
REVERT: G   20 LYS cc_start: 0.8117 (mttm) cc_final: 0.7877 (mtmm)
REVERT: G   21 MET cc_start: 0.7242 (mmm) cc_final: 0.6989 (ptm)
REVERT: G   32 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8512 (tptm)
REVERT: N    5 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7537 (mm110)
REVERT: N   19 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8229 (ttt180)
REVERT: N   34 MET cc_start: 0.9181 (mmm) cc_final: 0.8606 (mmm)
REVERT: N   76 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8520 (ptpt)
REVERT: R  206 MET cc_start: 0.8990 (mtm) cc_final: 0.8584 (mtm)
REVERT: R  333 ASN cc_start: 0.7968 (t0) cc_final: 0.7620 (t0)
REVERT: P   21 MET cc_start: 0.7663 (ttm) cc_final: 0.7345 (ttp)
  outliers start: 20
  outliers final: 9
  residues processed: 137
  average time/residue: 1.4732
  time to fit residues: 212.2663
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   chunk 74 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B  17 GLN
B 142 HIS
B 155 ASN
B 340 ASN
G  59 ASN
R 173 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.134026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.100378 restraints weight = 16201.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.41
r_work: 0.2849 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2820
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2820
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8346  Z= 0.166
  Angle     :  0.506  13.091  11305  Z= 0.265
  Chirality :  0.042   0.137   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.480  25.381   1119
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.21 %
    Favored  : 84.74 %
  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: -0.38 (0.26), residues: 1001
  helix:  0.36 (0.26), residues: 400
  sheet: -0.21 (0.33), residues: 227
  loop : -0.80 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.011   0.001   TYR R 363 
 ARG   0.011   0.000   ARG R 310 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7317 (tt0) cc_final: 0.7058 (tt0)
REVERT: A   20 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7234 (mtm110)
REVERT: A   25 LYS cc_start: 0.8390 (ttmm) cc_final: 0.7817 (tttp)
REVERT: A  389 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7360 (mtp180)
REVERT: B   23 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8018 (tppt)
REVERT: B   46 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7436 (mmt-90)
REVERT: B   76 ASP cc_start: 0.9003 (p0) cc_final: 0.8659 (p0)
REVERT: B   86 THR cc_start: 0.8789 (m) cc_final: 0.8499 (p)
REVERT: B  134 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6894 (mmp80)
REVERT: B  214 ARG cc_start: 0.7839 (mmt180) cc_final: 0.7627 (mmp80)
REVERT: B  217 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8702 (pmt)
REVERT: B  291 ASP cc_start: 0.7973 (p0) cc_final: 0.7684 (p0)
REVERT: G   20 LYS cc_start: 0.8092 (mttm) cc_final: 0.7848 (mtmm)
REVERT: G   21 MET cc_start: 0.7164 (mmm) cc_final: 0.6882 (ptm)
REVERT: G   32 LYS cc_start: 0.8789 (tmtt) cc_final: 0.8478 (tptm)
REVERT: N    5 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7436 (mm110)
REVERT: N   19 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8121 (ttt180)
REVERT: N   34 MET cc_start: 0.9187 (mmm) cc_final: 0.8561 (mmm)
REVERT: N   89 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7322 (pm20)
REVERT: R  333 ASN cc_start: 0.7891 (t0) cc_final: 0.7597 (t0)
REVERT: P   21 MET cc_start: 0.7752 (ttm) cc_final: 0.7298 (ttp)
  outliers start: 18
  outliers final: 6
  residues processed: 137
  average time/residue: 1.4609
  time to fit residues: 210.7253
Evaluate side-chains
  129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.132873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.099970 restraints weight = 17640.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.51
r_work: 0.2802 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8346  Z= 0.200
  Angle     :  0.528  14.211  11305  Z= 0.275
  Chirality :  0.043   0.135   1246
  Planarity :  0.004   0.045   1443
  Dihedral  :  4.482  24.718   1119
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.55 %
    Favored  : 83.83 %
  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: -0.13 (0.26), residues: 1001
  helix:  0.64 (0.26), residues: 400
  sheet: -0.17 (0.33), residues: 228
  loop : -0.68 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.016   0.001   PHE R 260 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.011   0.000   ARG R 310 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7327 (tt0) cc_final: 0.7048 (tt0)
REVERT: A   20 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7271 (mtm110)
REVERT: A   25 LYS cc_start: 0.8385 (ttmm) cc_final: 0.7824 (tttp)
REVERT: A  264 ASN cc_start: 0.7441 (p0) cc_final: 0.7117 (p0)
REVERT: A  389 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7386 (mtp180)
REVERT: B   23 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8024 (tppt)
REVERT: B   46 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7428 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8979 (p0) cc_final: 0.8582 (p0)
