Starting phenix.real_space_refine
on Wed Sep 17 08:06:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d9h_7835/09_2025/6d9h_7835.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d9h_7835/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2025/6d9h_7835.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2025/6d9h_7835.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2025/6d9h_7835.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2025/6d9h_7835.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.74, per 1000 atoms: 0.25
  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: 0.67
  Conformation dependent library (CDL) restraints added in 346.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.19
  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: 1.13

  Time building geometry restraints manager: 0.87 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: 9280
        1.97 -     3.94: 352
        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:             0.430
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.070
-------------------------------------------------------------------------------
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   7167  Z= 0.273
  Angle     :  0.933   9.857   9710  Z= 0.518
  Chirality :  0.056   0.291   1125
  Planarity :  0.007   0.050   1213
  Dihedral  :  9.573  76.099   2595
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.11
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG B  68 
 TYR   0.021   0.003   TYR R 179 
 PHE   0.039   0.004   PHE R 171 
 TRP   0.049   0.004   TRP R 146 
 HIS   0.007   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 7165)
  covalent geometry    : angle       0.93316 ( 9706)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       1.44368 (    4)
  hydrogen bonds       : bond        0.11970 (  396)
  hydrogen bonds       : angle       5.90794 ( 1161)

*********************** 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  : 0.316 
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: 0.7063 (t0)
REVERT: R   89 ILE cc_start: 0.8617 (mt) cc_final: 0.8366 (mt)
REVERT: R  117 MET cc_start: 0.7175 (ptm) cc_final: 0.6953 (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: 0.0897
  time to fit residues: 22.5428
Evaluate side-chains
  128 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 196 HIS
A 295 ASN
A 332 ASN
B   6 GLN
B  88 ASN
B 239 ASN
B 266 HIS
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 = 0.3827 r_free = 0.3827 target = 0.160865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.129856 restraints weight = 7675.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.130954 restraints weight = 6712.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.132279 restraints weight = 5720.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132817 restraints weight = 4797.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.133549 restraints weight = 4592.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7167  Z= 0.192
  Angle     :  0.591   5.841   9710  Z= 0.321
  Chirality :  0.044   0.174   1125
  Planarity :  0.005   0.063   1213
  Dihedral  :  6.098  60.042    976
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.28), residues: 876
  helix:  1.13 (0.25), residues: 414
  sheet: -0.45 (0.38), residues: 164
  loop : -2.23 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 108 
 TYR   0.016   0.002   TYR G  40 
 PHE   0.037   0.002   PHE R 275 
 TRP   0.027   0.003   TRP R 146 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 7165)
  covalent geometry    : angle       0.59065 ( 9706)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       0.83166 (    4)
  hydrogen bonds       : bond        0.04543 (  396)
  hydrogen bonds       : angle       4.73825 ( 1161)

*********************** 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
  153 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8439 (m110) cc_final: 0.7773 (m110)
REVERT: R  108 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8250 (mtp85)
REVERT: R  178 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7275 (mt-10)
REVERT: R  275 PHE cc_start: 0.8651 (p90) cc_final: 0.8289 (p90)
  outliers start: 13
  outliers final: 10
  residues processed: 146
  average time/residue: 0.0883
  time to fit residues: 17.3190
Evaluate side-chains
  140 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  340 ASN
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  286 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.151700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.120410 restraints weight = 7832.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123192 restraints weight = 6335.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124656 restraints weight = 4960.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.124883 restraints weight = 4230.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125447 restraints weight = 4032.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7167  Z= 0.123
  Angle     :  0.508   6.373   9710  Z= 0.275
  Chirality :  0.041   0.167   1125
  Planarity :  0.004   0.065   1213
  Dihedral  :  5.479  54.107    976
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.51 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.29), residues: 876
  helix:  1.78 (0.26), residues: 415
  sheet: -0.35 (0.38), residues: 169
  loop : -1.94 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 108 
 TYR   0.009   0.001   TYR R 115 
 PHE   0.033   0.002   PHE R 275 
 TRP   0.022   0.002   TRP R 188 
 HIS   0.002   0.000   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7165)
  covalent geometry    : angle       0.50748 ( 9706)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       0.60190 (    4)
  hydrogen bonds       : bond        0.03864 (  396)
  hydrogen bonds       : angle       4.36161 ( 1161)

