Starting phenix.real_space_refine
on Thu Mar 13 10:33:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jv5_22493/03_2025/7jv5_22493.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jv5_22493/03_2025/7jv5_22493.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jv5_22493/03_2025/7jv5_22493.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jv5_22493/03_2025/7jv5_22493.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jv5_22493/03_2025/7jv5_22493.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jv5_22493/03_2025/7jv5_22493.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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      54      5.16       5
     Cl      1      4.86       5
     C    5493      2.51       5
     N    1444      2.21       5
     O    1539      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8531
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2244
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 10, 'TRANS': 271}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1978
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2604
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 296
          Unusual residues: {'CLR': 6, 'PLM': 6, 'SK0': 1}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
  Time building chain proxies: 5.26, per 1000 atoms: 0.62
  Number of scatterers: 8531
  At special positions: 0
  Unit cell: (106.47, 98.358, 120.666, 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      1     17.00
     S      54     16.00
     O    1539      8.00
     N    1444      7.00
     C    5493      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 899.8 milliseconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      44.1% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 51
    Processing helix  chain 'R' and resid 52 through 57
      removed outlier: 3.826A  pdb=" N   LYS R  57 " --> pdb=" O   HIS R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 77
      removed outlier: 4.148A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
    Processing helix  chain 'R' and resid 94 through 127
      removed outlier: 4.477A  pdb=" N   ILE R  98 " --> pdb=" O   SER R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 135
    Processing helix  chain 'R' and resid 136 through 156
    Processing helix  chain 'R' and resid 157 through 162
    Processing helix  chain 'R' and resid 191 through 203
    Processing helix  chain 'R' and resid 203 through 240
    Processing helix  chain 'R' and resid 264 through 295
      removed outlier: 3.998A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 296 through 298
      No H-bonds generated for 'chain 'R' and resid 296 through 298'
    Processing helix  chain 'R' and resid 309 through 332
      removed outlier: 4.580A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU R 326 " --> pdb=" O   ALA R 322 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 346
    Processing helix  chain 'A' and resid 10 through 40
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 234 through 240
      removed outlier: 3.595A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 4.055A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 4.219A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.948A  pdb=" N   ASP A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.554A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.191A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    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 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.736A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 61 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.979A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.600A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.599A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.157A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.904A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.773A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.681A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.115A  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: 6.780A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.590A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1308 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: 2.38

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2419
        1.34 -     1.46: 1815
        1.46 -     1.58: 4404
        1.58 -     1.70: 0
        1.70 -     1.83: 74
  Bond restraints: 8712
  Sorted by residual:
  bond pdb=" C   MET R  78 "
       pdb=" N   PRO R  79 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.76e+00
  bond pdb=" C   ILE R 157 "
       pdb=" N   PRO R 158 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.20e-02 6.94e+03 3.59e+00
