Starting phenix.real_space_refine
on Fri Jul  3 12:25:58 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7zxe_15009/07_2026/7zxe_15009.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      93      5.49       5
     S      68      5.16       5
     C    8676      2.51       5
     N    2504      2.21       5
     O    2807      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 106 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14150
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "M"
      Number of atoms: 1567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1567
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 10, 'TRANS': 190}
    Chain: "N"
      Number of atoms: 987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 987
          Classifications: {'DNA': 47}
          Link IDs: {'rna3p': 46}
    Chain: "O"
      Number of atoms: 1422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1422
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 9, 'TRANS': 169}
    Chain: "T"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 921
          Classifications: {'DNA': 46}
          Link IDs: {'rna3p': 45}
    Chain: "U"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 734
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
          Chain breaks: 1
    Chain: "V"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 793
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 1, 'TRANS': 95}
    Chain: "a"
      Number of atoms: 1807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1807
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2977
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 347}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "c"
      Number of atoms: 2516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2516
          Classifications: {'peptide': 303}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
          Chain breaks: 1
    Chain: "d"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 424
          Classifications: {'peptide': 52}
          Link IDs: {'TRANS': 51}
    Chain: "b"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9621  SG  CYS b 221      76.488  68.528  26.048  1.00139.75           S
  ATOM  10418  SG  CYS b 317      72.705  68.101  26.856  1.00147.72           S
  ATOM  10740  SG  CYS b 354      88.563  47.824  28.607  1.00133.30           S
  ATOM  10764  SG  CYS b 357      92.447  47.927  28.524  1.00131.82           S
  ATOM  10955  SG  CYS b 380      90.426  48.557  25.390  1.00131.89           S
  ATOM  10976  SG  CYS b 383      90.645  45.098  26.867  1.00134.69           S

  Time building chain proxies: 3.10, per 1000 atoms: 0.22
  Number of scatterers: 14150
  At special positions: 0
  Unit cell: (135.45, 164.85, 110.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      68     16.00
     P      93     15.00
     O    2807      8.00
     N    2504      7.00
     C    8676      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 533.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN b 501 "
        pdb="ZN    ZN b 501 " - pdb=" NE2 HIS b 313 "
        pdb="ZN    ZN b 501 " - pdb=" NE2 HIS b 319 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 317 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 221 "
      pdb="  ZN b 502 "
        pdb="ZN    ZN b 502 " - pdb=" SG  CYS b 380 "
        pdb="ZN    ZN b 502 " - pdb=" SG  CYS b 383 "
        pdb="ZN    ZN b 502 " - pdb=" SG  CYS b 357 "
        pdb="ZN    ZN b 502 " - pdb=" SG  CYS b 354 "
      Number of angles added : 8


  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2874

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      53.3% alpha, 11.4% beta
      38 base pairs and 71 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'M' and resid 117 through 129
      removed outlier: 3.866A  pdb=" N   ILE M 128 " --> pdb=" O   MET M 124 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 131 through 149
      removed outlier: 3.800A  pdb=" N   VAL M 135 " --> pdb=" O   PRO M 131 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 155 through 171
    Processing helix  chain 'M' and resid 176 through 182
    Processing helix  chain 'M' and resid 187 through 203
    Processing helix  chain 'M' and resid 211 through 222
      removed outlier: 4.067A  pdb=" N   MET M 215 " --> pdb=" O   THR M 211 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   SER M 216 " --> pdb=" O   GLY M 212 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ARG M 217 " --> pdb=" O   ASP M 213 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER M 220 " --> pdb=" O   SER M 216 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 225 through 242
