Starting phenix.real_space_refine
on Wed Mar 12 01:06:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d9h_7835/03_2025/6d9h_7835.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d9h_7835/03_2025/6d9h_7835.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d9h_7835/03_2025/6d9h_7835.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d9h_7835/03_2025/6d9h_7835.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d9h_7835/03_2025/6d9h_7835.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d9h_7835/03_2025/6d9h_7835.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4503      2.51       5
     N    1196      2.21       5
     O    1272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 7023
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1691
          Classifications: {'peptide': 209}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 206}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    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: "R"
      Number of atoms: 2276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2276
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 14, 'TRANS': 273}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'ADN%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 4.33, per 1000 atoms: 0.62
  Number of scatterers: 7023
  At special positions: 0
  Unit cell: (76.32, 139.92, 100.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1272      8.00
     N    1196      7.00
     C    4503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  80 " - pdb=" SG  CYS R 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 260 " - pdb=" SG  CYS R 263 " 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: 1.69
  Conformation dependent library (CDL) restraints added in 965.8 milliseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 9 sheets defined
      49.2% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 32
      removed outlier: 4.203A  pdb=" N   ARG A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.770A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.171A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
      removed outlier: 3.610A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 214 through 217'
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 4.170A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.094A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.909A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 330 through 353
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.900A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    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: 3.550A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 6 through 37
      Proline residue:  R  25  - end of helix
      removed outlier: 3.737A  pdb=" N   ASN R  37 " --> pdb=" O   ALA R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 72
      removed outlier: 4.860A  pdb=" N   ILE R  63 " --> pdb=" O   GLY R  59 " (cutoff:3.500A)
      Proline residue:  R  64  - end of helix
    Processing helix  chain 'R' and resid 77 through 111
      Proline residue:  R  86  - end of helix
      removed outlier: 3.623A  pdb=" N   SER R  93 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   VAL R 109 " --> pdb=" O   ARG R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 114 through 119
    Processing helix  chain 'R' and resid 120 through 141
    Processing helix  chain 'R' and resid 148 through 160
    Processing helix  chain 'R' and resid 170 through 175
    Processing helix  chain 'R' and resid 176 through 182
    Processing helix  chain 'R' and resid 182 through 189
      removed outlier: 3.825A  pdb=" N   VAL R 189 " --> pdb=" O   PHE R 185 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 189 through 213
    Processing helix  chain 'R' and resid 224 through 260
      removed outlier: 3.610A  pdb=" N   LEU R 248 " --> pdb=" O   ALA R 244 " (cutoff:3.500A)
      Proline residue:  R 249  - end of helix
    Processing helix  chain 'R' and resid 266 through 289
      removed outlier: 4.025A  pdb=" N   THR R 270 " --> pdb=" O   PRO R 266 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   SER R 281 " --> pdb=" O   THR R 277 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA R 282 " --> pdb=" O   HIS R 278 " (cutoff:3.500A)
      Proline residue:  R 285  - end of helix
    Processing helix  chain 'R' and resid 292 through 301
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.976A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.885A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.666A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.514A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.294A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.912A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.660A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.090A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 74 through 76

    396 hydrogen bonds defined for protein.