  bond pdb=" CA  PHE R 297 "
       pdb=" C   PHE R 297 "
    ideal  model  delta    sigma   weight residual
    1.523  1.557 -0.033 1.80e-02 3.09e+03 3.42e+00
  bond pdb=" C   LEU R 295 "
       pdb=" N   PRO R 296 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 1.36e-02 5.41e+03 3.35e+00
  bond pdb=" C   ASN R 327 "
       pdb=" N   PRO R 328 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.27e+00
  ... (remaining 8707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10959
        2.05 -     4.09: 742
        4.09 -     6.14: 71
        6.14 -     8.18: 19
        8.18 -    10.23: 5
  Bond angle restraints: 11796
  Sorted by residual:
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     122.08  128.51   -6.43 1.47e+00 4.63e-01 1.91e+01
  angle pdb=" N   MET R  78 "
        pdb=" CA  MET R  78 "
        pdb=" C   MET R  78 "
      ideal   model   delta    sigma   weight residual
     109.81  119.30   -9.49 2.21e+00 2.05e-01 1.84e+01
  angle pdb=" N   GLU A  16 "
        pdb=" CA  GLU A  16 "
        pdb=" C   GLU A  16 "
      ideal   model   delta    sigma   weight residual
     111.11  116.04   -4.93 1.20e+00 6.94e-01 1.69e+01
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     110.62  115.17   -4.55 1.14e+00 7.69e-01 1.59e+01
  angle pdb=" N   LYS A  17 "
        pdb=" CA  LYS A  17 "
        pdb=" C   LYS A  17 "
      ideal   model   delta    sigma   weight residual
     111.37  117.33   -5.96 1.65e+00 3.67e-01 1.31e+01
  ... (remaining 11791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 5177
       15.04 -    30.07: 282
       30.07 -    45.11: 46
       45.11 -    60.15: 4
       60.15 -    75.18: 2
  Dihedral angle restraints: 5511
    sinusoidal: 2469
      harmonic: 3042
  Sorted by residual:
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.14   26.86     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  SER N  49 "
           pdb=" C   SER N  49 "
           pdb=" N   ASP N  50 "
           pdb=" CA  ASP N  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.23  -26.77     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  LEU B 198 "
           pdb=" C   LEU B 198 "
           pdb=" N   PHE B 199 "
           pdb=" CA  PHE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.33   25.67     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1127
       0.085 -    0.170: 169
       0.170 -    0.254: 24
       0.254 -    0.339: 7
       0.339 -    0.424: 7
  Chirality restraints: 1334
  Sorted by residual:
  chirality pdb=" C14 CLR R 502 "
            pdb=" C13 CLR R 502 "
            pdb=" C15 CLR R 502 "
            pdb=" C8  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.49e+00
  chirality pdb=" C14 CLR R 507 "
            pdb=" C13 CLR R 507 "
            pdb=" C15 CLR R 507 "
            pdb=" C8  CLR R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" C14 CLR R 504 "
            pdb=" C13 CLR R 504 "
            pdb=" C15 CLR R 504 "
            pdb=" C8  CLR R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.40 2.00e-01 2.50e+01 3.96e+00
  ... (remaining 1331 not shown)

  Planarity restraints: 1453
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 207 "    0.022 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        pdb=" C   VAL R 207 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   VAL R 207 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ALA R 208 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 218 "   -0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   TYR R 218 "    0.073 2.00e-02 2.50e+03
        pdb=" O   TYR R 218 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ARG R 219 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 272 "    0.021 2.00e-02 2.50e+03   4.19e-02 1.75e+01
        pdb=" C   LYS R 272 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   LYS R 272 "    0.027 2.00e-02 2.50e+03
        pdb=" N   THR R 273 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1450 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1224
        2.77 -     3.30: 7752
        3.30 -     3.84: 13286
        3.84 -     4.37: 15683
        4.37 -     4.90: 27429
  Nonbonded interactions: 65374
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   TRP N  47 "
            pdb=" OG1 THR N  61 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NE2 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.345 3.120
  ... (remaining 65369 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:             0.500
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.400
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
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   0.051   8712  Z= 0.308
  Angle     :  1.087  10.230  11796  Z= 0.624