    Processing helix  chain 'M' and resid 249 through 265
    Processing helix  chain 'M' and resid 270 through 279
      removed outlier: 3.828A  pdb=" N   ILE M 274 " --> pdb=" O   THR M 270 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 281 through 292
      removed outlier: 3.640A  pdb=" N   ILE M 292 " --> pdb=" O   SER M 288 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 295 through 300
      removed outlier: 3.773A  pdb=" N   LEU M 299 " --> pdb=" O   ARG M 295 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE M 300 " --> pdb=" O   ALA M 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 295 through 300'
    Processing helix  chain 'O' and resid 179 through 187
    Processing helix  chain 'O' and resid 226 through 244
    Processing helix  chain 'O' and resid 269 through 277
    Processing helix  chain 'O' and resid 317 through 335
      removed outlier: 3.506A  pdb=" N   ILE O 321 " --> pdb=" O   VAL O 317 " (cutoff:3.500A)
      Proline residue:  O 330  - end of helix
    Processing helix  chain 'U' and resid 10 through 33
      removed outlier: 4.422A  pdb=" N   ASP U  27 " --> pdb=" O   ASN U  23 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   ILE U  28 " --> pdb=" O   ASP U  24 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY U  33 " --> pdb=" O   PHE U  29 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 35 through 51
      removed outlier: 3.654A  pdb=" N   LEU U  39 " --> pdb=" O   ASP U  35 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 9 through 25
    Processing helix  chain 'V' and resid 29 through 49
    Processing helix  chain 'a' and resid 6 through 20
      removed outlier: 4.582A  pdb=" N   ASP a  10 " --> pdb=" O   GLY a   6 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 25 through 37
      removed outlier: 3.903A  pdb=" N   PHE a  29 " --> pdb=" O   ARG a  25 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 38 through 42
      removed outlier: 3.993A  pdb=" N   PHE a  42 " --> pdb=" O   GLY a  39 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 47 through 67
    Processing helix  chain 'a' and resid 71 through 88
    Processing helix  chain 'a' and resid 100 through 117
      removed outlier: 4.186A  pdb=" N   ASP a 105 " --> pdb=" O   LEU a 101 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU a 106 " --> pdb=" O   LYS a 102 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 119 through 132
    Processing helix  chain 'a' and resid 166 through 172
      removed outlier: 4.218A  pdb=" N   LYS a 170 " --> pdb=" O   ASP a 166 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 173 through 195
      removed outlier: 3.686A  pdb=" N   SER a 195 " --> pdb=" O   LYS a 191 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 210 through 232
      removed outlier: 4.384A  pdb=" N   ASP a 214 " --> pdb=" O   ASP a 210 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 44 through 55
    Processing helix  chain 'b' and resid 77 through 91
      removed outlier: 3.634A  pdb=" N   ARG b  81 " --> pdb=" O   ALA b  77 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 93 through 104
    Processing helix  chain 'b' and resid 127 through 144
    Processing helix  chain 'b' and resid 150 through 161
    Processing helix  chain 'b' and resid 192 through 196
      removed outlier: 3.698A  pdb=" N   LYS b 196 " --> pdb=" O   HIS b 193 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 221 through 226
      removed outlier: 3.717A  pdb=" N   GLN b 226 " --> pdb=" O   SER b 223 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 242 through 247
    Processing helix  chain 'b' and resid 270 through 280
      removed outlier: 4.448A  pdb=" N   ILE b 274 " --> pdb=" O   LEU b 270 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 380 through 389
      removed outlier: 3.650A  pdb=" N   TYR b 389 " --> pdb=" O   ARG b 385 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 82 through 123
      removed outlier: 4.229A  pdb=" N   CYS c  86 " --> pdb=" O   ASP c  82 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 162 through 171
    Processing helix  chain 'c' and resid 185 through 221
      Proline residue:  c 207  - end of helix
    Processing helix  chain 'c' and resid 225 through 247
    Processing helix  chain 'c' and resid 249 through 255
      removed outlier: 4.287A  pdb=" N   GLY c 255 " --> pdb=" O   GLU c 251 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 262 through 267
      removed outlier: 3.808A  pdb=" N   ILE c 266 " --> pdb=" O   ASP c 262 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 276 through 287
