Starting phenix.real_space_refine
on Thu Mar 13 08:35:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7evm_31329/03_2025/7evm_31329_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7evm_31329/03_2025/7evm_31329.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7evm_31329/03_2025/7evm_31329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7evm_31329/03_2025/7evm_31329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7evm_31329/03_2025/7evm_31329_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7evm_31329/03_2025/7evm_31329_trim.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     Cl      2      4.86       5
     C    5445      2.51       5
     N    1445      2.21       5
     O    1522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8462
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1957
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 2
    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: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2330
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 5, 'TRANS': 276}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 185
          Unusual residues: {'CLR': 6, 'HNO': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 5.69, per 1000 atoms: 0.67
  Number of scatterers: 8462
  At special positions: 0
  Unit cell: (82.555, 95.095, 131.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      48     16.00
     O    1522      8.00
     N    1445      7.00
     C    5445      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=2.06
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.05

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 998.9 milliseconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      43.1% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.736A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.723A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.912A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.638A  pdb=" N   TRP A 277 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 304
      removed outlier: 3.628A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.567A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.938A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 389
      removed outlier: 3.567A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.734A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 61 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.753A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 143
    Processing helix  chain 'R' and resid 144 through 169
      removed outlier: 3.773A  pdb=" N   PHE R 169 " --> pdb=" O   ILE R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 211
      removed outlier: 4.169A  pdb=" N   GLN R 211 " --> pdb=" O   THR R 207 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 222
      removed outlier: 3.911A  pdb=" N   GLN R 221 " --> pdb=" O   LEU R 217 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 226 through 257
    Processing helix  chain 'R' and resid 263 through 292
      removed outlier: 3.623A  pdb=" N   ARG R 267 " --> pdb=" O   GLN R 263 " (cutoff:3.500A)
      Proline residue:  R 277  - end of helix
      removed outlier: 3.544A  pdb=" N   PHE R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 302 through 337
      removed outlier: 3.501A  pdb=" N   TRP R 306 " --> pdb=" O   ASN R 302 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 361
      removed outlier: 3.714A  pdb=" N   LYS R 351 " --> pdb=" O   CYS R 347 " (cutoff:3.500A)
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 363 through 368
      removed outlier: 4.023A  pdb=" N   PHE R 367 " --> pdb=" O   HIS R 363 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 376 through 404
      removed outlier: 3.553A  pdb=" N   THR R 386 " --> pdb=" O   ILE R 382 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR R 391 " --> pdb=" O   GLU R 387 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 424
      removed outlier: 3.867A  pdb=" N   GLU R 418 " --> pdb=" O   ARG R 414 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   HIS R 424 " --> pdb=" O   TRP R 420 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.105A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.722A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.133A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.748A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.601A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.646A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.841A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.762A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 7.090A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA N  40 " --> pdb=" O   GLY N  44 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLY N  44 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)

    419 hydrogen bonds defined for protein.
    1188 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: 2.48

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1938
        1.33 -     1.45: 2088
        1.45 -     1.58: 4557
        1.58 -     1.71: 5
        1.71 -     1.83: 68
  Bond restraints: 8656
  Sorted by residual:
  bond pdb=" C14 HNO R 501 "
       pdb=" N15 HNO R 501 "
    ideal  model  delta    sigma   weight residual
    1.348  1.458 -0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" CA  CYS N  99 "
       pdb=" C   CYS N  99 "
    ideal  model  delta    sigma   weight residual
    1.527  1.474  0.053 1.32e-02 5.74e+03 1.59e+01
  bond pdb=" C13 CLR R 506 "
       pdb=" C18 CLR R 506 "
    ideal  model  delta    sigma   weight residual
    1.532  1.597 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" C   LEU R 311 "
       pdb=" O   LEU R 311 "
    ideal  model  delta    sigma   weight residual
    1.244  1.211  0.033 1.00e-02 1.00e+04 1.07e+01
  bond pdb=" C13 CLR R 507 "
       pdb=" C18 CLR R 507 "
    ideal  model  delta    sigma   weight residual
    1.532  1.597 -0.065 2.00e-02 2.50e+03 1.04e+01
  ... (remaining 8651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 11531
        2.63 -     5.26: 190