  Chirality :  0.070   0.424   1334
  Planarity :  0.009   0.076   1453
  Dihedral  :  9.419  75.182   3523
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.22), residues: 1024
  helix: -2.90 (0.18), residues: 413
  sheet: -0.01 (0.33), residues: 232
  loop : -2.01 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP N  36 
 HIS   0.010   0.003   HIS B 183 
 PHE   0.040   0.003   PHE B 234 
 TYR   0.020   0.002   TYR R 331 
 ARG   0.008   0.000   ARG A 385 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 LYS cc_start: 0.7224 (mmmt) cc_final: 0.5561 (tttm)
REVERT: A  317 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8225 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8387 (tt0) cc_final: 0.7943 (tp30)
REVERT: B   46 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7486 (mtp-110)
REVERT: B  134 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6768 (pmt170)
REVERT: B  163 ASP cc_start: 0.8713 (p0) cc_final: 0.8502 (p0)
REVERT: B  175 GLN cc_start: 0.8563 (mt0) cc_final: 0.7951 (mm-40)
REVERT: B  217 MET cc_start: 0.8622 (ptt) cc_final: 0.8300 (ppp)
REVERT: B  226 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8540 (mt-10)
REVERT: B  239 ASN cc_start: 0.8036 (m-40) cc_final: 0.7240 (t0)
REVERT: B  303 ASP cc_start: 0.7805 (t0) cc_final: 0.7469 (p0)
REVERT: B  315 VAL cc_start: 0.8675 (t) cc_final: 0.8259 (p)
REVERT: G   21 MET cc_start: 0.8095 (mtt) cc_final: 0.7405 (tmm)
REVERT: G   61 PHE cc_start: 0.8183 (m-80) cc_final: 0.7903 (m-80)
REVERT: N   72 ARG cc_start: 0.8322 (ptm160) cc_final: 0.8062 (ppp80)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 1.3050
  time to fit residues: 259.6469
Evaluate side-chains
  106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0020
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B  75 GLN
B 142 HIS
B 176 GLN
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.187311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.141300 restraints weight = 9283.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 3.20
r_work: 0.3764 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6130
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8712  Z= 0.183
  Angle     :  0.563   6.579  11796  Z= 0.300
  Chirality :  0.042   0.162   1334
  Planarity :  0.005   0.048   1453
  Dihedral  :  6.550  55.005   1625
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 10.59 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1024
  helix:  0.39 (0.23), residues: 422
  sheet:  0.43 (0.34), residues: 228
  loop : -1.35 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  53 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.014   0.001   TYR B 105 
 ARG   0.008   0.000   ARG G  27 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  227 ARG cc_start: 0.6548 (mtm-85) cc_final: 0.6285 (mtp180)
REVERT: A  229 ASP cc_start: 0.7839 (t0) cc_final: 0.7371 (p0)
REVERT: A  307 LYS cc_start: 0.6648 (mmmt) cc_final: 0.5344 (tttm)
REVERT: A  317 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7864 (ptt-90)
REVERT: A  343 ASP cc_start: 0.7740 (m-30) cc_final: 0.7531 (m-30)
REVERT: A  392 GLU cc_start: 0.7691 (tt0) cc_final: 0.7219 (tp30)
REVERT: B   46 ARG cc_start: 0.6651 (ttm-80) cc_final: 0.6184 (mtp-110)
REVERT: B   76 ASP cc_start: 0.6754 (p0) cc_final: 0.6364 (p0)
REVERT: B  134 ARG cc_start: 0.6211 (mtm-85) cc_final: 0.5654 (pmt170)
REVERT: B  138 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8305 (mm-30)
REVERT: B  175 GLN cc_start: 0.7636 (mt0) cc_final: 0.6926 (mm-40)
REVERT: B  189 SER cc_start: 0.8369 (p) cc_final: 0.8102 (m)
REVERT: B  205 ASP cc_start: 0.6874 (p0) cc_final: 0.6514 (p0)
REVERT: B  212 ASP cc_start: 0.6654 (t0) cc_final: 0.6251 (t0)
REVERT: B  214 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8525 (tpp80)
REVERT: B  217 MET cc_start: 0.7685 (ptt) cc_final: 0.7199 (ppp)
REVERT: B  226 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: B  239 ASN cc_start: 0.6934 (m-40) cc_final: 0.6278 (t0)
REVERT: B  254 ASP cc_start: 0.7613 (t0) cc_final: 0.7310 (t0)
REVERT: B  298 ASP cc_start: 0.7259 (t0) cc_final: 0.6794 (t70)
REVERT: B  303 ASP cc_start: 0.6505 (t0) cc_final: 0.6015 (p0)
REVERT: B  304 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7600 (mtm-85)
REVERT: B  315 VAL cc_start: 0.8458 (t) cc_final: 0.8212 (p)
REVERT: G   21 MET cc_start: 0.7490 (mtt) cc_final: 0.6924 (tmm)
  outliers start: 22
  outliers final: 8
  residues processed: 145
  average time/residue: 1.2541
  time to fit residues: 193.1054
Evaluate side-chains
  113 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.177974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.130376 restraints weight = 9563.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 3.25