    Processing helix  chain 'c' and resid 298 through 313
    Processing helix  chain 'c' and resid 316 through 324
    Processing helix  chain 'c' and resid 329 through 340
    Processing helix  chain 'c' and resid 350 through 365
    Processing helix  chain 'c' and resid 371 through 376
    Processing helix  chain 'c' and resid 383 through 394
    Processing helix  chain 'd' and resid 2 through 45
    Processing sheet with id=AA1, first strand: chain 'O' and resid 190 through 191
      removed outlier: 4.052A  pdb=" N   LYS O 218 " --> pdb=" O   PHE O 214 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU O 165 " --> pdb=" O   GLY O 260 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   GLY O 260 " --> pdb=" O   LEU O 165 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ASN O 167 " --> pdb=" O   MET O 258 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   MET O 258 " --> pdb=" O   ASN O 167 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   VAL O 169 " --> pdb=" O   GLN O 256 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ASN O 173 " --> pdb=" O   ASP O 252 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   ASP O 252 " --> pdb=" O   ASN O 173 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   MET O 258 " --> pdb=" O   GLY O 314 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLY O 314 " --> pdb=" O   MET O 258 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'U' and resid 363 through 367
      removed outlier: 4.280A  pdb=" N   PHE V  58 " --> pdb=" O   ILE U 371 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   PHE V  58 " --> pdb=" O   PHE V  81 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   PHE V  81 " --> pdb=" O   PHE V  58 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   GLY V  60 " --> pdb=" O   VAL V  79 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   VAL V  79 " --> pdb=" O   GLY V  60 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   LEU V  62 " --> pdb=" O   ASN V  77 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ASN V  77 " --> pdb=" O   LEU V  62 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ASP V  91 " --> pdb=" O   ASP V  78 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   GLU V  80 " --> pdb=" O   LYS V  89 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   LYS V  89 " --> pdb=" O   GLU V  80 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ARG V  82 " --> pdb=" O   LEU V  87 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU V  87 " --> pdb=" O   ARG V  82 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   VAL U 335 " --> pdb=" O   VAL V  96 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   CYS V  98 " --> pdb=" O   VAL U 335 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   CYS U 337 " --> pdb=" O   CYS V  98 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL U 335 " --> pdb=" O   MET U 358 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   MET U 358 " --> pdb=" O   VAL U 335 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   CYS U 337 " --> pdb=" O   GLY U 356 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   GLY U 356 " --> pdb=" O   CYS U 337 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   TYR U 339 " --> pdb=" O   LYS U 354 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   LYS U 354 " --> pdb=" O   TYR U 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'a' and resid 97 through 99
    Processing sheet with id=AA4, first strand: chain 'b' and resid 42 through 43
    Processing sheet with id=AA5, first strand: chain 'b' and resid 290 through 291
      removed outlier: 6.846A  pdb=" N   PHE b 258 " --> pdb=" O   ALA b 291 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   VAL b 320 " --> pdb=" O   LEU b 187 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR b 324 " --> pdb=" O   SER b 183 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   SER b 183 " --> pdb=" O   THR b 324 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ILE b 326 " --> pdb=" O   ILE b 181 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE b 181 " --> pdb=" O   ILE b 326 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   THR b 203 " --> pdb=" O   ILE b 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'b' and resid 377 through 379

    652 hydrogen bonds defined for protein.
    1908 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      98 hydrogen bonds
      196 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      71 stacking parallelities
  Total time for adding SS restraints: 2.68