    1161 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: 1.86

  Time building geometry restraints manager: 2.01 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: 2229
        1.34 -     1.46: 1578
        1.46 -     1.58: 3283
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 7165
  Sorted by residual:
  bond pdb=" C   VAL R  24 "
       pdb=" N   PRO R  25 "
    ideal  model  delta    sigma   weight residual
    1.335  1.364 -0.028 1.36e-02 5.41e+03 4.32e+00
  bond pdb=" C   THR R 141 "
       pdb=" N   PRO R 142 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.54e+00
  bond pdb=" C   CYS R  85 "
       pdb=" N   PRO R  86 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.19e-02 7.06e+03 3.20e+00
  bond pdb=" CA  CYS R  85 "
       pdb=" C   CYS R  85 "
    ideal  model  delta    sigma   weight residual
    1.524  1.546 -0.022 1.26e-02 6.30e+03 3.15e+00
  bond pdb=" CG  LEU B 192 "
       pdb=" CD1 LEU B 192 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.09e+00
  ... (remaining 7160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 9283
        1.97 -     3.94: 349
        3.94 -     5.91: 50
        5.91 -     7.89: 19
        7.89 -     9.86: 5
  Bond angle restraints: 9706
  Sorted by residual:
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  130.04   -8.50 1.91e+00 2.74e-01 1.98e+01
  angle pdb=" CA  LYS R  35 "
        pdb=" CB  LYS R  35 "
        pdb=" CG  LYS R  35 "
      ideal   model   delta    sigma   weight residual
     114.10  122.70   -8.60 2.00e+00 2.50e-01 1.85e+01
  angle pdb=" C   ILE R 274 "
        pdb=" N   PHE R 275 "
        pdb=" CA  PHE R 275 "
      ideal   model   delta    sigma   weight residual
     121.14  113.92    7.22 1.75e+00 3.27e-01 1.70e+01
  angle pdb=" N   LEU R 248 "
        pdb=" CA  LEU R 248 "
        pdb=" C   LEU R 248 "
      ideal   model   delta    sigma   weight residual
     113.16  118.55   -5.39 1.42e+00 4.96e-01 1.44e+01
  angle pdb=" C   PHE G  61 "
        pdb=" N   ARG G  62 "
        pdb=" CA  ARG G  62 "
      ideal   model   delta    sigma   weight residual
     121.70  128.51   -6.81 1.80e+00 3.09e-01 1.43e+01
  ... (remaining 9701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.22: 4095
       15.22 -    30.44: 145
       30.44 -    45.66: 43
       45.66 -    60.88: 6
       60.88 -    76.10: 4
  Dihedral angle restraints: 4293
    sinusoidal: 1691
      harmonic: 2602
  Sorted by residual:
  dihedral pdb=" CA  GLY A 293 "
           pdb=" C   GLY A 293 "
           pdb=" N   ALA A 294 "
           pdb=" CA  ALA A 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.06  -25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.19   22.81     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.94   19.06     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 4290 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 837
       0.058 -    0.116: 231
       0.116 -    0.174: 45
       0.174 -    0.232: 10
       0.232 -    0.291: 2
  Chirality restraints: 1125
  Sorted by residual:
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CA  PHE R 275 "
            pdb=" N   PHE R 275 "
            pdb=" C   PHE R 275 "
            pdb=" CB  PHE R 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  LYS R  35 "
            pdb=" N   LYS R  35 "
            pdb=" C   LYS R  35 "
            pdb=" CB  LYS R  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1122 not shown)

  Planarity restraints: 1213
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 181 "    0.025 2.00e-02 2.50e+03   5.00e-02 2.50e+01
        pdb=" C   VAL R 181 "   -0.087 2.00e-02 2.50e+03
        pdb=" O   VAL R 181 "    0.032 2.00e-02 2.50e+03
        pdb=" N   TYR R 182 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 182 "   -0.017 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   TYR R 182 "    0.057 2.00e-02 2.50e+03
        pdb=" O   TYR R 182 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PHE R 183 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 146 "    0.025 2.00e-02 2.50e+03   2.02e-02 1.02e+01
        pdb=" CG  TRP R 146 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 146 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 146 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 146 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 146 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 146 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 146 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 146 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 146 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1210 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 774
        2.76 -     3.29: 6666
        3.29 -     3.83: 11421
