Starting phenix.real_space_refine
on Wed Feb 12 01:25:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d9h_7835/02_2025/6d9h_7835.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d9h_7835/02_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_7835/02_2025/6d9h_7835.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d9h_7835/02_2025/6d9h_7835.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d9h_7835/02_2025/6d9h_7835.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d9h_7835/02_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-5592/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: 4.39, per 1000 atoms: 0.63
  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 987.5 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: 0.82
  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: 2.12

  Time building geometry restraints manager: 1.92 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:             0.240
  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:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.260
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.980
-------------------------------------------------------------------------------
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  : 0.755 
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: 0.1961
  time to fit residues: 48.5957
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  : 0.885 
-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.153477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.122081 restraints weight = 7779.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125334 restraints weight = 6257.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.126202 restraints weight = 4652.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
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 : 5.74
  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  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8297 (t0)
REVERT: A  322 THR cc_start: 0.8900 (m) cc_final: 0.8531 (p)
REVERT: B   88 ASN cc_start: 0.8411 (m110) cc_final: 0.7767 (m110)
REVERT: B   98 SER cc_start: 0.8156 (m) cc_final: 0.7849 (t)
REVERT: R  178 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7296 (mt-10)
REVERT: R  275 PHE cc_start: 0.8622 (p90) cc_final: 0.8283 (p90)
  outliers start: 11
  outliers final: 7
  residues processed: 146
  average time/residue: 0.1999
  time to fit residues: 38.9647
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  : 0.751 
-------------------------------------------------------------------------------
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:    2.9990
   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:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.148498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116351 restraints weight = 8007.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119326 restraints weight = 6312.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.120684 restraints weight = 4883.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7165  Z= 0.263
  Angle     :  0.562   6.193   9706  Z= 0.303
  Chirality :  0.043   0.170   1125
  Planarity :  0.004   0.049   1213
  Dihedral  :  5.661  56.628    976
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 10.25 %
    Favored  : 87.39 %
  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:  0.17 (0.29), residues: 876
  helix:  1.65 (0.26), residues: 415
  sheet: -0.35 (0.38), residues: 170
  loop : -1.88 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 146 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.031   0.002   PHE R 275 
 TYR   0.014   0.002   TYR R 115 
 ARG   0.005   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
  156 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8402 (m110) cc_final: 0.7811 (m-40)
REVERT: B  297 TRP cc_start: 0.8799 (m100) cc_final: 0.8216 (m-10)
REVERT: R  173 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7255 (ttpt)
REVERT: R  178 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7368 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2189
  time to fit residues: 43.0037
Evaluate side-chains
  143 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
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  260 GLU
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  315 VAL
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:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R  38 GLN

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 = 0.153183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.123421 restraints weight = 7932.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125772 restraints weight = 6080.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127420 restraints weight = 5025.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7165  Z= 0.172
  Angle     :  0.494   7.342   9706  Z= 0.267
  Chirality :  0.041   0.139   1125
  Planarity :  0.004   0.046   1213
  Dihedral  :  5.219  51.525    976
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.96 %
    Favored  : 85.41 %
  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:  0.43 (0.29), residues: 876
  helix:  1.97 (0.26), residues: 416
  sheet: -0.34 (0.37), residues: 169
  loop : -1.88 (0.34), 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  91 
 PHE   0.023   0.001   PHE R 275 
 TYR   0.017   0.001   TYR R 115 
 ARG   0.002   0.000   ARG A 243 

*********************** 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
  159 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8198 (ttpp)
REVERT: B   88 ASN cc_start: 0.8380 (m110) cc_final: 0.7810 (m-40)
REVERT: B  123 ILE cc_start: 0.8805 (mm) cc_final: 0.8559 (mt)
REVERT: R  173 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7284 (ttpt)
REVERT: R  178 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7368 (mt-10)
  outliers start: 20
  outliers final: 17
  residues processed: 147
  average time/residue: 0.2230
  time to fit residues: 43.9649
Evaluate side-chains
  142 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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  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  164 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  340 ASN
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  178 GLU
Chi-restraints excluded: chain R residue  275 PHE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    0.2980
   chunk 83 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.152928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.122790 restraints weight = 7867.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125213 restraints weight = 6071.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.126796 restraints weight = 5025.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2711

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= 0.179
  Angle     :  0.488   6.103   9706  Z= 0.265
  Chirality :  0.041   0.138   1125
  Planarity :  0.004   0.045   1213
  Dihedral  :  5.236  52.624    976
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.09 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.29), residues: 876
  helix:  2.11 (0.26), residues: 416
  sheet: -0.27 (0.37), residues: 172
  loop : -1.77 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 188 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.022   0.001   PHE R 275 
 TYR   0.017   0.001   TYR R 115 
 ARG   0.007   0.000   ARG R 108 