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3567
        1.33 -     1.45: 3101
        1.45 -     1.57: 7662
        1.57 -     1.69: 184
        1.69 -     1.81: 105
  Bond restraints: 14619
  Sorted by residual:
  bond pdb=" C1'  DC T  24 "
       pdb=" N1   DC T  24 "
    ideal  model  delta    sigma   weight residual
    1.468  1.521 -0.053 1.40e-02 5.10e+03 1.43e+01
  bond pdb=" C1'  DT T -16 "
       pdb=" N1   DT T -16 "
    ideal  model  delta    sigma   weight residual
    1.468  1.520 -0.052 1.40e-02 5.10e+03 1.40e+01
  bond pdb=" C1'  DT T  12 "
       pdb=" N1   DT T  12 "
    ideal  model  delta    sigma   weight residual
    1.468  1.518 -0.050 1.40e-02 5.10e+03 1.26e+01
  bond pdb=" C1'  DT T -18 "
       pdb=" N1   DT T -18 "
    ideal  model  delta    sigma   weight residual
    1.468  1.515 -0.047 1.40e-02 5.10e+03 1.12e+01
  bond pdb=" C1'  DC T   6 "
       pdb=" N1   DC T   6 "
    ideal  model  delta    sigma   weight residual
    1.468  1.515 -0.047 1.40e-02 5.10e+03 1.11e+01
  ... (remaining 14614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 19169
        1.26 -     2.53: 707
        2.53 -     3.79: 214
        3.79 -     5.06: 18
        5.06 -     6.32: 4
  Bond angle restraints: 20112
  Sorted by residual:
  angle pdb=" O4'  DT T   8 "
        pdb=" C1'  DT T   8 "
        pdb=" N1   DT T   8 "
      ideal   model   delta    sigma   weight residual
     108.00  111.05   -3.05 7.00e-01 2.04e+00 1.90e+01
  angle pdb=" N3   DT T -16 "
        pdb=" C4   DT T -16 "
        pdb=" O4   DT T -16 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.89e+01
  angle pdb=" N3   DT N -21 "
        pdb=" C4   DT N -21 "
        pdb=" O4   DT N -21 "
      ideal   model   delta    sigma   weight residual
     119.90  122.46   -2.56 6.00e-01 2.78e+00 1.82e+01
  angle pdb=" N3   DT T -18 "
        pdb=" C4   DT T -18 "
        pdb=" O4   DT T -18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.44   -2.54 6.00e-01 2.78e+00 1.79e+01
  angle pdb=" N3   DT N -23 "
        pdb=" C4   DT N -23 "
        pdb=" O4   DT N -23 "
      ideal   model   delta    sigma   weight residual
     119.90  122.42   -2.52 6.00e-01 2.78e+00 1.77e+01
  ... (remaining 20107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.18: 8000
       31.18 -    62.36: 596
       62.36 -    93.54: 35
       93.54 -   124.72: 1
      124.72 -   155.90: 2
  Dihedral angle restraints: 8634
    sinusoidal: 4224
      harmonic: 4410
  Sorted by residual:
  dihedral pdb=" CA  VAL V  52 "
           pdb=" C   VAL V  52 "
           pdb=" N   ARG V  53 "
           pdb=" CA  ARG V  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.59   27.41     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CA  LYS O 297 "
           pdb=" C   LYS O 297 "
           pdb=" N   PRO O 298 "
           pdb=" CA  PRO O 298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  TYR b  32 "
           pdb=" C   TYR b  32 "
           pdb=" N   GLU b  33 "
           pdb=" CA  GLU b  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 8631 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1715
       0.041 -    0.081: 293
       0.081 -    0.122: 109
       0.122 -    0.162: 86
       0.162 -    0.203: 3
  Chirality restraints: 2206
  Sorted by residual:
  chirality pdb=" CG  LEU d  22 "
            pdb=" CB  LEU d  22 "
            pdb=" CD1 LEU d  22 "
            pdb=" CD2 LEU d  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C3'  DG N  -6 "
            pdb=" C4'  DG N  -6 "
            pdb=" O3'  DG N  -6 "
            pdb=" C2'  DG N  -6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.73e-01
  chirality pdb=" C3'  DG N -18 "
            pdb=" C4'  DG N -18 "
            pdb=" O3'  DG N -18 "
            pdb=" C2'  DG N -18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.73e-01
  ... (remaining 2203 not shown)

  Planarity restraints: 2263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE b 307 "    0.069 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO b 308 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO b 308 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO b 308 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU M 130 "    0.055 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO M 131 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO M 131 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO M 131 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP a 226 "    0.010 2.00e-02 2.50e+03   1.01e-02 2.55e+00