r_work: 0.3634 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6234
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8712  Z= 0.240
  Angle     :  0.572   6.567  11796  Z= 0.298
  Chirality :  0.043   0.166   1334
  Planarity :  0.004   0.047   1453
  Dihedral  :  6.627  59.002   1625
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.26 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1024
  helix:  1.82 (0.25), residues: 432
  sheet:  0.40 (0.34), residues: 220
  loop : -1.18 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N  36 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B 199 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.007   0.000   ARG G  27 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6522 (tppt)
REVERT: A  221 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7473 (mtp)
REVERT: A  229 ASP cc_start: 0.8021 (t0) cc_final: 0.7680 (t70)
REVERT: A  314 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: A  317 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7947 (ptt90)
REVERT: A  392 GLU cc_start: 0.7928 (tt0) cc_final: 0.7261 (tp30)
REVERT: B  134 ARG cc_start: 0.6420 (mtm-85) cc_final: 0.5610 (pmt170)
REVERT: B  175 GLN cc_start: 0.7468 (mt0) cc_final: 0.6901 (mm-40)
REVERT: B  205 ASP cc_start: 0.6934 (p0) cc_final: 0.6588 (p0)
REVERT: B  212 ASP cc_start: 0.6740 (t0) cc_final: 0.6378 (t0)
REVERT: B  217 MET cc_start: 0.7743 (ptt) cc_final: 0.7247 (ppp)
REVERT: B  226 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7780 (mt-10)
REVERT: B  239 ASN cc_start: 0.7225 (m-40) cc_final: 0.6741 (t0)
REVERT: B  254 ASP cc_start: 0.7701 (t0) cc_final: 0.7412 (t0)
REVERT: B  277 SER cc_start: 0.8985 (t) cc_final: 0.8773 (p)
REVERT: B  303 ASP cc_start: 0.6740 (t0) cc_final: 0.6286 (p0)
REVERT: B  304 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7684 (mtm110)
REVERT: B  339 TRP cc_start: 0.8612 (m100) cc_final: 0.7990 (m-10)
REVERT: G   21 MET cc_start: 0.7363 (mtt) cc_final: 0.6858 (tmm)
  outliers start: 27
  outliers final: 13
  residues processed: 134
  average time/residue: 1.1792
  time to fit residues: 168.8406
Evaluate side-chains
  113 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  152 VAL
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0070
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   overall best weight:    1.7802

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.174370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.127101 restraints weight = 9679.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 3.22
r_work: 0.3598 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6276
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8712  Z= 0.259
  Angle     :  0.563   6.473  11796  Z= 0.294
  Chirality :  0.043   0.152   1334
  Planarity :  0.004   0.045   1453
  Dihedral  :  6.657  54.437   1625
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 12.37 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1024
  helix:  2.17 (0.25), residues: 429
  sheet:  0.15 (0.34), residues: 230
  loop : -1.11 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B 199 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.008   0.000   ARG G  27 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  132 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7529 (mt-10)
REVERT: R  283 CYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (m)
REVERT: A   34 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6496 (tppt)
REVERT: A   60 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6721 (mpt)
REVERT: A  221 MET cc_start: 0.7809 (ttm) cc_final: 0.7476 (mtp)
REVERT: A  229 ASP cc_start: 0.8031 (t0) cc_final: 0.7526 (t0)
REVERT: A  314 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7210 (pm20)
REVERT: A  317 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7963 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8025 (tt0) cc_final: 0.7260 (tp30)
REVERT: B   46 ARG cc_start: 0.6812 (ttm-80) cc_final: 0.6282 (mtp-110)
REVERT: B   58 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7831 (mm)
REVERT: B   61 MET cc_start: 0.8466 (ppp) cc_final: 0.8179 (pp-130)
REVERT: B   75 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7917 (mm110)
REVERT: B  134 ARG cc_start: 0.6483 (mtm-85) cc_final: 0.5524 (pmt170)
REVERT: B  138 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8076 (mm-30)
REVERT: B  175 GLN cc_start: 0.7660 (mt0) cc_final: 0.7130 (mp10)
REVERT: B  180 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.2578 (p90)
REVERT: B  205 ASP cc_start: 0.7081 (p0) cc_final: 0.6742 (p0)
REVERT: B  214 ARG cc_start: 0.8900 (tpp80) cc_final: 0.8598 (tpp80)
REVERT: B  217 MET cc_start: 0.7821 (ptt) cc_final: 0.7351 (ppp)
REVERT: B  220 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (mt0)