        5.26 -     7.89: 31
        7.89 -    10.52: 5
       10.52 -    13.15: 1
  Bond angle restraints: 11758
  Sorted by residual:
  angle pdb=" N   PHE R 143 "
        pdb=" CA  PHE R 143 "
        pdb=" C   PHE R 143 "
      ideal   model   delta    sigma   weight residual
     112.92   99.77   13.15 1.23e+00 6.61e-01 1.14e+02
  angle pdb=" N   VAL R 150 "
        pdb=" CA  VAL R 150 "
        pdb=" C   VAL R 150 "
      ideal   model   delta    sigma   weight residual
     110.42  103.67    6.75 9.60e-01 1.09e+00 4.94e+01
  angle pdb=" N   PRO N 100 "
        pdb=" CA  PRO N 100 "
        pdb=" C   PRO N 100 "
      ideal   model   delta    sigma   weight residual
     114.03  122.66   -8.63 1.23e+00 6.61e-01 4.93e+01
  angle pdb=" N   GLU R 292 "
        pdb=" CA  GLU R 292 "
        pdb=" C   GLU R 292 "
      ideal   model   delta    sigma   weight residual
     110.17  120.09   -9.92 1.51e+00 4.39e-01 4.31e+01
  angle pdb=" N   LEU R 411 "
        pdb=" CA  LEU R 411 "
        pdb=" C   LEU R 411 "
      ideal   model   delta    sigma   weight residual
     111.24  104.26    6.98 1.29e+00 6.01e-01 2.93e+01
  ... (remaining 11753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 4745
       17.00 -    34.01: 495
       34.01 -    51.01: 123
       51.01 -    68.01: 34
       68.01 -    85.02: 8
  Dihedral angle restraints: 5405
    sinusoidal: 2383
      harmonic: 3022
  Sorted by residual:
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.72  -67.72     1      1.00e+01 1.00e-02 5.96e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.90   22.10     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" C   TYR R 148 "
           pdb=" N   TYR R 148 "
           pdb=" CA  TYR R 148 "
           pdb=" CB  TYR R 148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.03    9.43     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 5402 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1158
       0.079 -    0.159: 142
       0.159 -    0.238: 14
       0.238 -    0.318: 5
       0.318 -    0.397: 6
  Chirality restraints: 1325
  Sorted by residual:
  chirality pdb=" CA  TYR R 148 "
            pdb=" N   TYR R 148 "
            pdb=" C   TYR R 148 "
            pdb=" CB  TYR R 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  GLU R 292 "
            pdb=" N   GLU R 292 "
            pdb=" C   GLU R 292 "
            pdb=" CB  GLU R 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.82e+00
  chirality pdb=" C14 CLR R 505 "
            pdb=" C13 CLR R 505 "
            pdb=" C15 CLR R 505 "
            pdb=" C8  CLR R 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.71    0.39 2.00e-01 2.50e+01 3.77e+00
  ... (remaining 1322 not shown)

  Planarity restraints: 1454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 410 "    0.025 2.00e-02 2.50e+03   5.22e-02 2.73e+01
        pdb=" C   GLN R 410 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   GLN R 410 "    0.035 2.00e-02 2.50e+03
        pdb=" N   LEU R 411 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 198 "    0.022 2.00e-02 2.50e+03   4.49e-02 2.02e+01
        pdb=" C   ASP R 198 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   ASP R 198 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ALA R 199 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG N  98 "    0.020 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   ARG N  98 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   ARG N  98 "    0.030 2.00e-02 2.50e+03
        pdb=" N   CYS N  99 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1451 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 438
        2.72 -     3.26: 8758
        3.26 -     3.81: 14360
        3.81 -     4.35: 18359
        4.35 -     4.90: 30257
  Nonbonded interactions: 72172
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.282 3.040
  ... (remaining 72167 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.770
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
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      :  0.005   0.110   8656  Z= 0.335
  Angle     :  0.855  13.151  11758  Z= 0.499
  Chirality :  0.061   0.397   1325
  Planarity :  0.005   0.052   1454
  Dihedral  : 15.260  85.018   3442
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  :  7.51 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.10 %
  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: -2.23 (0.24), residues: 1019
  helix: -1.35 (0.23), residues: 384
  sheet: -1.43 (0.31), residues: 209
  loop : -1.41 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 234 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.017   0.002   PHE R 280 
 TYR   0.028   0.002   TYR R 148 
 ARG   0.005   0.001   ARG B 129 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 282
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.8536 (tt0) cc_final: 0.8030 (tt0)
REVERT: A  215 ASP cc_start: 0.7802 (t0) cc_final: 0.7307 (t0)
REVERT: A  325 THR cc_start: 0.8755 (m) cc_final: 0.8499 (p)
REVERT: A  339 TYR cc_start: 0.7798 (m-80) cc_final: 0.7525 (m-80)
REVERT: A  343 ASP cc_start: 0.8072 (m-30) cc_final: 0.7510 (m-30)
REVERT: A  370 GLU cc_start: 0.7996 (pm20) cc_final: 0.7631 (pm20)
REVERT: A  378 ASP cc_start: 0.7259 (m-30) cc_final: 0.6767 (m-30)
REVERT: A  381 ASP cc_start: 0.8350 (t0) cc_final: 0.8112 (t0)
REVERT: B   44 GLN cc_start: 0.7955 (pt0) cc_final: 0.7693 (pt0)
REVERT: B   47 THR cc_start: 0.8847 (t) cc_final: 0.8562 (m)
REVERT: B  124 TYR cc_start: 0.8361 (m-80) cc_final: 0.7914 (m-80)
REVERT: B  132 ASN cc_start: 0.6821 (p0) cc_final: 0.6370 (p0)
REVERT: B  138 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: B  175 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7223 (pp30)
REVERT: B  217 MET cc_start: 0.7127 (ptt) cc_final: 0.6894 (ptt)
REVERT: B  226 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6920 (mt-10)
REVERT: B  228 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7705 (m-30)
REVERT: B  230 ASN cc_start: 0.8282 (m-40) cc_final: 0.8033 (m-40)
REVERT: B  243 THR cc_start: 0.7847 (p) cc_final: 0.7568 (p)