        pdb=" CG  TRP a 226 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP a 226 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP a 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP a 226 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP a 226 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP a 226 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP a 226 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP a 226 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP a 226 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2260 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 142
        2.56 -     3.15: 11688
        3.15 -     3.73: 23746
        3.73 -     4.32: 32168
        4.32 -     4.90: 51251
  Nonbonded interactions: 118995
  Sorted by model distance:
  nonbonded pdb=" O   LEU a 207 "
            pdb=" NH2 ARG d  28 "
     model   vdw
     1.978 3.120
  nonbonded pdb=" OP1  DG N   8 "
            pdb=" OG  SER O 216 "
     model   vdw
     2.016 3.040
  nonbonded pdb=" OH  TYR V   3 "
            pdb=" O   CYS V  98 "
     model   vdw
     2.044 3.040
  nonbonded pdb=" O   SER M 216 "
            pdb=" OG  SER M 220 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OG  SER b 209 "
            pdb=" OD1 ASN b 299 "
     model   vdw
     2.104 3.040
  ... (remaining 118990 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=0.00 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:             4.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.610
  Find NCS groups from input model:        0.070
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
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      :  0.004   0.053  14627  Z= 0.302
  Angle     :  0.605   6.319  20120  Z= 0.439
  Chirality :  0.045   0.203   2206
  Planarity :  0.004   0.103   2263
  Dihedral  : 19.337 155.905   5760
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.71 (0.23), residues: 1474
  helix:  1.79 (0.20), residues: 747
  sheet: -0.34 (0.42), residues: 136
  loop : -1.07 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG V  82 
 TYR   0.018   0.001   TYR c 141 
 PHE   0.025   0.001   PHE V  81 
 TRP   0.028   0.001   TRP a 226 
 HIS   0.006   0.001   HIS c 369 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.30 (14619)
  covalent geometry    : angle       0.60424 /  0.44 (20112)
  hydrogen bonds       : bond        0.10980 /  6.95 (  750)
  hydrogen bonds       : angle       5.30184 /  3.93 ( 2104)
  metal coordination   : bond        0.00436 /  0.22 (    8)
  metal coordination   : angle       1.96029 /  1.09 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  129 ASN cc_start: 0.8640 (m110) cc_final: 0.7964 (t0)
REVERT: M  227 GLN cc_start: 0.9361 (mp10) cc_final: 0.9150 (mp10)
REVERT: M  259 TYR cc_start: 0.9308 (t80) cc_final: 0.8919 (t80)
REVERT: O  229 GLN cc_start: 0.8435 (mp10) cc_final: 0.8199 (mp10)
REVERT: U   24 ASP cc_start: 0.8080 (p0) cc_final: 0.7791 (p0)
REVERT: U   35 ASP cc_start: 0.7804 (p0) cc_final: 0.7463 (p0)
REVERT: U   37 GLN cc_start: 0.9118 (mp-120) cc_final: 0.8340 (mp10)
REVERT: U   43 LYS cc_start: 0.9262 (ttpp) cc_final: 0.9013 (ttpt)
REVERT: U   47 GLU cc_start: 0.8976 (mp0) cc_final: 0.8634 (mp0)
REVERT: V   21 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8670 (mm-30)
REVERT: V   83 GLU cc_start: 0.7587 (pp20) cc_final: 0.7384 (pp20)
REVERT: a   53 MET cc_start: 0.8920 (tmm) cc_final: 0.8687 (tmm)
REVERT: a   57 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8201 (tt0)
REVERT: a   83 TYR cc_start: 0.8783 (t80) cc_final: 0.8368 (t80)
REVERT: a  119 HIS cc_start: 0.8874 (m-70) cc_final: 0.8161 (m90)
REVERT: a  226 TRP cc_start: 0.8955 (t60) cc_final: 0.8739 (t60)
REVERT: c  248 LEU cc_start: 0.9070 (tp) cc_final: 0.8769 (tp)
REVERT: c  259 ASP cc_start: 0.7831 (p0) cc_final: 0.7522 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1078
  time to fit residues: 34.2255
Evaluate side-chains
  140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M 287 GLN
b 139 HIS
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.088580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.068208 restraints weight = 68498.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.069725 restraints weight = 32719.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.070532 restraints weight = 21000.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.071056 restraints weight = 16721.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.071392 restraints weight = 14909.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14627  Z= 0.178
  Angle     :  0.649   9.563  20120  Z= 0.358
  Chirality :  0.043   0.315   2206
  Planarity :  0.005   0.074   2263
  Dihedral  : 21.836 150.981   2641