REVERT: B  239 ASN cc_start: 0.7342 (m-40) cc_final: 0.6816 (t0)
REVERT: B  246 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7901 (t0)
REVERT: B  254 ASP cc_start: 0.7755 (t0) cc_final: 0.7536 (t0)
REVERT: B  290 ASP cc_start: 0.6898 (m-30) cc_final: 0.6663 (m-30)
REVERT: B  303 ASP cc_start: 0.6702 (t0) cc_final: 0.6258 (p0)
REVERT: B  304 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7631 (mtm-85)
REVERT: B  339 TRP cc_start: 0.8660 (m100) cc_final: 0.8036 (m-10)
REVERT: G   21 MET cc_start: 0.7159 (mtt) cc_final: 0.6686 (tmm)
REVERT: N   38 ARG cc_start: 0.7587 (ptt180) cc_final: 0.6937 (ptt-90)
REVERT: N   98 ARG cc_start: 0.8437 (ttp80) cc_final: 0.7815 (ttt-90)
  outliers start: 34
  outliers final: 13
  residues processed: 129
  average time/residue: 1.3001
  time to fit residues: 178.2531
Evaluate side-chains
  120 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  132 GLU
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
** A 220 HIS ** 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 = 0.4248 r_free = 0.4248 target = 0.177260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.130161 restraints weight = 9548.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 3.22
r_work: 0.3629 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8712  Z= 0.173
  Angle     :  0.518   6.982  11796  Z= 0.267
  Chirality :  0.041   0.181   1334
  Planarity :  0.004   0.048   1453
  Dihedral  :  6.397  56.446   1625
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.27 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 1024
  helix:  2.43 (0.25), residues: 429
  sheet: -0.02 (0.33), residues: 234
  loop : -0.99 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.009   0.001   TYR N  80 
 ARG   0.008   0.000   ARG G  27 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: R  132 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7490 (mt-10)
REVERT: R  283 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7294 (m)
REVERT: A   34 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6551 (tppt)
REVERT: A   60 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6655 (mpt)
REVERT: A  221 MET cc_start: 0.7709 (ttm) cc_final: 0.7425 (mtp)
REVERT: A  229 ASP cc_start: 0.8024 (t0) cc_final: 0.7454 (t0)
REVERT: A  314 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7209 (pm20)
REVERT: A  317 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7991 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8018 (tt0) cc_final: 0.7278 (tp30)
REVERT: B   61 MET cc_start: 0.8459 (ppp) cc_final: 0.8222 (pp-130)
REVERT: B  134 ARG cc_start: 0.6439 (mtm-85) cc_final: 0.5537 (pmt170)
REVERT: B  138 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8039 (mm-30)
REVERT: B  161 SER cc_start: 0.8945 (t) cc_final: 0.8582 (p)
REVERT: B  175 GLN cc_start: 0.7657 (mt0) cc_final: 0.7011 (mm110)
REVERT: B  180 PHE cc_start: 0.4625 (OUTLIER) cc_final: 0.2387 (p90)
REVERT: B  205 ASP cc_start: 0.7011 (p0) cc_final: 0.6702 (p0)
REVERT: B  214 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8655 (tpp80)
REVERT: B  217 MET cc_start: 0.7753 (ptt) cc_final: 0.7281 (ppp)
REVERT: B  239 ASN cc_start: 0.7287 (m-40) cc_final: 0.6824 (t0)
REVERT: B  246 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7869 (t0)
REVERT: B  254 ASP cc_start: 0.7751 (t0) cc_final: 0.7507 (t0)
REVERT: B  290 ASP cc_start: 0.6856 (m-30) cc_final: 0.6616 (m-30)
REVERT: B  298 ASP cc_start: 0.7426 (t70) cc_final: 0.7020 (t70)
REVERT: B  304 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7572 (mtm-85)
REVERT: B  339 TRP cc_start: 0.8629 (m100) cc_final: 0.7995 (m-10)
REVERT: G   21 MET cc_start: 0.6998 (mtt) cc_final: 0.6552 (tmm)
  outliers start: 24
  outliers final: 12
  residues processed: 118
  average time/residue: 1.4918
  time to fit residues: 187.5279
Evaluate side-chains
  105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0770
   chunk 77 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.179518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.132752 restraints weight = 9435.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 3.20
r_work: 0.3670 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6208
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   8712  Z= 0.149
  Angle     :  0.497   8.390  11796  Z= 0.256
  Chirality :  0.040   0.152   1334
  Planarity :  0.003   0.050   1453
  Dihedral  :  6.101  56.779   1625
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.38 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 1024
  helix:  2.66 (0.25), residues: 430
  sheet: -0.05 (0.33), residues: 234
  loop : -1.01 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 123 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.007   0.001   TYR B 111 