*********************** 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
  156 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8182 (ttpp)
REVERT: B   88 ASN cc_start: 0.8397 (m110) cc_final: 0.7838 (m-40)
REVERT: B  105 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8513 (t80)
REVERT: B  123 ILE cc_start: 0.8815 (mm) cc_final: 0.8570 (mt)
REVERT: R  173 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7325 (ttpt)
  outliers start: 24
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1927
  time to fit residues: 37.7377
Evaluate side-chains
  145 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
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  330 THR
Chi-restraints excluded: chain B residue  105 TYR
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  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
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:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.149603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.119421 restraints weight = 7928.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.120967 restraints weight = 6465.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122423 restraints weight = 5470.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7165  Z= 0.273
  Angle     :  0.531   5.885   9706  Z= 0.288
  Chirality :  0.043   0.138   1125
  Planarity :  0.004   0.048   1213
  Dihedral  :  5.544  57.400    976
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.96 %
    Favored  : 85.41 %
  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:  0.42 (0.29), residues: 876
  helix:  1.95 (0.26), residues: 416
  sheet: -0.47 (0.36), residues: 181
  loop : -1.79 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 188 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.020   0.002   PHE R 275 
 TYR   0.014   0.001   TYR R 115 
 ARG   0.005   0.000   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
  159 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8176 (ttpp)
REVERT: B   88 ASN cc_start: 0.8435 (m110) cc_final: 0.7859 (m-40)
REVERT: B  105 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8564 (t80)
REVERT: B  147 SER cc_start: 0.8856 (p) cc_final: 0.8566 (t)
REVERT: R  144 PHE cc_start: 0.6749 (m-10) cc_final: 0.6475 (m-10)
REVERT: R  173 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7494 (ttpt)
REVERT: R  290 PHE cc_start: 0.8108 (t80) cc_final: 0.7896 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 148
  average time/residue: 0.2145
  time to fit residues: 42.6380
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  : 0.810 
-------------------------------------------------------------------------------
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  330 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  105 TYR
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0870
   chunk 49 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** 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 = 0.3759 r_free = 0.3759 target = 0.153077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.123207 restraints weight = 7806.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125483 restraints weight = 6005.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.127045 restraints weight = 5017.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2980

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= 0.159
  Angle     :  0.486   8.874   9706  Z= 0.262
  Chirality :  0.041   0.142   1125
  Planarity :  0.004   0.044   1213
  Dihedral  :  5.216  54.140    976
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.01 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 876
  helix:  2.25 (0.26), residues: 416
  sheet: -0.45 (0.37), residues: 176
  loop : -1.69 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 189 
 PHE   0.020   0.001   PHE R 275 
 TYR   0.018   0.001   TYR R 115 
 ARG   0.006   0.000   ARG R 108 