        3.83 -     4.36: 12948
        4.36 -     4.90: 23105
  Nonbonded interactions: 54914
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R  55 "
            pdb=" OG  SER R 281 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   ILE B 123 "
            pdb=" OG  SER B 136 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OG1 THR R  44 "
            pdb=" OD2 ASP R 104 "
     model   vdw
     2.335 3.040
  ... (remaining 54909 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 group one per residue
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:             0.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.110
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.060
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
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      :  0.006   0.084   7165  Z= 0.388
  Angle     :  0.932   9.857   9706  Z= 0.518
  Chirality :  0.056   0.291   1125
  Planarity :  0.007   0.050   1213
  Dihedral  :  9.574  76.099   2595
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.25), residues: 876
  helix:  0.08 (0.23), residues: 404
  sheet: -0.57 (0.39), residues: 154
  loop : -2.65 (0.28), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.004   TRP R 146 
 HIS   0.007   0.002   HIS B 311 
 PHE   0.039   0.004   PHE R 171 
 TYR   0.021   0.003   TYR R 179 
 ARG   0.008   0.001   ARG B  68 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8049 (m-40) cc_final: 0.7667 (m110)
REVERT: B  118 ASP cc_start: 0.7416 (p0) cc_final: 0.7065 (t0)
REVERT: R   89 ILE cc_start: 0.8617 (mt) cc_final: 0.8365 (mt)
REVERT: R  117 MET cc_start: 0.7175 (ptm) cc_final: 0.6941 (mmm)
REVERT: R  275 PHE cc_start: 0.8534 (p90) cc_final: 0.7706 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1942
  time to fit residues: 48.6360
Evaluate side-chains
  127 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
A 295 ASN
A 332 ASN
B   6 GLN
B  88 ASN
B 239 ASN
B 266 HIS
B 340 ASN
R  38 GLN
R 184 ASN
R 251 HIS
R 280 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.121956 restraints weight = 7788.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125151 restraints weight = 6259.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.126039 restraints weight = 4667.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7165  Z= 0.185
  Angle     :  0.544   5.759   9706  Z= 0.295
  Chirality :  0.042   0.172   1125
  Planarity :  0.004   0.046   1213
  Dihedral  :  5.765  57.039    976
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.46 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.28), residues: 876
  helix:  1.35 (0.25), residues: 414
  sheet: -0.29 (0.38), residues: 164
  loop : -2.16 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 188 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.039   0.002   PHE R 275 
 TYR   0.018   0.001   TYR R 115 
 ARG   0.009   0.001   ARG B 197 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8296 (t0)
REVERT: A  322 THR cc_start: 0.8899 (m) cc_final: 0.8531 (p)
REVERT: B   88 ASN cc_start: 0.8410 (m110) cc_final: 0.7764 (m110)
REVERT: B   98 SER cc_start: 0.8155 (m) cc_final: 0.7848 (t)
REVERT: R  178 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7296 (mt-10)
REVERT: R  275 PHE cc_start: 0.8623 (p90) cc_final: 0.8286 (p90)
  outliers start: 11
  outliers final: 7
  residues processed: 146
  average time/residue: 0.1904
  time to fit residues: 37.4119
Evaluate side-chains
  131 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  178 GLU
Chi-restraints excluded: chain R residue  281 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 79 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0270
   chunk 25 optimal weight:    0.0770
   chunk 33 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.154435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122643 restraints weight = 7808.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125190 restraints weight = 7382.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.126479 restraints weight = 5362.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7165  Z= 0.169
  Angle     :  0.508   6.384   9706  Z= 0.274
  Chirality :  0.041   0.165   1125
  Planarity :  0.004   0.046   1213
  Dihedral  :  5.253  51.821    976
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  9.72 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.29), residues: 876
  helix:  1.91 (0.26), residues: 415
  sheet: -0.14 (0.39), residues: 164
  loop : -1.86 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 188 
 HIS   0.002   0.001   HIS R 251 
 PHE   0.033   0.001   PHE R 275 
 TYR   0.017   0.001   TYR R 115 
 ARG   0.004   0.000   ARG B 214 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 THR cc_start: 0.8875 (m) cc_final: 0.8479 (p)