REVERT: B   86 THR cc_start: 0.8778 (m) cc_final: 0.8548 (p)
REVERT: B  134 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6913 (mmp80)
REVERT: B  214 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7539 (mmp80)
REVERT: B  217 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8670 (pmt)
REVERT: B  291 ASP cc_start: 0.8009 (p0) cc_final: 0.7705 (p0)
REVERT: G   20 LYS cc_start: 0.8102 (mttm) cc_final: 0.7852 (mtmm)
REVERT: G   21 MET cc_start: 0.7096 (mmm) cc_final: 0.6833 (ptm)
REVERT: G   32 LYS cc_start: 0.8738 (tmtt) cc_final: 0.8423 (tptm)
REVERT: N    5 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7472 (mm110)
REVERT: N   19 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8227 (ttt180)
REVERT: N   34 MET cc_start: 0.9170 (mmm) cc_final: 0.8679 (mmm)
REVERT: N   89 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7404 (pm20)
REVERT: R  206 MET cc_start: 0.8962 (mtm) cc_final: 0.8600 (mtm)
REVERT: R  333 ASN cc_start: 0.7876 (t0) cc_final: 0.7528 (t0)
  outliers start: 23
  outliers final: 9
  residues processed: 126
  average time/residue: 1.5229
  time to fit residues: 201.7066
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0670
   chunk 55 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6922

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.135036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102835 restraints weight = 16971.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.40
r_work: 0.2862 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   8346  Z= 0.145
  Angle     :  0.484  11.563  11305  Z= 0.255
  Chirality :  0.042   0.135   1246
  Planarity :  0.004   0.045   1443
  Dihedral  :  4.264  22.218   1119
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.01 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.26), residues: 1001
  helix:  0.97 (0.26), residues: 400
  sheet: -0.04 (0.33), residues: 228
  loop : -0.59 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.009   0.000   ARG R 310 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7290 (tt0) cc_final: 0.6997 (tt0)
REVERT: A   20 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7125 (mtm110)
REVERT: A   25 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7779 (tttp)
REVERT: A  389 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7443 (mtp180)
REVERT: B   23 LYS cc_start: 0.8305 (ttpp) cc_final: 0.8022 (tppt)
REVERT: B   46 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7467 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8907 (p0) cc_final: 0.8521 (p0)
REVERT: B  134 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6891 (mmp80)
REVERT: B  214 ARG cc_start: 0.7762 (mmt180) cc_final: 0.7503 (mmp80)
REVERT: B  217 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8647 (pmt)
REVERT: B  291 ASP cc_start: 0.7913 (p0) cc_final: 0.7626 (p0)
REVERT: B  312 ASP cc_start: 0.8287 (m-30) cc_final: 0.8018 (m-30)
REVERT: G   20 LYS cc_start: 0.8075 (mttm) cc_final: 0.7695 (mtmm)
REVERT: G   21 MET cc_start: 0.7037 (mmm) cc_final: 0.6803 (ptm)
REVERT: G   32 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8375 (tptm)
REVERT: N    5 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7427 (mm110)
REVERT: N   19 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8267 (ttt180)
REVERT: N   34 MET cc_start: 0.9158 (mmm) cc_final: 0.8648 (mmm)
REVERT: N   87 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (ptpp)
REVERT: N   89 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7069 (pm20)
REVERT: R  333 ASN cc_start: 0.7797 (t0) cc_final: 0.7459 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 124
  average time/residue: 1.5784
  time to fit residues: 205.8136
Evaluate side-chains
  121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 40 optimal weight:    0.1980
   chunk 58 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
B 220 GLN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.134690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.103013 restraints weight = 17936.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.59
r_work: 0.2842 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8346  Z= 0.177
  Angle     :  0.501  12.465  11305  Z= 0.262
  Chirality :  0.042   0.135   1246
  Planarity :  0.004   0.044   1443
  Dihedral  :  4.296  21.759   1119
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.90 %
    Favored  : 83.26 %
  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:  0.34 (0.26), residues: 1001
  helix:  1.09 (0.26), residues: 400
  sheet:  0.10 (0.34), residues: 219
  loop : -0.51 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.016   0.001   PHE R 260 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.009   0.000   ARG R 292 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7334 (tt0) cc_final: 0.7068 (tt0)
REVERT: A   20 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7297 (mtm110)
REVERT: A   25 LYS cc_start: 0.8387 (ttmm) cc_final: 0.7864 (tttp)