 ARG   0.002   0.000   ARG B 150 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: R   36 SER cc_start: 0.7671 (t) cc_final: 0.7414 (m)
REVERT: R  132 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7502 (mt-10)
REVERT: R  283 CYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7286 (m)
REVERT: A   34 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6526 (tppt)
REVERT: A   60 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6522 (mpt)
REVERT: A  229 ASP cc_start: 0.8020 (t0) cc_final: 0.7432 (t0)
REVERT: A  265 ARG cc_start: 0.6736 (ptt90) cc_final: 0.5864 (ptt90)
REVERT: A  314 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7219 (pm20)
REVERT: A  317 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7986 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8005 (tt0) cc_final: 0.7281 (tp30)
REVERT: B   68 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7072 (mmm-85)
REVERT: B  134 ARG cc_start: 0.6495 (mtm-85) cc_final: 0.5612 (pmt170)
REVERT: B  138 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7971 (mm-30)
REVERT: B  175 GLN cc_start: 0.7640 (mt0) cc_final: 0.6993 (mm110)
REVERT: B  180 PHE cc_start: 0.4672 (OUTLIER) cc_final: 0.2220 (p90)
REVERT: B  205 ASP cc_start: 0.7001 (p0) cc_final: 0.6678 (p0)
REVERT: B  214 ARG cc_start: 0.8854 (tpp80) cc_final: 0.8640 (tpp80)
REVERT: B  217 MET cc_start: 0.7766 (ptt) cc_final: 0.7278 (ppp)
REVERT: B  239 ASN cc_start: 0.7203 (m-40) cc_final: 0.6948 (t0)
REVERT: B  246 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7817 (t0)
REVERT: B  254 ASP cc_start: 0.7733 (t0) cc_final: 0.6922 (p0)
REVERT: B  298 ASP cc_start: 0.7293 (t70) cc_final: 0.6687 (t0)
REVERT: B  339 TRP cc_start: 0.8654 (m100) cc_final: 0.7982 (m-10)
REVERT: G   21 MET cc_start: 0.6844 (mtt) cc_final: 0.6416 (tmm)
REVERT: N  105 ARG cc_start: 0.7074 (mtm180) cc_final: 0.6640 (mtm180)
  outliers start: 26
  outliers final: 12
  residues processed: 116
  average time/residue: 1.4723
  time to fit residues: 182.8517
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    0.0970
   chunk 14 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 96 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0370
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
A 220 HIS
B 142 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.179478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.134334 restraints weight = 9478.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 3.11
r_work: 0.3698 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6221
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.079   8712  Z= 0.153
  Angle     :  0.491   7.911  11796  Z= 0.254
  Chirality :  0.040   0.151   1334
  Planarity :  0.003   0.050   1453
  Dihedral  :  5.909  59.761   1625
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.72 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.27), residues: 1024
  helix:  2.82 (0.25), residues: 429
  sheet:  0.04 (0.33), residues: 223
  loop : -0.96 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.006   0.001   TYR A 339 
 ARG   0.002   0.000   ARG A 265 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: R   36 SER cc_start: 0.7697 (t) cc_final: 0.7435 (m)
REVERT: R  132 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7484 (mt-10)
REVERT: R  283 CYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7282 (m)
REVERT: A   34 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6565 (tppt)
REVERT: A   60 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6518 (mpt)
REVERT: A  229 ASP cc_start: 0.8058 (t0) cc_final: 0.7463 (t0)
REVERT: A  314 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7279 (pm20)
REVERT: A  317 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8018 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7971 (tt0) cc_final: 0.7264 (tp30)
REVERT: B   45 MET cc_start: 0.7690 (mtt) cc_final: 0.6840 (mtt)
REVERT: B   58 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7747 (mm)
REVERT: B   68 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7111 (mmm-85)
REVERT: B  134 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.5624 (pmt170)
REVERT: B  138 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7944 (mm-30)
REVERT: B  175 GLN cc_start: 0.7690 (mt0) cc_final: 0.7160 (mp10)
REVERT: B  180 PHE cc_start: 0.4629 (OUTLIER) cc_final: 0.2099 (p90)
REVERT: B  205 ASP cc_start: 0.6951 (p0) cc_final: 0.6637 (t0)
REVERT: B  214 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8586 (tpp80)
REVERT: B  217 MET cc_start: 0.7782 (ptt) cc_final: 0.7282 (ppp)
REVERT: B  239 ASN cc_start: 0.7158 (m-40) cc_final: 0.6871 (t0)
REVERT: B  246 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7826 (t0)