*********************** 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
  162 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8389 (m110) cc_final: 0.7795 (m-40)
REVERT: R   45 PHE cc_start: 0.6890 (m-80) cc_final: 0.6627 (m-80)
REVERT: R  173 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7273 (ttpt)
REVERT: R  178 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7378 (mt-10)
  outliers start: 17
  outliers final: 11
  residues processed: 154
  average time/residue: 0.0789
  time to fit residues: 16.5985
Evaluate side-chains
  134 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  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  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 2 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 68 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.150894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.121368 restraints weight = 7923.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123514 restraints weight = 6125.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125108 restraints weight = 5117.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126363 restraints weight = 4501.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127151 restraints weight = 4099.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
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      :  0.004   0.035   7167  Z= 0.162
  Angle     :  0.535   6.909   9710  Z= 0.288
  Chirality :  0.042   0.145   1125
  Planarity :  0.005   0.086   1213
  Dihedral  :  5.458  53.060    976
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 11.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.29), residues: 876
  helix:  1.84 (0.26), residues: 416
  sheet: -0.46 (0.38), residues: 173
  loop : -1.94 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 108 
 TYR   0.010   0.001   TYR R 115 
 PHE   0.023   0.002   PHE R 275 
 TRP   0.020   0.002   TRP R 188 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7165)
  covalent geometry    : angle       0.53497 ( 9706)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.67896 (    4)
  hydrogen bonds       : bond        0.04009 (  396)
  hydrogen bonds       : angle       4.31945 ( 1161)

*********************** 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
  154 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8418 (m110) cc_final: 0.7825 (m-40)
REVERT: B  297 TRP cc_start: 0.8815 (m100) cc_final: 0.8285 (m-10)
REVERT: R  173 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7350 (ttpt)
REVERT: R  178 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7369 (mt-10)
REVERT: R  290 PHE cc_start: 0.8009 (t80) cc_final: 0.7800 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0809
  time to fit residues: 15.6949
Evaluate side-chains
  141 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  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  294 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 76 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.146294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117482 restraints weight = 8151.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.117542 restraints weight = 7439.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.118917 restraints weight = 6516.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.119399 restraints weight = 5600.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.119843 restraints weight = 5220.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7167  Z= 0.224
  Angle     :  0.587   6.183   9710  Z= 0.317
  Chirality :  0.045   0.145   1125
  Planarity :  0.005   0.094   1213
  Dihedral  :  5.841  56.333    976
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 12.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.29), residues: 876
  helix:  1.59 (0.26), residues: 416
  sheet: -0.51 (0.37), residues: 171
  loop : -1.86 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 108 
 TYR   0.010   0.001   TYR B 124 
 PHE   0.021   0.002   PHE R 275 
 TRP   0.024   0.003   TRP R 188 
 HIS   0.005   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 7165)
  covalent geometry    : angle       0.58704 ( 9706)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       0.78006 (    4)
  hydrogen bonds       : bond        0.04487 (  396)
  hydrogen bonds       : angle       4.53195 ( 1161)

*********************** 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
  160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8431 (m110) cc_final: 0.7845 (m-40)
REVERT: B  147 SER cc_start: 0.8896 (p) cc_final: 0.8560 (t)
REVERT: B  155 ASN cc_start: 0.8577 (t0) cc_final: 0.8282 (t0)
REVERT: R   35 LYS cc_start: 0.6307 (pttt) cc_final: 0.6092 (tppt)
REVERT: R  144 PHE cc_start: 0.6795 (m-10) cc_final: 0.6536 (m-10)
REVERT: R  178 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7384 (mt-10)
  outliers start: 25
  outliers final: 21
  residues processed: 147
  average time/residue: 0.0919
  time to fit residues: 17.9308
Evaluate side-chains
  154 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  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  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  315 VAL
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  104 ASP
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   chunk 70 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R  38 GLN
R 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.163146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131332 restraints weight = 7604.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.133220 restraints weight = 6891.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.134389 restraints weight = 5601.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.135150 restraints weight = 4965.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.135926 restraints weight = 4467.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7167  Z= 0.107
  Angle     :  0.479   6.248   9710  Z= 0.259
  Chirality :  0.040   0.142   1125
  Planarity :  0.004   0.071   1213
  Dihedral  :  5.137  51.287    976
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.29), residues: 876
  helix:  2.14 (0.26), residues: 416
  sheet: -0.42 (0.37), residues: 174
  loop : -1.78 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  68 
 TYR   0.013   0.001   TYR R 115 
 PHE   0.039   0.001   PHE R 290 
 TRP   0.020   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7165)
  covalent geometry    : angle       0.47920 ( 9706)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       0.55663 (    4)
  hydrogen bonds       : bond        0.03525 (  396)
  hydrogen bonds       : angle       4.11303 ( 1161)