*********************** 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
  154 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8168 (ttpp)
REVERT: B   88 ASN cc_start: 0.8399 (m110) cc_final: 0.7839 (m-40)
REVERT: B  105 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (t80)
REVERT: B  123 ILE cc_start: 0.8828 (mm) cc_final: 0.8610 (mt)
REVERT: B  234 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8140 (m-80)
REVERT: B  297 TRP cc_start: 0.8777 (m100) cc_final: 0.8241 (m100)
REVERT: R  144 PHE cc_start: 0.6801 (m-10) cc_final: 0.6570 (m-10)
REVERT: R  173 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7521 (ttpt)
  outliers start: 19
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1885
  time to fit residues: 36.8152
Evaluate side-chains
  154 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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  105 TYR
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  234 PHE
Chi-restraints excluded: chain B residue  260 GLU
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   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:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 80 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0670
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.125265 restraints weight = 7799.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126258 restraints weight = 6702.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127384 restraints weight = 5903.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7165  Z= 0.159
  Angle     :  0.499   9.744   9706  Z= 0.263
  Chirality :  0.040   0.142   1125
  Planarity :  0.004   0.043   1213
  Dihedral  :  4.988  51.399    976
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.80 %
    Favored  : 83.44 %
  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:  0.89 (0.30), residues: 876
  helix:  2.39 (0.26), residues: 416
  sheet: -0.39 (0.37), residues: 177
  loop : -1.55 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 169 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.037   0.001   PHE R 290 
 TYR   0.017   0.001   TYR R 115 
 ARG   0.005   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
  162 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8168 (ttpp)
REVERT: B   88 ASN cc_start: 0.8398 (m110) cc_final: 0.7869 (m-40)
REVERT: B  105 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8561 (t80)
REVERT: B  123 ILE cc_start: 0.8855 (mm) cc_final: 0.8643 (mt)
REVERT: B  234 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8143 (m-80)
REVERT: B  297 TRP cc_start: 0.8807 (m100) cc_final: 0.8434 (m100)
REVERT: B  339 TRP cc_start: 0.8664 (m100) cc_final: 0.8302 (m-10)
REVERT: R  173 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7621 (ttpt)
  outliers start: 21
  outliers final: 15
  residues processed: 154
  average time/residue: 0.1788
  time to fit residues: 37.2910
Evaluate side-chains
  150 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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  105 TYR
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  234 PHE
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.147676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118079 restraints weight = 8014.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.120241 restraints weight = 6148.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.121812 restraints weight = 5139.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7165  Z= 0.320
  Angle     :  0.577   9.018   9706  Z= 0.309
  Chirality :  0.044   0.154   1125
  Planarity :  0.004   0.052   1213
  Dihedral  :  5.527  57.209    976
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.19 %
    Favored  : 82.79 %
  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:  0.52 (0.29), residues: 876
  helix:  1.98 (0.26), residues: 416
  sheet: -0.51 (0.37), residues: 175
  loop : -1.59 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 189 
 PHE   0.035   0.002   PHE R 290 
 TYR   0.013   0.001   TYR R 115 
 ARG   0.007   0.000   ARG R 108 

*********************** 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
  160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 ASP cc_start: 0.7388 (t70) cc_final: 0.7103 (m-30)
REVERT: B   88 ASN cc_start: 0.8406 (m110) cc_final: 0.7833 (m-40)
REVERT: B  147 SER cc_start: 0.8917 (p) cc_final: 0.8620 (t)
REVERT: R  144 PHE cc_start: 0.6873 (m-10) cc_final: 0.6630 (m-10)
REVERT: R  173 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7807 (ttpt)
  outliers start: 23
  outliers final: 20
  residues processed: 147
  average time/residue: 0.1837
  time to fit residues: 36.3351
Evaluate side-chains
  153 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
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   44 GLN
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.152012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.122936 restraints weight = 7954.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124148 restraints weight = 6747.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125463 restraints weight = 5871.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7165  Z= 0.178
  Angle     :  0.521   8.912   9706  Z= 0.278
  Chirality :  0.041   0.176   1125
  Planarity :  0.004   0.049   1213
  Dihedral  :  5.193  53.447    976
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.98 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.29), residues: 876
  helix:  2.21 (0.26), residues: 416
  sheet: -0.42 (0.38), residues: 167
  loop : -1.50 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.031   0.002   PHE R 290 
 TYR   0.018   0.001   TYR R 115 
 ARG   0.008   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
  156 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7435 (mp10) cc_final: 0.7101 (mp10)
REVERT: B   88 ASN cc_start: 0.8380 (m110) cc_final: 0.7855 (m-40)
REVERT: B  123 ILE cc_start: 0.8845 (mm) cc_final: 0.8628 (mt)
REVERT: B  234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8111 (m-10)
REVERT: B  297 TRP cc_start: 0.8767 (m100) cc_final: 0.8271 (m100)
REVERT: R  144 PHE cc_start: 0.6792 (m-10) cc_final: 0.6575 (m-10)
REVERT: R  173 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7714 (ttpt)
  outliers start: 19
  outliers final: 16
  residues processed: 147
  average time/residue: 0.1801
  time to fit residues: 35.7067
Evaluate side-chains
  152 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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   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  234 PHE
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 210 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.120623 restraints weight = 8006.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.121380 restraints weight = 6590.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122535 restraints weight = 5940.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7165  Z= 0.260
  Angle     :  0.562   9.417   9706  Z= 0.299
  Chirality :  0.043   0.207   1125
  Planarity :  0.004   0.050   1213
  Dihedral  :  5.359  54.987    976
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.16 %
    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:  0.60 (0.29), residues: 876
  helix:  2.09 (0.26), residues: 416
  sheet: -0.60 (0.37), residues: 175
  loop : -1.53 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.032   0.002   PHE R 290 
 TYR   0.021   0.002   TYR R 179 
 ARG   0.007   0.000   ARG R 108 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2253.52 seconds
wall clock time: 41 minutes 25.67 seconds (2485.67 seconds total)