REVERT: B  254 ASP cc_start: 0.7658 (t0) cc_final: 0.6889 (p0)
REVERT: B  298 ASP cc_start: 0.7231 (t70) cc_final: 0.6613 (t0)
REVERT: B  339 TRP cc_start: 0.8606 (m100) cc_final: 0.7858 (m-10)
REVERT: G   21 MET cc_start: 0.6896 (mtt) cc_final: 0.6501 (tmm)
REVERT: N   38 ARG cc_start: 0.7671 (ptt180) cc_final: 0.7229 (ptt-90)
  outliers start: 23
  outliers final: 11
  residues processed: 106
  average time/residue: 1.3304
  time to fit residues: 150.1961
Evaluate side-chains
  102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    0.0670
   chunk 47 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0980
   chunk 86 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.0324

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.177991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.130849 restraints weight = 9733.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 3.25
r_work: 0.3650 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6202
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   8712  Z= 0.190
  Angle     :  0.515   8.490  11796  Z= 0.267
  Chirality :  0.041   0.151   1334
  Planarity :  0.003   0.050   1453
  Dihedral  :  5.843  56.785   1625
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.28 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.27), residues: 1024
  helix:  2.98 (0.25), residues: 420
  sheet: -0.00 (0.33), residues: 234
  loop : -0.89 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R  80 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.004   0.000   ARG R 130 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6531 (tppt)
REVERT: A   60 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6375 (mpt)
REVERT: A  229 ASP cc_start: 0.8010 (t0) cc_final: 0.7421 (t0)
REVERT: A  314 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7290 (pm20)
REVERT: A  317 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8017 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7910 (tt0) cc_final: 0.7154 (tp30)
REVERT: B   45 MET cc_start: 0.7945 (mtt) cc_final: 0.7117 (mtt)
REVERT: B   68 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7105 (mmm-85)
REVERT: B  134 ARG cc_start: 0.6534 (mtm-85) cc_final: 0.5614 (pmt170)
REVERT: B  138 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7873 (mm-30)
REVERT: B  175 GLN cc_start: 0.7609 (mt0) cc_final: 0.7112 (mp10)
REVERT: B  180 PHE cc_start: 0.4642 (OUTLIER) cc_final: 0.2198 (p90)
REVERT: B  205 ASP cc_start: 0.6936 (p0) cc_final: 0.6611 (p0)
REVERT: B  214 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8590 (tpp80)
REVERT: B  217 MET cc_start: 0.7769 (ptt) cc_final: 0.7424 (ppp)
REVERT: B  239 ASN cc_start: 0.7177 (m-40) cc_final: 0.6727 (t0)
REVERT: B  246 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7857 (t0)
REVERT: B  298 ASP cc_start: 0.7301 (t70) cc_final: 0.6848 (t70)
REVERT: B  339 TRP cc_start: 0.8634 (m100) cc_final: 0.7903 (m-10)
REVERT: G   21 MET cc_start: 0.6820 (mtt) cc_final: 0.6453 (tmm)
REVERT: N   38 ARG cc_start: 0.7691 (ptt180) cc_final: 0.7232 (ptm-80)
REVERT: N  105 ARG cc_start: 0.6894 (mtm180) cc_final: 0.6653 (mtm180)
  outliers start: 22
  outliers final: 13
  residues processed: 100
  average time/residue: 1.2997
  time to fit residues: 138.3439
Evaluate side-chains
  103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 93 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.178262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.132971 restraints weight = 9617.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 3.13
r_work: 0.3706 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6176
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.075   8712  Z= 0.159
  Angle     :  0.497   8.967  11796  Z= 0.258
  Chirality :  0.040   0.147   1334
  Planarity :  0.003   0.050   1453
  Dihedral  :  5.625  57.025   1625
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.50 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.27), residues: 1024
  helix:  3.04 (0.25), residues: 421
  sheet: -0.08 (0.32), residues: 240
  loop : -0.77 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.009   0.001   TYR B 111 
 ARG   0.004   0.000   ARG R 130 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6549 (ttpt)
REVERT: A   60 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6472 (mpt)
REVERT: A  229 ASP cc_start: 0.7956 (t0) cc_final: 0.7379 (t0)
REVERT: A  314 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7345 (pm20)
REVERT: A  317 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8035 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7954 (tt0) cc_final: 0.7183 (tp30)
REVERT: B   45 MET cc_start: 0.8076 (mtt) cc_final: 0.7213 (mtt)
REVERT: B   58 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7703 (mm)