*********************** 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
  166 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8530 (ptp90) cc_final: 0.8323 (ttm110)
REVERT: B   88 ASN cc_start: 0.8416 (m110) cc_final: 0.7854 (m-40)
REVERT: B  123 ILE cc_start: 0.8835 (mm) cc_final: 0.8589 (mt)
REVERT: B  234 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8087 (m-10)
REVERT: B  297 TRP cc_start: 0.8789 (m100) cc_final: 0.8298 (m-10)
REVERT: R  173 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7453 (ttpt)
  outliers start: 21
  outliers final: 15
  residues processed: 156
  average time/residue: 0.0917
  time to fit residues: 19.1402
Evaluate side-chains
  153 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  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 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  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  283 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.151494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120074 restraints weight = 7836.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122794 restraints weight = 5720.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.124867 restraints weight = 4630.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126025 restraints weight = 3971.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127178 restraints weight = 3591.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7167  Z= 0.126
  Angle     :  0.500   9.273   9710  Z= 0.266
  Chirality :  0.041   0.139   1125
  Planarity :  0.004   0.075   1213
  Dihedral  :  5.121  51.141    976
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.40 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.29), residues: 876
  helix:  2.26 (0.26), residues: 416
  sheet: -0.47 (0.37), residues: 182
  loop : -1.68 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.010   0.001   TYR R 115 
 PHE   0.031   0.002   PHE R 290 
 TRP   0.021   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7165)
  covalent geometry    : angle       0.50029 ( 9706)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       0.58460 (    4)
  hydrogen bonds       : bond        0.03621 (  396)
  hydrogen bonds       : angle       4.12091 ( 1161)

*********************** 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
  163 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8432 (m110) cc_final: 0.7846 (m-40)
REVERT: B  123 ILE cc_start: 0.8851 (mm) cc_final: 0.8607 (mt)
REVERT: B  197 ARG cc_start: 0.7354 (mmm160) cc_final: 0.7051 (mmm-85)
REVERT: B  297 TRP cc_start: 0.8811 (m100) cc_final: 0.8328 (m-10)
REVERT: R  173 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7496 (ttpt)
  outliers start: 20
  outliers final: 17
  residues processed: 155
  average time/residue: 0.0888
  time to fit residues: 18.5371
Evaluate side-chains
  153 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  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  290 ASP
Chi-restraints excluded: chain B residue  294 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  175 ILE
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  283 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0030
   chunk 26 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.7392

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.152804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121324 restraints weight = 7894.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124193 restraints weight = 5734.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.126290 restraints weight = 4601.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.127730 restraints weight = 3947.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.128850 restraints weight = 3533.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7167  Z= 0.112
  Angle     :  0.498   8.844   9710  Z= 0.265
  Chirality :  0.040   0.140   1125
  Planarity :  0.004   0.071   1213
  Dihedral  :  4.942  48.958    976
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.88 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.30), residues: 876
  helix:  2.40 (0.26), residues: 416
  sheet: -0.36 (0.38), residues: 176
  loop : -1.58 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 214 
 TYR   0.013   0.001   TYR R 115 
 PHE   0.028   0.001   PHE R 290 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7165)
  covalent geometry    : angle       0.49799 ( 9706)
  SS BOND              : bond        0.00112 (    2)
  SS BOND              : angle       0.50400 (    4)
  hydrogen bonds       : bond        0.03442 (  396)
  hydrogen bonds       : angle       4.00976 ( 1161)

*********************** 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
  163 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8367 (m110) cc_final: 0.7818 (m-40)
REVERT: B  123 ILE cc_start: 0.8854 (mm) cc_final: 0.8615 (mt)
REVERT: B  197 ARG cc_start: 0.7358 (mmm160) cc_final: 0.6924 (mmm-85)
REVERT: B  234 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8003 (m-10)
REVERT: B  297 TRP cc_start: 0.8768 (m100) cc_final: 0.8361 (m100)
  outliers start: 23
  outliers final: 21
  residues processed: 153
  average time/residue: 0.0906
  time to fit residues: 18.6761
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  : 0.284 
-------------------------------------------------------------------------------
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  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  290 ASP
Chi-restraints excluded: chain B residue  294 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  104 ASP
Chi-restraints excluded: chain R residue  111 ILE
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  175 ILE
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  283 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.153651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123546 restraints weight = 7808.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126116 restraints weight = 5866.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.127786 restraints weight = 4797.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.129266 restraints weight = 4177.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.129972 restraints weight = 3769.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7167  Z= 0.110
  Angle     :  0.507   8.751   9710  Z= 0.267
  Chirality :  0.040   0.142   1125
  Planarity :  0.005   0.091   1213
  Dihedral  :  4.826  47.233    976
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.06 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.30), residues: 876
  helix:  2.50 (0.26), residues: 416
  sheet: -0.28 (0.38), residues: 176
  loop : -1.46 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 214 
 TYR   0.013   0.001   TYR R 115 
 PHE   0.025   0.001   PHE R 290 
 TRP   0.023   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7165)
  covalent geometry    : angle       0.50700 ( 9706)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       0.50199 (    4)
  hydrogen bonds       : bond        0.03343 (  396)
  hydrogen bonds       : angle       3.98042 ( 1161)