REVERT: B  291 ASP cc_start: 0.7545 (p0) cc_final: 0.7336 (p0)
REVERT: B  312 ASP cc_start: 0.8278 (m-30) cc_final: 0.7999 (m-30)
REVERT: G   21 MET cc_start: 0.7174 (tpt) cc_final: 0.6694 (ttp)
REVERT: N    3 GLN cc_start: 0.7288 (tp40) cc_final: 0.6468 (tm-30)
REVERT: N   31 ASN cc_start: 0.7938 (m-40) cc_final: 0.7691 (t0)
REVERT: N   77 ASN cc_start: 0.7551 (m-40) cc_final: 0.7238 (p0)
REVERT: R  136 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7166 (p)
REVERT: R  142 LEU cc_start: 0.8305 (tp) cc_final: 0.8034 (tm)
REVERT: R  144 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7534 (tp)
REVERT: R  148 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5614 (p90)
REVERT: R  197 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7718 (tmmm)
REVERT: R  262 GLU cc_start: 0.8326 (pt0) cc_final: 0.7912 (pt0)
REVERT: R  292 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7300 (mm-30)
REVERT: R  346 LYS cc_start: 0.7558 (mttt) cc_final: 0.6956 (pttm)
REVERT: R  383 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8330 (tmtp)
REVERT: R  423 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6876 (pt0)
  outliers start: 30
  outliers final: 5
  residues processed: 301
  average time/residue: 1.2166
  time to fit residues: 388.4530
Evaluate side-chains
  162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue  136 SER
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  197 LYS
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  326 ARG
Chi-restraints excluded: chain R residue  412 GLU
Chi-restraints excluded: chain R residue  421 ARG
Chi-restraints excluded: chain R residue  423 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 220 GLN
B 259 GLN
N  35 ASN
R 171 HIS
** R 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.133421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.096845 restraints weight = 12585.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.87
r_work: 0.3169 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8656  Z= 0.249
  Angle     :  0.633   7.652  11758  Z= 0.337
  Chirality :  0.045   0.157   1325
  Planarity :  0.005   0.085   1454
  Dihedral  :  8.447  63.755   1557
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.51 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    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: -1.00 (0.26), residues: 1019
  helix: -0.02 (0.26), residues: 399
  sheet: -0.86 (0.33), residues: 209
  loop : -1.03 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R 214 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.021   0.002   PHE A 273 
 TYR   0.026   0.002   TYR R 148 
 ARG   0.006   0.001   ARG A 347 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 169
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7690 (ttm-80)
REVERT: A   31 GLN cc_start: 0.8042 (tp40) cc_final: 0.7819 (tp-100)
REVERT: A  213 GLN cc_start: 0.8819 (tt0) cc_final: 0.8235 (tt0)
REVERT: A  215 ASP cc_start: 0.7782 (t0) cc_final: 0.7246 (t0)
REVERT: A  294 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7579 (mm110)
REVERT: A  325 THR cc_start: 0.8858 (m) cc_final: 0.8546 (p)
REVERT: A  339 TYR cc_start: 0.8050 (m-80) cc_final: 0.7845 (m-80)
REVERT: A  343 ASP cc_start: 0.8293 (m-30) cc_final: 0.7789 (m-30)
REVERT: A  349 SER cc_start: 0.8693 (t) cc_final: 0.7798 (p)
REVERT: A  352 SER cc_start: 0.8129 (t) cc_final: 0.6895 (t)
REVERT: A  378 ASP cc_start: 0.7469 (m-30) cc_final: 0.7217 (m-30)
REVERT: B   38 ASP cc_start: 0.8566 (p0) cc_final: 0.7976 (p0)
REVERT: B   44 GLN cc_start: 0.8204 (pt0) cc_final: 0.7901 (pt0)
REVERT: B  124 TYR cc_start: 0.8708 (m-80) cc_final: 0.8270 (m-80)
REVERT: B  138 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8170 (mt-10)
REVERT: B  197 ARG cc_start: 0.8351 (ttt90) cc_final: 0.8145 (mmm160)
REVERT: B  217 MET cc_start: 0.8027 (ptt) cc_final: 0.7675 (ptt)
REVERT: B  228 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7845 (m-30)
REVERT: B  243 THR cc_start: 0.7895 (p) cc_final: 0.7491 (p)
REVERT: G   38 MET cc_start: 0.7518 (ptp) cc_final: 0.7142 (ttp)
REVERT: G   42 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7133 (mp0)
REVERT: N    3 GLN cc_start: 0.7687 (tp40) cc_final: 0.6980 (tm-30)
REVERT: N   31 ASN cc_start: 0.8312 (m-40) cc_final: 0.7947 (t0)
REVERT: N   65 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8227 (ttpt)
REVERT: N   77 ASN cc_start: 0.7661 (m-40) cc_final: 0.7323 (p0)
REVERT: N  110 VAL cc_start: 0.8937 (m) cc_final: 0.8643 (t)
REVERT: N  120 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8774 (tp40)
REVERT: R  139 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8368 (tt0)
REVERT: R  142 LEU cc_start: 0.8274 (tp) cc_final: 0.7979 (tm)
REVERT: R  262 GLU cc_start: 0.8321 (pt0) cc_final: 0.7922 (pt0)
REVERT: R  305 TYR cc_start: 0.7286 (m-80) cc_final: 0.7071 (m-10)
REVERT: R  346 LYS cc_start: 0.7377 (mttt) cc_final: 0.6800 (pttm)
REVERT: R  394 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7749 (tt0)
REVERT: R  397 MET cc_start: 0.7740 (mmt) cc_final: 0.7426 (mmt)
REVERT: R  407 ASN cc_start: 0.8910 (m-40) cc_final: 0.8564 (m110)
REVERT: R  412 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7593 (tm-30)
REVERT: R  413 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8201 (m-80)
  outliers start: 34
  outliers final: 12
  residues processed: 193
  average time/residue: 1.6213
  time to fit residues: 332.7155
Evaluate side-chains
  162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  349 LEU
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  413 PHE
Chi-restraints excluded: chain R residue  423 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    0.0870
   chunk 59 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0770
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B 176 GLN
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 171 HIS
R 263 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.134832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.101764 restraints weight = 13515.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.80
r_work: 0.3283 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8656  Z= 0.193