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.97 %
    Favored  : 92.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.56 (0.22), residues: 1474
  helix:  1.62 (0.19), residues: 760
  sheet: -0.22 (0.45), residues: 112
  loop : -1.16 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG d  17 
 TYR   0.026   0.002   TYR O 237 
 PHE   0.018   0.002   PHE U 351 
 TRP   0.015   0.002   TRP a 226 
 HIS   0.008   0.001   HIS a 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.18 (14619)
  covalent geometry    : angle       0.64591 /  0.36 (20112)
  hydrogen bonds       : bond        0.04473 /  2.95 (  750)
  hydrogen bonds       : angle       4.55710 /  3.35 ( 2104)
  metal coordination   : bond        0.00957 /  0.44 (    8)
  metal coordination   : angle       3.20081 /  1.68 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  215 MET cc_start: 0.8159 (mpp) cc_final: 0.7870 (mpp)
REVERT: M  259 TYR cc_start: 0.9168 (t80) cc_final: 0.8940 (t80)
REVERT: M  267 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7952 (mt-10)
REVERT: O  220 VAL cc_start: 0.9388 (t) cc_final: 0.9165 (m)
REVERT: O  237 TYR cc_start: 0.7758 (m-80) cc_final: 0.7446 (m-80)
REVERT: O  307 SER cc_start: 0.9121 (m) cc_final: 0.8882 (p)
REVERT: U   24 ASP cc_start: 0.7817 (p0) cc_final: 0.7558 (p0)
REVERT: U   37 GLN cc_start: 0.8873 (mp-120) cc_final: 0.8598 (mp10)
REVERT: a   35 ASN cc_start: 0.9241 (m110) cc_final: 0.9026 (m110)
REVERT: a   57 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8230 (tt0)
REVERT: a  119 HIS cc_start: 0.8764 (m-70) cc_final: 0.8119 (m90)
REVERT: b  143 THR cc_start: 0.8640 (m) cc_final: 0.8250 (p)
REVERT: c  214 TYR cc_start: 0.8974 (t80) cc_final: 0.8732 (t80)
REVERT: c  248 LEU cc_start: 0.9086 (tp) cc_final: 0.8800 (tp)
REVERT: c  356 MET cc_start: 0.8636 (ttt) cc_final: 0.8166 (tpp)
REVERT: d   17 ARG cc_start: 0.8504 (mtm180) cc_final: 0.8245 (ptt180)
  outliers start: 11
  outliers final: 7
  residues processed: 166
  average time/residue: 0.1072
  time to fit residues: 27.7152
Evaluate side-chains
  143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  334 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 147 optimal weight:    0.9980
   chunk 144 optimal weight:    0.7980
   chunk 123 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 121 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M 116 ASN
** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 166 GLN
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.087507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.067137 restraints weight = 68886.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.068646 restraints weight = 32744.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.069574 restraints weight = 21076.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.069970 restraints weight = 16555.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.070274 restraints weight = 14910.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14627  Z= 0.157
  Angle     :  0.623   8.750  20120  Z= 0.343
  Chirality :  0.042   0.312   2206
  Planarity :  0.005   0.068   2263
  Dihedral  : 21.977 150.811   2641
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.79 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.39 (0.22), residues: 1474
  helix:  1.42 (0.19), residues: 764
  sheet: -0.41 (0.44), residues: 119
  loop : -1.14 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG V  55 
 TYR   0.019   0.001   TYR O 237 
 PHE   0.013   0.001   PHE U 351 
 TRP   0.013   0.001   TRP c 317 
 HIS   0.010   0.001   HIS a 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.16 (14619)
  covalent geometry    : angle       0.62079 /  0.34 (20112)
  hydrogen bonds       : bond        0.04116 /  2.71 (  750)
  hydrogen bonds       : angle       4.33959 /  3.18 ( 2104)
  metal coordination   : bond        0.00814 /  0.37 (    8)
  metal coordination   : angle       2.96990 /  1.59 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: M  215 MET cc_start: 0.8122 (mpp) cc_final: 0.7920 (mpp)
REVERT: M  221 ASN cc_start: 0.9057 (m110) cc_final: 0.8788 (m110)
REVERT: M  259 TYR cc_start: 0.9180 (t80) cc_final: 0.8953 (t80)
REVERT: U   24 ASP cc_start: 0.7805 (p0) cc_final: 0.7286 (p0)
REVERT: a   35 ASN cc_start: 0.9226 (m110) cc_final: 0.9013 (m110)
REVERT: a   57 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8239 (tt0)
REVERT: a   87 ASN cc_start: 0.9259 (m-40) cc_final: 0.8942 (m110)
REVERT: a  119 HIS cc_start: 0.8699 (m-70) cc_final: 0.7976 (m90)
REVERT: b  143 THR cc_start: 0.8735 (m) cc_final: 0.8291 (p)