REVERT: A  389 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.7411 (mtp180)
REVERT: B   23 LYS cc_start: 0.8328 (ttpp) cc_final: 0.8052 (tppt)
REVERT: B   46 ARG cc_start: 0.8272 (mtm180) cc_final: 0.7517 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8923 (p0) cc_final: 0.8536 (p0)
REVERT: B  134 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6923 (mmp80)
REVERT: B  214 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7512 (mmp80)
REVERT: B  217 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8742 (pmt)
REVERT: B  291 ASP cc_start: 0.7994 (p0) cc_final: 0.7679 (p0)
REVERT: B  312 ASP cc_start: 0.8314 (m-30) cc_final: 0.8037 (m-30)
REVERT: G   20 LYS cc_start: 0.8048 (mttm) cc_final: 0.7655 (mtmm)
REVERT: G   21 MET cc_start: 0.7038 (mmm) cc_final: 0.6773 (ptm)
REVERT: G   32 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8394 (tptm)
REVERT: N    5 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7484 (mm110)
REVERT: N   19 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8354 (ttt180)
REVERT: N   34 MET cc_start: 0.9173 (mmm) cc_final: 0.8636 (mmm)
REVERT: N   87 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7632 (ptpp)
REVERT: N   89 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7104 (pm20)
REVERT: R  333 ASN cc_start: 0.7847 (t0) cc_final: 0.7513 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 127
  average time/residue: 1.4405
  time to fit residues: 192.7274
Evaluate side-chains
  129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.128229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.095058 restraints weight = 22514.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.31
r_work: 0.2720 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063   8346  Z= 0.502
  Angle     :  0.687  19.364  11305  Z= 0.352
  Chirality :  0.049   0.172   1246
  Planarity :  0.005   0.042   1443
  Dihedral  :  4.979  26.886   1119
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.01 %
    Favored  : 82.80 %
  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: -0.12 (0.26), residues: 1001
  helix:  0.57 (0.25), residues: 405
  sheet: -0.11 (0.34), residues: 229
  loop : -0.64 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP N  47 
 HIS   0.015   0.002   HIS A 220 
 PHE   0.026   0.003   PHE N 108 
 TYR   0.016   0.002   TYR R 212 
 ARG   0.010   0.001   ARG R 292 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7413 (tt0) cc_final: 0.6984 (tp30)
REVERT: A   20 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7234 (mtm110)
REVERT: A   25 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7852 (tttp)
REVERT: A  389 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7483 (mtp180)
REVERT: B   23 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8050 (tppt)
REVERT: B   42 ARG cc_start: 0.6540 (tpt170) cc_final: 0.5989 (tpt170)
REVERT: B   46 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7401 (mmt-90)
REVERT: B   76 ASP cc_start: 0.9009 (p0) cc_final: 0.8566 (p0)
REVERT: B  134 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6873 (mmp80)
REVERT: B  214 ARG cc_start: 0.7947 (mmt180) cc_final: 0.7707 (mmp80)
REVERT: B  217 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8730 (pmt)
REVERT: B  291 ASP cc_start: 0.8087 (p0) cc_final: 0.7810 (p0)
REVERT: G   20 LYS cc_start: 0.7918 (mttm) cc_final: 0.7550 (mtmm)
REVERT: G   32 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8459 (tptm)
REVERT: N    5 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7522 (mm110)
REVERT: N   19 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8309 (ttt180)
REVERT: N   34 MET cc_start: 0.9191 (mmm) cc_final: 0.8760 (mmm)
REVERT: N   76 LYS cc_start: 0.8762 (ptpt) cc_final: 0.8495 (ptpt)
REVERT: N   89 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7320 (pm20)
REVERT: P   21 MET cc_start: 0.7821 (ttm) cc_final: 0.7589 (ttp)
  outliers start: 28
  outliers final: 14
  residues processed: 127
  average time/residue: 1.5110
  time to fit residues: 201.7524
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.133439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.100253 restraints weight = 23395.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 3.34
r_work: 0.2811 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2799
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2799 r_free = 0.2799    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2799
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8346  Z= 0.168
  Angle     :  0.509  12.668  11305  Z= 0.268
  Chirality :  0.042   0.136   1246
  Planarity :  0.004   0.045   1443
  Dihedral  :  4.489  24.022   1119
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.03 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.26), residues: 1001
  helix:  1.13 (0.26), residues: 391
  sheet:  0.10 (0.34), residues: 228
  loop : -0.53 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.009   0.000   ARG R 292 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7335 (tt0) cc_final: 0.6916 (tp30)