  Angle     :  0.582   7.352  11758  Z= 0.308
  Chirality :  0.043   0.145   1325
  Planarity :  0.005   0.060   1454
  Dihedral  :  7.190  58.923   1533
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.64 %
    Favored  : 74.33 %
  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: -0.44 (0.26), residues: 1019
  helix:  0.66 (0.26), residues: 400
  sheet: -0.65 (0.34), residues: 210
  loop : -0.95 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 277 
 HIS   0.004   0.001   HIS R 363 
 PHE   0.030   0.002   PHE N  27 
 TYR   0.022   0.001   TYR R 148 
 ARG   0.008   0.001   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8030 (ttm170) cc_final: 0.7813 (ttm-80)
REVERT: A   60 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7938 (mpt)
REVERT: A  213 GLN cc_start: 0.8824 (tt0) cc_final: 0.8276 (tt0)
REVERT: A  215 ASP cc_start: 0.7784 (t0) cc_final: 0.7242 (t0)
REVERT: A  220 HIS cc_start: 0.7424 (m90) cc_final: 0.7114 (m90)
REVERT: A  278 ASN cc_start: 0.7917 (m-40) cc_final: 0.7487 (m-40)
REVERT: A  296 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8652 (tp)
REVERT: A  325 THR cc_start: 0.8922 (m) cc_final: 0.8608 (p)
REVERT: A  343 ASP cc_start: 0.8419 (m-30) cc_final: 0.8023 (m-30)
REVERT: B   13 GLN cc_start: 0.8183 (mm110) cc_final: 0.7924 (mm110)
REVERT: B   38 ASP cc_start: 0.8544 (p0) cc_final: 0.7967 (p0)
REVERT: B   44 GLN cc_start: 0.8212 (pt0) cc_final: 0.7948 (pt0)
REVERT: B   57 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8350 (ptpp)
REVERT: B  138 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8274 (mt-10)
REVERT: B  172 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7706 (mp0)
REVERT: B  226 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7275 (mt-10)
REVERT: B  228 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7758 (m-30)
REVERT: B  243 THR cc_start: 0.8133 (p) cc_final: 0.7722 (p)
REVERT: G   21 MET cc_start: 0.7273 (ttp) cc_final: 0.6752 (ttp)
REVERT: G   38 MET cc_start: 0.7678 (ptp) cc_final: 0.7373 (ttp)
REVERT: G   42 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7454 (mp0)
REVERT: N    3 GLN cc_start: 0.7663 (tp40) cc_final: 0.7066 (tm-30)
REVERT: N   31 ASN cc_start: 0.8388 (m-40) cc_final: 0.8111 (t0)
REVERT: N   77 ASN cc_start: 0.7666 (m-40) cc_final: 0.7216 (p0)
REVERT: N  110 VAL cc_start: 0.8942 (m) cc_final: 0.8727 (t)
REVERT: N  120 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8779 (tp40)
REVERT: R  139 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8361 (tt0)
REVERT: R  142 LEU cc_start: 0.8280 (tp) cc_final: 0.8022 (tm)
REVERT: R  262 GLU cc_start: 0.8266 (pt0) cc_final: 0.8012 (pt0)
REVERT: R  346 LYS cc_start: 0.7610 (mttt) cc_final: 0.7020 (pmmt)
REVERT: R  394 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8037 (tt0)
REVERT: R  412 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7600 (tm-30)
REVERT: R  413 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8171 (m-80)
REVERT: R  423 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5935 (tm-30)
  outliers start: 36
  outliers final: 11
  residues processed: 194
  average time/residue: 1.0900
  time to fit residues: 226.6376
Evaluate side-chains
  170 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  349 LEU
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  412 GLU
Chi-restraints excluded: chain R residue  413 PHE
Chi-restraints excluded: chain R residue  423 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 ASN
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 302 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.132286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.098502 restraints weight = 13514.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.82
r_work: 0.3217 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8656  Z= 0.242
  Angle     :  0.567   7.304  11758  Z= 0.299
  Chirality :  0.043   0.153   1325
  Planarity :  0.004   0.044   1454
  Dihedral  :  7.042  59.337   1533
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 21.52 %
    Favored  : 73.21 %
  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: 1019
  helix:  0.90 (0.26), residues: 405
  sheet: -0.51 (0.34), residues: 216
  loop : -0.84 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 277 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.022   0.002   PHE N  27 
 TYR   0.019   0.002   TYR R 148 
 ARG   0.015   0.001   ARG B 214 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 155
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7861 (ttm-80)
REVERT: A   60 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7268 (mpt)
REVERT: A  211 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8130 (mmtm)
REVERT: A  213 GLN cc_start: 0.8803 (tt0) cc_final: 0.8207 (tt0)
REVERT: A  215 ASP cc_start: 0.7720 (t0) cc_final: 0.7165 (t0)
REVERT: A  325 THR cc_start: 0.8952 (m) cc_final: 0.8676 (p)
REVERT: A  343 ASP cc_start: 0.8420 (m-30) cc_final: 0.8078 (m-30)
REVERT: A  370 GLU cc_start: 0.8050 (pm20) cc_final: 0.7756 (pm20)
REVERT: B   13 GLN cc_start: 0.8222 (mm110) cc_final: 0.7913 (mm110)
REVERT: B   19 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8216 (ttp80)
REVERT: B   38 ASP cc_start: 0.8541 (p0) cc_final: 0.7968 (p0)
REVERT: B   44 GLN cc_start: 0.8295 (pt0) cc_final: 0.7966 (pt0)
REVERT: B  138 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8345 (mt-10)
REVERT: B  172 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7730 (mp0)
REVERT: B  215 GLU cc_start: 0.8209 (mp0) cc_final: 0.7815 (mp0)
REVERT: B  243 THR cc_start: 0.8128 (p) cc_final: 0.7706 (p)
REVERT: G   21 MET cc_start: 0.7425 (ttp) cc_final: 0.6777 (ttp)
REVERT: G   38 MET cc_start: 0.7799 (ptp) cc_final: 0.7368 (ttp)
REVERT: G   42 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7572 (mp0)
REVERT: N    3 GLN cc_start: 0.7681 (tp40) cc_final: 0.7133 (tm-30)
REVERT: N   31 ASN cc_start: 0.8462 (m-40) cc_final: 0.8135 (t0)
REVERT: N   67 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.5523 (ptm-80)
REVERT: N  110 VAL cc_start: 0.8894 (m) cc_final: 0.8685 (t)
REVERT: N  120 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8780 (tp40)