*********************** 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
  168 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8371 (m110) cc_final: 0.7808 (m-40)
REVERT: B  123 ILE cc_start: 0.8831 (mm) cc_final: 0.8610 (mt)
REVERT: B  197 ARG cc_start: 0.7267 (mmm160) cc_final: 0.6981 (mmm-85)
REVERT: B  234 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7948 (m-10)
REVERT: B  297 TRP cc_start: 0.8785 (m100) cc_final: 0.8397 (m-10)
  outliers start: 22
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0811
  time to fit residues: 17.4167
Evaluate side-chains
  157 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  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  290 ASP
Chi-restraints excluded: chain B residue  294 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  104 ASP
Chi-restraints excluded: chain R residue  111 ILE
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  175 ILE
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  283 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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**
R 280 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.152526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.122204 restraints weight = 7866.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.124573 restraints weight = 5934.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.126609 restraints weight = 4881.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128027 restraints weight = 4237.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128359 restraints weight = 3806.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7167  Z= 0.124
  Angle     :  0.525   8.683   9710  Z= 0.277
  Chirality :  0.041   0.183   1125
  Planarity :  0.005   0.092   1213
  Dihedral  :  4.906  47.951    976
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.30), residues: 876
  helix:  2.48 (0.26), residues: 416
  sheet: -0.31 (0.38), residues: 176
  loop : -1.39 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 214 
 TYR   0.013   0.001   TYR G  40 
 PHE   0.025   0.001   PHE R 290 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7165)
  covalent geometry    : angle       0.52483 ( 9706)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       0.50601 (    4)
  hydrogen bonds       : bond        0.03452 (  396)
  hydrogen bonds       : angle       3.96720 ( 1161)

********************** 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
  160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8373 (m110) cc_final: 0.7811 (m-40)
REVERT: B  123 ILE cc_start: 0.8845 (mm) cc_final: 0.8614 (mt)
REVERT: B  197 ARG cc_start: 0.7258 (mmm160) cc_final: 0.6964 (mmm-85)
REVERT: B  234 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7974 (m-10)
REVERT: B  297 TRP cc_start: 0.8799 (m100) cc_final: 0.8387 (m-10)
  outliers start: 22
  outliers final: 20
  residues processed: 150
  average time/residue: 0.0848
  time to fit residues: 17.3811
Evaluate side-chains
  159 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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  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  290 ASP
Chi-restraints excluded: chain B residue  294 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  104 ASP
Chi-restraints excluded: chain R residue  111 ILE
Chi-restraints excluded: chain R residue  159 ASN
Chi-restraints excluded: chain R residue  175 ILE
Chi-restraints excluded: chain R residue  275 PHE
Chi-restraints excluded: chain R residue  281 SER
Chi-restraints excluded: chain R residue  283 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 54 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0030
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7992

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.153357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.123034 restraints weight = 7791.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.125652 restraints weight = 5880.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127525 restraints weight = 4812.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.128737 restraints weight = 4190.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.129641 restraints weight = 3793.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7167  Z= 0.117
  Angle     :  0.522   9.464   9710  Z= 0.276
  Chirality :  0.041   0.202   1125
  Planarity :  0.005   0.088   1213
  Dihedral  :  4.835  47.040    976
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.45 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.30), residues: 876
  helix:  2.48 (0.26), residues: 416
  sheet: -0.38 (0.38), residues: 175
  loop : -1.30 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 214 
 TYR   0.012   0.001   TYR R 115 
 PHE   0.025   0.001   PHE R 290 
 TRP   0.026   0.002   TRP B 169 
 HIS   0.002   0.000   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7165)
  covalent geometry    : angle       0.52242 ( 9706)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       0.48741 (    4)
  hydrogen bonds       : bond        0.03419 (  396)
  hydrogen bonds       : angle       3.95070 ( 1161)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1272.48 seconds
wall clock time: 22 minutes 48.56 seconds (1368.56 seconds total)