REVERT: B   68 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6999 (mmm-85)
REVERT: B  138 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7871 (mm-30)
REVERT: B  175 GLN cc_start: 0.7603 (mt0) cc_final: 0.7113 (mp10)
REVERT: B  180 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.2173 (p90)
REVERT: B  214 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8594 (tpp80)
REVERT: B  217 MET cc_start: 0.7761 (ptt) cc_final: 0.7424 (ppp)
REVERT: B  226 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: B  239 ASN cc_start: 0.7188 (m-40) cc_final: 0.6705 (t0)
REVERT: B  246 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7816 (t0)
REVERT: B  298 ASP cc_start: 0.7207 (t70) cc_final: 0.6554 (t0)
REVERT: B  339 TRP cc_start: 0.8604 (m100) cc_final: 0.7863 (m-10)
REVERT: G   21 MET cc_start: 0.6865 (mtt) cc_final: 0.6566 (tmm)
REVERT: N   38 ARG cc_start: 0.7702 (ptt180) cc_final: 0.7256 (ptm-80)
REVERT: N  105 ARG cc_start: 0.6936 (mtm180) cc_final: 0.6697 (mtm180)
  outliers start: 18
  outliers final: 11
  residues processed: 100
  average time/residue: 1.3552
  time to fit residues: 144.7487
Evaluate side-chains
  99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.175877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.130416 restraints weight = 9537.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 3.11
r_work: 0.3640 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8712  Z= 0.193
  Angle     :  0.521   8.476  11796  Z= 0.273
  Chirality :  0.041   0.149   1334
  Planarity :  0.004   0.049   1453
  Dihedral  :  5.707  57.349   1625
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.28 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.27), residues: 1024
  helix:  2.96 (0.25), residues: 421
  sheet: -0.16 (0.32), residues: 240
  loop : -0.70 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  80 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.004   0.000   ARG R 130 

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6712 (ttpt)
REVERT: A   60 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6566 (mpt)
REVERT: A  229 ASP cc_start: 0.8047 (t0) cc_final: 0.7477 (t0)
REVERT: A  314 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7553 (pm20)
REVERT: A  317 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8068 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8092 (tt0) cc_final: 0.7325 (tp30)
REVERT: B   45 MET cc_start: 0.8401 (mtt) cc_final: 0.7949 (mtt)
REVERT: B   46 ARG cc_start: 0.6910 (ttm-80) cc_final: 0.6398 (mtp-110)
REVERT: B   68 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7311 (mmm-85)
REVERT: B  118 ASP cc_start: 0.8119 (p0) cc_final: 0.7880 (p0)
REVERT: B  138 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7839 (mm-30)
REVERT: B  175 GLN cc_start: 0.7768 (mt0) cc_final: 0.7250 (mp10)
REVERT: B  180 PHE cc_start: 0.4988 (OUTLIER) cc_final: 0.2737 (p90)
REVERT: B  214 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8439 (mmt180)
REVERT: B  217 MET cc_start: 0.7948 (ptt) cc_final: 0.7606 (ppp)
REVERT: B  239 ASN cc_start: 0.7371 (m-40) cc_final: 0.6956 (t0)
REVERT: B  246 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7884 (t0)
REVERT: B  298 ASP cc_start: 0.7549 (t70) cc_final: 0.7122 (t70)
REVERT: B  339 TRP cc_start: 0.8695 (m100) cc_final: 0.8027 (m-10)
REVERT: G   21 MET cc_start: 0.6971 (mtt) cc_final: 0.6674 (tmm)
REVERT: N   38 ARG cc_start: 0.7948 (ptt180) cc_final: 0.7452 (ptm-80)
REVERT: N  105 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6895 (mtm180)
  outliers start: 22
  outliers final: 12
  residues processed: 99
  average time/residue: 1.2992
  time to fit residues: 136.8944
Evaluate side-chains
  99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 76 optimal weight:    0.2980
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.176470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.130730 restraints weight = 9688.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 3.16
r_work: 0.3666 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6268
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8712  Z= 0.178
  Angle     :  0.510   9.328  11796  Z= 0.267
  Chirality :  0.041   0.147   1334
  Planarity :  0.003   0.049   1453
  Dihedral  :  5.653  57.522   1625
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.61 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.27), residues: 1024
  helix:  3.01 (0.25), residues: 421
  sheet: -0.14 (0.33), residues: 229
  loop : -0.68 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 123 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.002   0.000   ARG A 265 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5894.52 seconds
wall clock time: 102 minutes 4.12 seconds (6124.12 seconds total)