REVERT: R  139 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8428 (tt0)
REVERT: R  142 LEU cc_start: 0.8262 (tp) cc_final: 0.8014 (tm)
REVERT: R  148 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6696 (p90)
REVERT: R  197 LYS cc_start: 0.8294 (tppp) cc_final: 0.8093 (tppt)
REVERT: R  203 TRP cc_start: 0.7120 (t-100) cc_final: 0.6886 (t-100)
REVERT: R  260 LEU cc_start: 0.8190 (pt) cc_final: 0.7823 (mm)
REVERT: R  346 LYS cc_start: 0.7526 (mttt) cc_final: 0.6942 (pttm)
REVERT: R  394 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8029 (tt0)
REVERT: R  413 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8238 (m-80)
  outliers start: 47
  outliers final: 23
  residues processed: 191
  average time/residue: 1.2698
  time to fit residues: 257.8663
Evaluate side-chains
  175 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  412 GLU
Chi-restraints excluded: chain R residue  413 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 96 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 29 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
N  35 ASN
** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 363 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.094599 restraints weight = 13316.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.85
r_work: 0.3152 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8656  Z= 0.327
  Angle     :  0.598   7.421  11758  Z= 0.311
  Chirality :  0.044   0.160   1325
  Planarity :  0.004   0.042   1454
  Dihedral  :  6.868  59.879   1528
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.88 %
    Favored  : 72.09 %
  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: 1019
  helix:  0.95 (0.26), residues: 412
  sheet: -0.53 (0.34), residues: 223
  loop : -0.82 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 277 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.037   0.002   PHE N  27 
 TYR   0.019   0.002   TYR N  95 
 ARG   0.013   0.001   ARG N 105 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.8135 (mpt) cc_final: 0.7580 (mpt)
REVERT: A  215 ASP cc_start: 0.7793 (t0) cc_final: 0.7229 (t0)
REVERT: A  325 THR cc_start: 0.8953 (m) cc_final: 0.8664 (p)
REVERT: A  343 ASP cc_start: 0.8453 (m-30) cc_final: 0.8124 (m-30)
REVERT: A  370 GLU cc_start: 0.8005 (pm20) cc_final: 0.7739 (pm20)
REVERT: B   13 GLN cc_start: 0.8262 (mm110) cc_final: 0.7968 (mm110)
REVERT: B   19 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8236 (ttp80)
REVERT: B   38 ASP cc_start: 0.8664 (p0) cc_final: 0.8135 (p0)
REVERT: B   57 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8388 (ptpp)
REVERT: B  138 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: B  172 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7746 (mp0)
REVERT: B  215 GLU cc_start: 0.8115 (mp0) cc_final: 0.7621 (mp0)
REVERT: B  228 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7637 (m-30)
REVERT: B  243 THR cc_start: 0.8136 (p) cc_final: 0.7709 (p)
REVERT: G   21 MET cc_start: 0.7381 (ttp) cc_final: 0.6680 (ttp)
REVERT: G   38 MET cc_start: 0.7987 (ptp) cc_final: 0.6252 (ttp)
REVERT: G   42 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7276 (mp0)
REVERT: N    3 GLN cc_start: 0.7707 (tp40) cc_final: 0.7133 (tm-30)
REVERT: N   31 ASN cc_start: 0.8600 (m-40) cc_final: 0.8343 (t0)
REVERT: N   67 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.5506 (ptm-80)
REVERT: N  110 VAL cc_start: 0.8887 (m) cc_final: 0.8686 (t)
REVERT: N  120 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8758 (tp40)
REVERT: R  139 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8353 (tt0)
REVERT: R  142 LEU cc_start: 0.8314 (tp) cc_final: 0.7993 (tm)
REVERT: R  146 ILE cc_start: 0.6649 (tt) cc_final: 0.6355 (tp)
REVERT: R  148 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6710 (p90)
REVERT: R  346 LYS cc_start: 0.7610 (mttt) cc_final: 0.7005 (pttm)
REVERT: R  394 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8113 (tt0)
REVERT: R  397 MET cc_start: 0.7920 (mmt) cc_final: 0.7637 (mmt)
REVERT: R  414 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.6031 (mpt180)
  outliers start: 36
  outliers final: 23
  residues processed: 171
  average time/residue: 1.1745
  time to fit residues: 213.9820
Evaluate side-chains
  175 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  414 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 7 optimal weight:    0.1980
   chunk 100 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0670
   chunk 45 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 16 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 230 ASN
N   1 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 363 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.131575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.097398 restraints weight = 13111.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.81
r_work: 0.3200 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8656  Z= 0.201
  Angle     :  0.567   8.357  11758  Z= 0.294
  Chirality :  0.042   0.154   1325
  Planarity :  0.004   0.043   1454
  Dihedral  :  6.690  57.827   1528
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 24.55 %
    Favored  : 71.30 %
  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:  0.08 (0.27), residues: 1019
  helix:  1.18 (0.26), residues: 406
  sheet: -0.46 (0.34), residues: 221
  loop : -0.73 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 277 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.055   0.001   PHE N  27 
 TYR   0.019   0.002   TYR N  32 
 ARG   0.011   0.000   ARG N 105 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.7659 (t0) cc_final: 0.7119 (t0)
REVERT: A  325 THR cc_start: 0.8949 (m) cc_final: 0.8683 (p)
REVERT: A  343 ASP cc_start: 0.8437 (m-30) cc_final: 0.8089 (m-30)
REVERT: A  370 GLU cc_start: 0.7943 (pm20) cc_final: 0.7647 (pm20)
REVERT: B   13 GLN cc_start: 0.8258 (mm110) cc_final: 0.7942 (mm110)
REVERT: B   38 ASP cc_start: 0.8638 (p0) cc_final: 0.8122 (p0)
REVERT: B   57 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8438 (ptpp)