REVERT: A   20 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7147 (mtm110)
REVERT: A   25 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7853 (tttp)
REVERT: A  389 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7356 (mtp180)
REVERT: B   23 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8049 (tppt)
REVERT: B   46 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7434 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8943 (p0) cc_final: 0.8546 (p0)
REVERT: B  134 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6955 (mmp80)
REVERT: B  214 ARG cc_start: 0.7937 (mmt180) cc_final: 0.7689 (mmp80)
REVERT: B  291 ASP cc_start: 0.7915 (p0) cc_final: 0.7629 (p0)
REVERT: B  312 ASP cc_start: 0.8390 (m-30) cc_final: 0.8091 (m-30)
REVERT: G   20 LYS cc_start: 0.8052 (mttm) cc_final: 0.7691 (mtmm)
REVERT: G   21 MET cc_start: 0.6983 (mmm) cc_final: 0.6704 (ptm)
REVERT: G   32 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8315 (tptm)
REVERT: N   19 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8299 (ttt180)
REVERT: N   34 MET cc_start: 0.9183 (mmm) cc_final: 0.8754 (mmm)
REVERT: N   89 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7584 (pm20)
  outliers start: 20
  outliers final: 11
  residues processed: 123
  average time/residue: 1.4700
  time to fit residues: 190.3271
Evaluate side-chains
  119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0270
   chunk 4 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.7442

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 155 ASN
B 268 ASN
R 173 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.134601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.102837 restraints weight = 16796.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.41
r_work: 0.2867 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8346  Z= 0.155
  Angle     :  0.498  12.202  11305  Z= 0.262
  Chirality :  0.042   0.139   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.322  22.168   1119
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.38 %
    Favored  : 82.57 %
  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:  0.58 (0.27), residues: 1001
  helix:  1.34 (0.26), residues: 395
  sheet:  0.24 (0.34), residues: 219
  loop : -0.43 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.008   0.000   ARG B  96 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.885 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.7363 (tt0) cc_final: 0.7127 (tt0)
REVERT: A   20 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7257 (mtm110)
REVERT: A   25 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7866 (tttp)
REVERT: A  389 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7424 (mtp180)
REVERT: B   23 LYS cc_start: 0.8341 (ttpp) cc_final: 0.8072 (tppt)
REVERT: B   46 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7502 (mmt-90)
REVERT: B   76 ASP cc_start: 0.8899 (p0) cc_final: 0.8505 (p0)
REVERT: B  134 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6858 (mmp80)
REVERT: B  214 ARG cc_start: 0.7815 (mmt180) cc_final: 0.7550 (mmp80)
REVERT: B  219 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8091 (mmm160)
REVERT: B  291 ASP cc_start: 0.7955 (p0) cc_final: 0.7644 (p0)
REVERT: B  312 ASP cc_start: 0.8332 (m-30) cc_final: 0.8064 (m-30)
REVERT: G   20 LYS cc_start: 0.8029 (mttm) cc_final: 0.7669 (mtmm)
REVERT: G   21 MET cc_start: 0.6926 (mmm) cc_final: 0.6720 (ptm)
REVERT: G   32 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8330 (tptm)
REVERT: N   19 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8299 (ttt180)
REVERT: N   34 MET cc_start: 0.9162 (mmm) cc_final: 0.8686 (mmm)
REVERT: N   89 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7557 (pm20)
  outliers start: 18
  outliers final: 12
  residues processed: 113
  average time/residue: 1.5027
  time to fit residues: 178.6877
Evaluate side-chains
  117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0050
   chunk 92 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 28 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  36 ASN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.135451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.102347 restraints weight = 19700.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.80
r_work: 0.2864 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   8346  Z= 0.139
  Angle     :  0.484  11.131  11305  Z= 0.255
  Chirality :  0.042   0.141   1246
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.212  21.138   1119
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.03 %
    Favored  : 82.57 %
  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:  0.72 (0.27), residues: 1001
  helix:  1.52 (0.26), residues: 395
  sheet:  0.29 (0.34), residues: 219
  loop : -0.42 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 260 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.009   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6272.56 seconds
wall clock time: 111 minutes 23.63 seconds (6683.63 seconds total)