REVERT: c  214 TYR cc_start: 0.8886 (t80) cc_final: 0.8650 (t80)
REVERT: c  248 LEU cc_start: 0.9046 (tp) cc_final: 0.8763 (tp)
REVERT: c  356 MET cc_start: 0.8591 (ttt) cc_final: 0.8169 (tpp)
REVERT: d   29 LEU cc_start: 0.4710 (mt) cc_final: 0.4447 (mm)
  outliers start: 11
  outliers final: 6
  residues processed: 165
  average time/residue: 0.1104
  time to fit residues: 28.0784
Evaluate side-chains
  144 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 138
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue  174 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 151 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 140 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 256 GLN
a  73 GLN
a 232 ASN
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 144 HIS
** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.087242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.066712 restraints weight = 67978.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.068231 restraints weight = 32377.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.069127 restraints weight = 20822.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.069554 restraints weight = 16396.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.069843 restraints weight = 14681.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14627  Z= 0.146
  Angle     :  0.624   9.344  20120  Z= 0.343
  Chirality :  0.042   0.316   2206
  Planarity :  0.004   0.060   2263
  Dihedral  : 22.024 150.170   2641
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.69 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.38 (0.22), residues: 1474
  helix:  1.33 (0.19), residues: 770
  sheet: -0.09 (0.46), residues: 107
  loop : -1.11 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG d   9 
 TYR   0.021   0.001   TYR b 340 
 PHE   0.012   0.001   PHE b  47 
 TRP   0.011   0.001   TRP c 317 
 HIS   0.006   0.001   HIS a 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.15 (14619)
  covalent geometry    : angle       0.62162 /  0.34 (20112)
  hydrogen bonds       : bond        0.03997 /  2.62 (  750)
  hydrogen bonds       : angle       4.32038 /  3.16 ( 2104)
  metal coordination   : bond        0.00661 /  0.30 (    8)
  metal coordination   : angle       2.83610 /  1.52 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9014 (m110) cc_final: 0.8776 (m110)
REVERT: O  237 TYR cc_start: 0.7834 (m-80) cc_final: 0.7529 (m-80)
REVERT: U   24 ASP cc_start: 0.7751 (p0) cc_final: 0.7464 (p0)
REVERT: a   35 ASN cc_start: 0.9224 (m110) cc_final: 0.8996 (m110)
REVERT: a   46 MET cc_start: 0.7481 (tmm) cc_final: 0.6662 (tmm)
REVERT: a   57 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8209 (tt0)
REVERT: a  119 HIS cc_start: 0.8652 (m-70) cc_final: 0.7904 (m90)
REVERT: b  143 THR cc_start: 0.8733 (m) cc_final: 0.8298 (p)
REVERT: c  214 TYR cc_start: 0.8886 (t80) cc_final: 0.8639 (t80)
REVERT: c  248 LEU cc_start: 0.9072 (tp) cc_final: 0.8781 (tp)
  outliers start: 17
  outliers final: 11
  residues processed: 171
  average time/residue: 0.0928
  time to fit residues: 24.9756
Evaluate side-chains
  146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  144 GLN
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  317 VAL
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  334 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 144 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 136 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0060
   overall best weight:    0.9200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 188 GLN
b 299 ASN
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.086507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.065610 restraints weight = 67814.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.067006 restraints weight = 32578.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.067957 restraints weight = 21381.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.068329 restraints weight = 16889.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.068636 restraints weight = 15300.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14627  Z= 0.147
  Angle     :  0.637  10.344  20120  Z= 0.343
  Chirality :  0.042   0.312   2206
  Planarity :  0.004   0.060   2263
  Dihedral  : 22.073 149.866   2641
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.61 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.45 (0.22), residues: 1474
  helix:  1.38 (0.19), residues: 771
  sheet:  0.03 (0.47), residues: 107
  loop : -1.10 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG d   9 
 TYR   0.016   0.001   TYR b 340 