REVERT: B  138 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: B  169 TRP cc_start: 0.9109 (m100) cc_final: 0.8817 (m100)
REVERT: B  172 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7749 (mp0)
REVERT: B  215 GLU cc_start: 0.8219 (mp0) cc_final: 0.7861 (mp0)
REVERT: B  228 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7470 (m-30)
REVERT: B  243 THR cc_start: 0.8101 (p) cc_final: 0.7669 (p)
REVERT: G   21 MET cc_start: 0.7377 (ttp) cc_final: 0.6630 (ttp)
REVERT: G   38 MET cc_start: 0.7919 (ptp) cc_final: 0.6155 (ttp)
REVERT: G   42 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7292 (mp0)
REVERT: N    3 GLN cc_start: 0.7687 (tp40) cc_final: 0.7001 (tm-30)
REVERT: N   31 ASN cc_start: 0.8501 (m-40) cc_final: 0.8234 (t0)
REVERT: N   67 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.5012 (ptm-80)
REVERT: N   90 ASP cc_start: 0.8805 (m-30) cc_final: 0.8595 (m-30)
REVERT: R  139 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8424 (tt0)
REVERT: R  142 LEU cc_start: 0.8305 (tp) cc_final: 0.8024 (tm)
REVERT: R  146 ILE cc_start: 0.6787 (tt) cc_final: 0.6473 (tp)
REVERT: R  148 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6813 (p90)
REVERT: R  260 LEU cc_start: 0.8246 (pt) cc_final: 0.7944 (mm)
REVERT: R  262 GLU cc_start: 0.8280 (pt0) cc_final: 0.7725 (pm20)
REVERT: R  299 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7545 (ttm170)
REVERT: R  346 LYS cc_start: 0.7607 (mttt) cc_final: 0.7023 (pttm)
REVERT: R  394 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7870 (tt0)
REVERT: R  406 ASN cc_start: 0.7845 (t0) cc_final: 0.6801 (t0)
REVERT: R  408 GLU cc_start: 0.7923 (mp0) cc_final: 0.7482 (mp0)
REVERT: R  412 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7811 (tp30)
REVERT: R  413 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8179 (m-80)
REVERT: R  414 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5920 (mpt180)
  outliers start: 37
  outliers final: 18
  residues processed: 181
  average time/residue: 1.3433
  time to fit residues: 260.1532
Evaluate side-chains
  176 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  413 PHE
Chi-restraints excluded: chain R residue  414 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 47 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.131736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.097197 restraints weight = 13316.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.85
r_work: 0.3194 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8656  Z= 0.216
  Angle     :  0.562   7.303  11758  Z= 0.293
  Chirality :  0.042   0.149   1325
  Planarity :  0.004   0.050   1454
  Dihedral  :  6.606  57.428   1528
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 24.55 %
    Favored  : 70.52 %
  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:  0.19 (0.27), residues: 1019
  helix:  1.26 (0.26), residues: 406
  sheet: -0.35 (0.36), residues: 215
  loop : -0.70 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 277 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.042   0.002   PHE N  27 
 TYR   0.018   0.002   TYR N  95 
 ARG   0.013   0.001   ARG N 105 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 150
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.8459 (pp20) cc_final: 0.8248 (pp20)
REVERT: A  215 ASP cc_start: 0.7652 (t0) cc_final: 0.7129 (t0)
REVERT: A  325 THR cc_start: 0.8957 (m) cc_final: 0.8702 (p)
REVERT: A  343 ASP cc_start: 0.8458 (m-30) cc_final: 0.8099 (m-30)
REVERT: A  370 GLU cc_start: 0.7855 (pm20) cc_final: 0.7505 (pm20)
REVERT: B   13 GLN cc_start: 0.8226 (mm110) cc_final: 0.7908 (mm110)
REVERT: B   38 ASP cc_start: 0.8629 (p0) cc_final: 0.8130 (p0)
REVERT: B   57 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8428 (ptpp)
REVERT: B  138 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8461 (mt-10)
REVERT: B  169 TRP cc_start: 0.9122 (m100) cc_final: 0.8827 (m100)
REVERT: B  172 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7794 (mp0)
REVERT: B  215 GLU cc_start: 0.8235 (mp0) cc_final: 0.7974 (mp0)
REVERT: B  228 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7550 (m-30)
REVERT: B  243 THR cc_start: 0.8156 (p) cc_final: 0.7711 (p)
REVERT: G   21 MET cc_start: 0.7375 (ttp) cc_final: 0.6598 (ttp)
REVERT: G   38 MET cc_start: 0.7948 (ptp) cc_final: 0.6368 (ptp)
REVERT: G   42 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7347 (mp0)
REVERT: N    3 GLN cc_start: 0.7558 (tp40) cc_final: 0.6989 (tm-30)
REVERT: N   31 ASN cc_start: 0.8475 (m-40) cc_final: 0.8090 (t0)
REVERT: N   67 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.5043 (ptm-80)
REVERT: N   90 ASP cc_start: 0.8722 (m-30) cc_final: 0.8448 (m-30)
REVERT: N  120 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8700 (tp40)
REVERT: R  139 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8399 (tt0)
REVERT: R  142 LEU cc_start: 0.8297 (tp) cc_final: 0.8049 (tm)
REVERT: R  146 ILE cc_start: 0.6950 (tt) cc_final: 0.6685 (tp)
REVERT: R  148 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6851 (p90)
REVERT: R  182 ASN cc_start: 0.9149 (m-40) cc_final: 0.8907 (m-40)
REVERT: R  260 LEU cc_start: 0.8306 (pt) cc_final: 0.7991 (mm)
REVERT: R  262 GLU cc_start: 0.8248 (pt0) cc_final: 0.7592 (pm20)
REVERT: R  299 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7555 (ttm170)
REVERT: R  346 LYS cc_start: 0.7640 (mttt) cc_final: 0.7038 (pttm)
REVERT: R  394 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7985 (tt0)
REVERT: R  406 ASN cc_start: 0.7810 (t0) cc_final: 0.6858 (t0)
REVERT: R  408 GLU cc_start: 0.7916 (mp0) cc_final: 0.7448 (mp0)
REVERT: R  413 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8193 (m-80)
REVERT: R  414 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5895 (mpt180)
  outliers start: 44
  outliers final: 24
  residues processed: 181
  average time/residue: 1.1364
  time to fit residues: 219.8041
Evaluate side-chains
  182 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  281 VAL
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  413 PHE
Chi-restraints excluded: chain R residue  414 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0870