REVERT: A  342 ASP cc_start: 0.8620 (t0) cc_final: 0.8354 (t0)
REVERT: B   88 ASN cc_start: 0.8329 (m110) cc_final: 0.7772 (m-40)
REVERT: B  123 ILE cc_start: 0.8759 (mm) cc_final: 0.8475 (mt)
REVERT: B  297 TRP cc_start: 0.8751 (m100) cc_final: 0.8300 (m-10)
REVERT: R   45 PHE cc_start: 0.7167 (m-80) cc_final: 0.6842 (m-80)
REVERT: R  178 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7388 (mt-10)
  outliers start: 17
  outliers final: 11
  residues processed: 155
  average time/residue: 0.1802
  time to fit residues: 38.1167
Evaluate side-chains
  132 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  178 GLU
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  283 MET
Chi-restraints excluded: chain R residue  286 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  38 GLN
R  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.171632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137820 restraints weight = 7334.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139845 restraints weight = 6639.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.141460 restraints weight = 5344.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7165  Z= 0.188
  Angle     :  0.499   7.288   9706  Z= 0.270
  Chirality :  0.042   0.145   1125
  Planarity :  0.004   0.047   1213
  Dihedral  :  5.170  51.613    976
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.96 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.29), residues: 876
  helix:  2.08 (0.26), residues: 416
  sheet: -0.36 (0.37), residues: 172
  loop : -1.79 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 188 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.022   0.002   PHE R 275 
 TYR   0.016   0.001   TYR R 115 
 ARG   0.003   0.000   ARG B 214 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 TYR cc_start: 0.7502 (m-80) cc_final: 0.7302 (m-80)
REVERT: B   88 ASN cc_start: 0.8371 (m110) cc_final: 0.7845 (m-40)
REVERT: B  123 ILE cc_start: 0.8730 (mm) cc_final: 0.8502 (mt)
REVERT: B  297 TRP cc_start: 0.8824 (m100) cc_final: 0.8358 (m-10)
REVERT: R  173 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7313 (ttpt)
REVERT: R  178 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7378 (mt-10)
  outliers start: 19
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1916
  time to fit residues: 35.8974
Evaluate side-chains
  143 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  178 GLU
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  286 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0270
   chunk 18 optimal weight:    0.0060
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.4654

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

Flipped N/Q/H residues before XYZ refinement:
R  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.127700 restraints weight = 7747.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.130070 restraints weight = 5852.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132056 restraints weight = 4800.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7165  Z= 0.132
  Angle     :  0.473   8.993   9706  Z= 0.252
  Chirality :  0.040   0.139   1125
  Planarity :  0.003   0.044   1213
  Dihedral  :  4.825  47.850    976
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.88 %
    Favored  : 85.02 %
  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:  0.88 (0.29), residues: 876
  helix:  2.34 (0.26), residues: 416
  sheet: -0.14 (0.37), residues: 169
  loop : -1.65 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 188 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.021   0.001   PHE R 275 
 TYR   0.017   0.001   TYR R 115 
 ARG   0.002   0.000   ARG B 214 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8134 (ttpp)
REVERT: B   88 ASN cc_start: 0.8310 (m110) cc_final: 0.7766 (m-40)
REVERT: B  197 ARG cc_start: 0.7185 (mmm160) cc_final: 0.6367 (mmm160)
REVERT: B  297 TRP cc_start: 0.8778 (m100) cc_final: 0.8384 (m-10)
REVERT: R   35 LYS cc_start: 0.6242 (pttt) cc_final: 0.6008 (mptt)
REVERT: R  173 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7248 (ttpt)
  outliers start: 16
  outliers final: 14
  residues processed: 155
  average time/residue: 0.1854
  time to fit residues: 39.0662
Evaluate side-chains
  146 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  286 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.147805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.118842 restraints weight = 8035.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.120960 restraints weight = 6176.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122621 restraints weight = 5152.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7165  Z= 0.367