   chunk 50 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 71 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0050
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4172

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.099180 restraints weight = 13401.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.86
r_work: 0.3233 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8656  Z= 0.186
  Angle     :  0.567   7.258  11758  Z= 0.296
  Chirality :  0.041   0.147   1325
  Planarity :  0.004   0.044   1454
  Dihedral  :  6.500  56.952   1528
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 25.78 %
    Favored  : 70.40 %
  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:  0.28 (0.27), residues: 1019
  helix:  1.34 (0.26), residues: 404
  sheet: -0.30 (0.36), residues: 212
  loop : -0.63 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 277 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.021   0.001   PHE A 212 
 TYR   0.017   0.002   TYR N  95 
 ARG   0.013   0.001   ARG B  19 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.7632 (t0) cc_final: 0.7108 (t0)
REVERT: A  325 THR cc_start: 0.8938 (m) cc_final: 0.8735 (p)
REVERT: A  343 ASP cc_start: 0.8462 (m-30) cc_final: 0.8094 (m-30)
REVERT: A  370 GLU cc_start: 0.7857 (pm20) cc_final: 0.7531 (pm20)
REVERT: B   13 GLN cc_start: 0.8171 (mm110) cc_final: 0.7866 (mm110)
REVERT: B   38 ASP cc_start: 0.8616 (p0) cc_final: 0.8156 (p0)
REVERT: B   57 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8451 (ptpp)
REVERT: B  138 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8458 (mt-10)
REVERT: B  169 TRP cc_start: 0.9080 (m100) cc_final: 0.8802 (m100)
REVERT: B  172 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7807 (mp0)
REVERT: B  215 GLU cc_start: 0.8292 (mp0) cc_final: 0.8011 (mp0)
REVERT: B  228 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7399 (m-30)
REVERT: B  243 THR cc_start: 0.8117 (p) cc_final: 0.7688 (p)
REVERT: G   21 MET cc_start: 0.7354 (ttp) cc_final: 0.6569 (ttp)
REVERT: G   38 MET cc_start: 0.7920 (ptp) cc_final: 0.7530 (ptp)
REVERT: G   42 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7639 (mp0)
REVERT: N    3 GLN cc_start: 0.7551 (tp40) cc_final: 0.6900 (tm-30)
REVERT: N   31 ASN cc_start: 0.8389 (m-40) cc_final: 0.7979 (t0)
REVERT: N   67 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.4992 (ptm-80)
REVERT: N   90 ASP cc_start: 0.8671 (m-30) cc_final: 0.8382 (m-30)
REVERT: N  120 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8677 (tp40)
REVERT: R  139 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8429 (tt0)
REVERT: R  142 LEU cc_start: 0.8227 (tp) cc_final: 0.7842 (tm)
REVERT: R  148 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6884 (p90)
REVERT: R  260 LEU cc_start: 0.8299 (pt) cc_final: 0.7983 (mm)
REVERT: R  262 GLU cc_start: 0.8258 (pt0) cc_final: 0.7576 (pm20)
REVERT: R  299 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7557 (ttm170)
REVERT: R  346 LYS cc_start: 0.7604 (mttt) cc_final: 0.7002 (pttm)
REVERT: R  394 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7993 (tt0)
REVERT: R  406 ASN cc_start: 0.7735 (t0) cc_final: 0.6732 (t0)
REVERT: R  408 GLU cc_start: 0.7965 (mp0) cc_final: 0.7500 (mp0)
REVERT: R  413 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8226 (m-80)
REVERT: R  414 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5906 (mpt180)
  outliers start: 34
  outliers final: 18
  residues processed: 179
  average time/residue: 1.2257
  time to fit residues: 233.7143
Evaluate side-chains
  185 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  413 PHE
Chi-restraints excluded: chain R residue  414 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0050
   chunk 98 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.132263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.097976 restraints weight = 13435.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.86
r_work: 0.3205 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8656  Z= 0.234
  Angle     :  0.588   7.483  11758  Z= 0.308
  Chirality :  0.042   0.161   1325
  Planarity :  0.004   0.058   1454
  Dihedral  :  6.492  56.558   1528
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 25.90 %
    Favored  : 69.62 %
  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:  0.27 (0.27), residues: 1019
  helix:  1.32 (0.26), residues: 404
  sheet: -0.32 (0.35), residues: 213
  loop : -0.63 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 277 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.025   0.001   PHE N  27 
 TYR   0.023   0.002   TYR N  32 
 ARG   0.013   0.001   ARG N 105 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 157
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.7647 (t0) cc_final: 0.7145 (t0)
REVERT: A  343 ASP cc_start: 0.8468 (m-30) cc_final: 0.8092 (m-30)
REVERT: A  370 GLU cc_start: 0.7844 (pm20) cc_final: 0.7462 (mp0)
REVERT: B   13 GLN cc_start: 0.8162 (mm110) cc_final: 0.7857 (mm110)
REVERT: B   57 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8451 (ptpp)
REVERT: B  138 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8467 (mt-10)
REVERT: B  169 TRP cc_start: 0.9128 (m100) cc_final: 0.8844 (m100)
REVERT: B  172 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7798 (mp0)
REVERT: B  215 GLU cc_start: 0.8305 (mp0) cc_final: 0.8031 (mp0)
REVERT: B  228 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7380 (m-30)
REVERT: B  243 THR cc_start: 0.8175 (p) cc_final: 0.7804 (p)
REVERT: G   21 MET cc_start: 0.7377 (ttp) cc_final: 0.6500 (ttp)
REVERT: G   38 MET cc_start: 0.7970 (ptp) cc_final: 0.7585 (ptp)
REVERT: G   42 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7649 (mp0)
REVERT: G   47 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7167 (mp0)
REVERT: N    3 GLN cc_start: 0.7599 (tp40) cc_final: 0.6880 (tm-30)
REVERT: N   31 ASN cc_start: 0.8479 (m-40) cc_final: 0.8076 (t0)
REVERT: N   67 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.5054 (ptm-80)
REVERT: N   90 ASP cc_start: 0.8673 (m-30) cc_final: 0.8387 (m-30)
REVERT: N  120 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8669 (tp40)
REVERT: R  139 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8337 (tt0)
REVERT: R  142 LEU cc_start: 0.8311 (tp) cc_final: 0.8097 (tm)
REVERT: R  148 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6827 (p90)
REVERT: R  260 LEU cc_start: 0.8348 (pt) cc_final: 0.8017 (mm)
REVERT: R  262 GLU cc_start: 0.8307 (pt0) cc_final: 0.7596 (pm20)
REVERT: R  299 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7464 (ttm170)
REVERT: R  346 LYS cc_start: 0.7594 (mttt) cc_final: 0.7014 (pttm)
REVERT: R  388 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7898 (mm)
REVERT: R  394 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7928 (tt0)
REVERT: R  406 ASN cc_start: 0.7776 (t0) cc_final: 0.6718 (t0)
REVERT: R  408 GLU cc_start: 0.7966 (mp0) cc_final: 0.7419 (mp0)
REVERT: R  414 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.5851 (mpt180)
  outliers start: 40
  outliers final: 21
  residues processed: 183
  average time/residue: 1.1292
  time to fit residues: 220.5489
Evaluate side-chains
  183 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  363 HIS
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  414 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.131549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.097290 restraints weight = 13284.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.84
r_work: 0.3200 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.5296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8656  Z= 0.257
  Angle     :  0.626   8.569  11758  Z= 0.325
  Chirality :  0.043   0.215   1325
  Planarity :  0.004   0.052   1454
  Dihedral  :  6.511  55.868   1528
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 27.13 %
    Favored  : 69.28 %
  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:  0.25 (0.27), residues: 1019
  helix:  1.28 (0.26), residues: 404
  sheet: -0.31 (0.36), residues: 203
  loop : -0.62 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 277 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.019   0.001   PHE A 212 
 TYR   0.019   0.002   TYR N  95 
 ARG   0.013   0.001   ARG N 105 

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 161
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7516 (mpt)
REVERT: A  215 ASP cc_start: 0.7665 (t0) cc_final: 0.7141 (t0)
REVERT: A  343 ASP cc_start: 0.8470 (m-30) cc_final: 0.8094 (m-30)
REVERT: A  370 GLU cc_start: 0.7836 (pm20) cc_final: 0.7458 (mp0)
REVERT: B   13 GLN cc_start: 0.8155 (mm110) cc_final: 0.7852 (mm110)
REVERT: B   38 ASP cc_start: 0.8601 (p0) cc_final: 0.8139 (p0)
REVERT: B   57 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8468 (ptpp)
REVERT: B  138 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: B  169 TRP cc_start: 0.9149 (m100) cc_final: 0.8863 (m100)
REVERT: B  172 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7792 (mp0)
REVERT: B  215 GLU cc_start: 0.8269 (mp0) cc_final: 0.7980 (mp0)
REVERT: B  243 THR cc_start: 0.8171 (p) cc_final: 0.7803 (p)
REVERT: G   21 MET cc_start: 0.7373 (ttp) cc_final: 0.6487 (ttp)
REVERT: G   38 MET cc_start: 0.8085 (ptp) cc_final: 0.7728 (ptp)
REVERT: G   42 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7640 (mp0)
REVERT: G   47 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7088 (mp0)
REVERT: N    3 GLN cc_start: 0.7488 (tp40) cc_final: 0.6706 (tm-30)
REVERT: N   31 ASN cc_start: 0.8529 (m-40) cc_final: 0.8251 (t0)
REVERT: N   67 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.4984 (ptm-80)
REVERT: N   84 ASN cc_start: 0.8671 (m-40) cc_final: 0.8386 (m-40)
REVERT: N   90 ASP cc_start: 0.8590 (m-30) cc_final: 0.8324 (m-30)
REVERT: N  120 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8719 (tp40)
REVERT: R  139 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8355 (tt0)
REVERT: R  148 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6785 (p90)
REVERT: R  260 LEU cc_start: 0.8369 (pt) cc_final: 0.8038 (mm)
REVERT: R  262 GLU cc_start: 0.8248 (pt0) cc_final: 0.7543 (pm20)
REVERT: R  299 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7449 (ttm170)
REVERT: R  346 LYS cc_start: 0.7616 (mttt) cc_final: 0.6943 (ptpp)
REVERT: R  388 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7869 (mm)
REVERT: R  394 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8011 (tt0)
REVERT: R  406 ASN cc_start: 0.7944 (t0) cc_final: 0.6837 (t0)
REVERT: R  408 GLU cc_start: 0.7998 (mp0) cc_final: 0.7566 (mp0)
REVERT: R  414 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.6247 (mmp-170)
REVERT: R  418 GLU cc_start: 0.6657 (pp20) cc_final: 0.6255 (pp20)
  outliers start: 32
  outliers final: 19
  residues processed: 180
  average time/residue: 1.2924
  time to fit residues: 246.8038
Evaluate side-chains
  181 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  277 TRP
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  363 HIS
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain R residue  394 GLN
Chi-restraints excluded: chain R residue  414 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0570
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.132757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.098685 restraints weight = 13501.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.90
r_work: 0.3229 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.5429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8656  Z= 0.198
  Angle     :  0.616   9.733  11758  Z= 0.319
  Chirality :  0.043   0.203   1325
  Planarity :  0.004   0.055   1454
  Dihedral  :  6.433  55.225   1528
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 27.91 %
    Favored  : 68.83 %
  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:  0.23 (0.27), residues: 1019
  helix:  1.28 (0.26), residues: 404
  sheet: -0.36 (0.36), residues: 196
  loop : -0.62 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 264 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.048   0.002   PHE N  27 
 TYR   0.019   0.002   TYR B 124 
 ARG   0.016   0.001   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7338.87 seconds
wall clock time: 129 minutes 16.52 seconds (7756.52 seconds total)