  Angle     :  0.592   7.940   9706  Z= 0.320
  Chirality :  0.045   0.141   1125
  Planarity :  0.005   0.066   1213
  Dihedral  :  5.600  57.718    976
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.01 %
    Favored  : 84.23 %
  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 (0.29), residues: 876
  helix:  1.86 (0.26), residues: 416
  sheet: -0.36 (0.37), residues: 176
  loop : -1.81 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP R 188 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.027   0.002   PHE B 199 
 TYR   0.014   0.001   TYR R 115 
 ARG   0.010   0.001   ARG R 108 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.7880 (mtt) cc_final: 0.7662 (mtt)
REVERT: A  210 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8188 (ttpp)
REVERT: A  258 LYS cc_start: 0.8362 (pttt) cc_final: 0.8030 (pttm)
REVERT: B   88 ASN cc_start: 0.8397 (m110) cc_final: 0.7785 (m-40)
REVERT: B  147 SER cc_start: 0.8874 (p) cc_final: 0.8592 (t)
REVERT: B  197 ARG cc_start: 0.7240 (mmm160) cc_final: 0.7037 (mmm-85)
REVERT: R   35 LYS cc_start: 0.6367 (pttt) cc_final: 0.6162 (tppt)
REVERT: R  144 PHE cc_start: 0.6705 (m-80) cc_final: 0.6324 (m-10)
REVERT: R  173 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7422 (ttpt)
  outliers start: 21
  outliers final: 15
  residues processed: 148
  average time/residue: 0.1931
  time to fit residues: 38.0749
Evaluate side-chains
  148 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.152153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122425 restraints weight = 7847.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124696 restraints weight = 6038.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126442 restraints weight = 5008.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7165  Z= 0.182
  Angle     :  0.497   7.469   9706  Z= 0.269
  Chirality :  0.041   0.134   1125
  Planarity :  0.004   0.045   1213
  Dihedral  :  5.244  54.031    976
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.93 %
    Favored  : 83.31 %
  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:  0.70 (0.29), residues: 876
  helix:  2.17 (0.26), residues: 416
  sheet: -0.21 (0.37), residues: 174
  loop : -1.73 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 188 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.036   0.002   PHE R 290 
 TYR   0.015   0.001   TYR B  85 
 ARG   0.004   0.000   ARG B  68 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.8377 (pttt) cc_final: 0.8041 (pttm)
REVERT: B   88 ASN cc_start: 0.8378 (m110) cc_final: 0.7779 (m-40)
REVERT: B  197 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6993 (mmm-85)
REVERT: B  297 TRP cc_start: 0.8774 (m100) cc_final: 0.8239 (m100)
REVERT: R  144 PHE cc_start: 0.6638 (m-80) cc_final: 0.6322 (m-10)
REVERT: R  173 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7527 (ttpt)
  outliers start: 21
  outliers final: 17
  residues processed: 148
  average time/residue: 0.1919
  time to fit residues: 38.4117
Evaluate side-chains
  156 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue   78 HIS
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.145657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.115707 restraints weight = 8081.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117962 restraints weight = 6241.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.119480 restraints weight = 5194.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   7165  Z= 0.402
  Angle     :  0.619   7.531   9706  Z= 0.335
  Chirality :  0.045   0.141   1125
  Planarity :  0.004   0.048   1213
  Dihedral  :  5.889  59.676    976
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.85 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.29), residues: 876
  helix:  1.66 (0.26), residues: 419
  sheet: -0.54 (0.37), residues: 169
  loop : -1.75 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B 169 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.036   0.003   PHE R 290 
 TYR   0.013   0.002   TYR B  85 
 ARG   0.004   0.000   ARG R 108 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 ASP cc_start: 0.7331 (t70) cc_final: 0.7121 (m-30)
REVERT: B   88 ASN cc_start: 0.8463 (m110) cc_final: 0.7882 (m-40)
REVERT: B  147 SER cc_start: 0.8910 (p) cc_final: 0.8601 (t)
REVERT: B  164 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8551 (p)
REVERT: R  144 PHE cc_start: 0.6636 (m-80) cc_final: 0.6347 (m-10)
  outliers start: 22
  outliers final: 20
  residues processed: 147
  average time/residue: 0.1933
  time to fit residues: 37.9442
Evaluate side-chains
  148 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue   71 ILE
Chi-restraints excluded: chain R residue   78 HIS
Chi-restraints excluded: chain R residue  111 ILE
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  281 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0980
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.120355 restraints weight = 7904.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123132 restraints weight = 5735.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125106 restraints weight = 4617.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7165  Z= 0.164
  Angle     :  0.497   6.954   9706  Z= 0.270
  Chirality :  0.041   0.142   1125
  Planarity :  0.004   0.044   1213
  Dihedral  :  5.238  53.394    976
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.90 %
    Favored  : 81.73 %
  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:  0.64 (0.29), residues: 876
  helix:  2.18 (0.26), residues: 415
  sheet: -0.48 (0.37), residues: 175
  loop : -1.67 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP R 188 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.030   0.002   PHE R 290 
 TYR   0.020   0.001   TYR R 179 
 ARG   0.002   0.000   ARG B 256 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.7714 (mtt) cc_final: 0.7443 (mtm)
REVERT: B   88 ASN cc_start: 0.8482 (m110) cc_final: 0.7885 (m-40)
REVERT: B  297 TRP cc_start: 0.8743 (m100) cc_final: 0.8205 (m100)
REVERT: R  144 PHE cc_start: 0.6735 (m-80) cc_final: 0.6422 (m-10)
REVERT: R  173 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7775 (ttpt)
  outliers start: 18
  outliers final: 17
  residues processed: 144
  average time/residue: 0.1818
  time to fit residues: 35.2925
Evaluate side-chains
  149 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue   78 HIS
Chi-restraints excluded: chain R residue  111 ILE
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  281 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0050
   chunk 30 optimal weight:    0.0270
   chunk 83 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.7254

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.123160 restraints weight = 7938.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.125785 restraints weight = 5994.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127535 restraints weight = 4885.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7165  Z= 0.164
  Angle     :  0.494   6.998   9706  Z= 0.266
  Chirality :  0.041   0.144   1125
  Planarity :  0.004   0.045   1213
  Dihedral  :  4.977  50.715    976
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.90 %
    Favored  : 81.60 %
  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:  0.88 (0.30), residues: 876
  helix:  2.37 (0.26), residues: 415
  sheet: -0.45 (0.37), residues: 177
  loop : -1.48 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP R 188 
 HIS   0.002   0.000   HIS A 214 
 PHE   0.029   0.001   PHE R 290 
 TYR   0.020   0.001   TYR R 179 
 ARG   0.002   0.000   ARG R 108 

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8429 (m110) cc_final: 0.7852 (m-40)
REVERT: B  297 TRP cc_start: 0.8748 (m100) cc_final: 0.8257 (m100)
REVERT: R  144 PHE cc_start: 0.6793 (m-80) cc_final: 0.6474 (m-10)
REVERT: R  173 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7711 (ttpt)
  outliers start: 19
  outliers final: 17
  residues processed: 154
  average time/residue: 0.1793
  time to fit residues: 37.5202
Evaluate side-chains
  157 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   49 VAL
Chi-restraints excluded: chain R residue   78 HIS
Chi-restraints excluded: chain R residue  111 ILE
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  173 LYS
Chi-restraints excluded: chain R residue  281 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.152671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.122982 restraints weight = 7921.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.125449 restraints weight = 5963.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127414 restraints weight = 4888.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7165  Z= 0.183
  Angle     :  0.507   6.967   9706  Z= 0.272
  Chirality :  0.041   0.184   1125
  Planarity :  0.004   0.045   1213
  Dihedral  :  5.006  51.159    976
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.37 %
    Favored  : 82.00 %
  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:  0.94 (0.30), residues: 876
  helix:  2.39 (0.26), residues: 415
  sheet: -0.41 (0.37), residues: 177
  loop : -1.41 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP R 188 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.030   0.002   PHE R 290 
 TYR   0.021   0.001   TYR R 179 
 ARG   0.001   0.000   ARG R 108 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2292.78 seconds
wall clock time: 40 minutes 49.80 seconds (2449.80 seconds total)