 PHE   0.017   0.001   PHE M 304 
 TRP   0.011   0.001   TRP V  72 
 HIS   0.005   0.001   HIS a 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.15 (14619)
  covalent geometry    : angle       0.63446 /  0.34 (20112)
  hydrogen bonds       : bond        0.03899 /  2.58 (  750)
  hydrogen bonds       : angle       4.26495 /  3.14 ( 2104)
  metal coordination   : bond        0.00665 /  0.30 (    8)
  metal coordination   : angle       2.83161 /  1.54 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9031 (m110) cc_final: 0.8756 (m110)
REVERT: M  259 TYR cc_start: 0.9176 (t80) cc_final: 0.8692 (t80)
REVERT: O  237 TYR cc_start: 0.7970 (m-80) cc_final: 0.7718 (m-80)
REVERT: V   84 VAL cc_start: 0.8755 (t) cc_final: 0.8455 (p)
REVERT: a   11 CYS cc_start: 0.9034 (m) cc_final: 0.8705 (m)
REVERT: a   35 ASN cc_start: 0.9255 (m110) cc_final: 0.9013 (m-40)
REVERT: a   57 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8193 (tt0)
REVERT: a  119 HIS cc_start: 0.8700 (m-70) cc_final: 0.7919 (m90)
REVERT: a  140 MET cc_start: 0.8506 (mmt) cc_final: 0.8277 (mmt)
REVERT: b  143 THR cc_start: 0.8724 (m) cc_final: 0.8094 (p)
REVERT: c  214 TYR cc_start: 0.8939 (t80) cc_final: 0.8664 (t80)
REVERT: c  248 LEU cc_start: 0.9060 (tp) cc_final: 0.8769 (tp)
REVERT: c  356 MET cc_start: 0.8618 (tpp) cc_final: 0.8032 (tpp)
  outliers start: 23
  outliers final: 15
  residues processed: 161
  average time/residue: 0.0931
  time to fit residues: 23.4000
Evaluate side-chains
  150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  144 GLN
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue   86 VAL
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  334 LEU
Chi-restraints excluded: chain d residue   22 LEU
Chi-restraints excluded: chain d residue   48 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 120 optimal weight:    7.9990
   chunk 111 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 237 GLN
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.083422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.062289 restraints weight = 67915.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.063783 restraints weight = 32860.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.064605 restraints weight = 21382.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.065190 restraints weight = 16963.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.065432 restraints weight = 14922.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14627  Z= 0.211
  Angle     :  0.712  12.051  20120  Z= 0.378
  Chirality :  0.044   0.297   2206
  Planarity :  0.005   0.059   2263
  Dihedral  : 22.270 148.720   2641
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.23 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.42 (0.22), residues: 1474
  helix:  1.37 (0.19), residues: 761
  sheet:  0.10 (0.48), residues: 107
  loop : -1.10 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG b 135 
 TYR   0.021   0.002   TYR b 340 
 PHE   0.015   0.002   PHE b 410 
 TRP   0.013   0.001   TRP c 317 
 HIS   0.007   0.001   HIS b 313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.21 (14619)
  covalent geometry    : angle       0.70861 /  0.38 (20112)
  hydrogen bonds       : bond        0.04296 /  2.86 (  750)
  hydrogen bonds       : angle       4.33270 /  3.16 ( 2104)
  metal coordination   : bond        0.01216 /  0.56 (    8)
  metal coordination   : angle       3.64901 /  1.97 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9138 (m110) cc_final: 0.8833 (m110)
REVERT: M  227 GLN cc_start: 0.8960 (mp10) cc_final: 0.8686 (pm20)
REVERT: M  229 GLN cc_start: 0.9209 (tp40) cc_final: 0.8620 (tp40)
REVERT: M  259 TYR cc_start: 0.9240 (t80) cc_final: 0.8786 (t80)
REVERT: O  237 TYR cc_start: 0.8183 (m-80) cc_final: 0.7982 (m-80)
REVERT: U   36 GLU cc_start: 0.8679 (tp30) cc_final: 0.7935 (tp30)
REVERT: V   83 GLU cc_start: 0.7630 (pp20) cc_final: 0.7256 (pp20)
REVERT: a   11 CYS cc_start: 0.9197 (m) cc_final: 0.8804 (m)
REVERT: a   35 ASN cc_start: 0.9307 (m110) cc_final: 0.9063 (m110)
REVERT: a   46 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6834 (tmm)
REVERT: a   57 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8305 (tt0)
REVERT: a  119 HIS cc_start: 0.8830 (m-70) cc_final: 0.8031 (m90)
REVERT: a  140 MET cc_start: 0.8628 (mmt) cc_final: 0.7473 (mmt)
REVERT: b  143 THR cc_start: 0.8553 (m) cc_final: 0.8214 (p)
REVERT: b  340 TYR cc_start: 0.6796 (t80) cc_final: 0.6462 (t80)
REVERT: c  142 MET cc_start: 0.8053 (tpp) cc_final: 0.7284 (mpp)
REVERT: c  248 LEU cc_start: 0.9132 (tp) cc_final: 0.8830 (tp)
  outliers start: 22
  outliers final: 13
  residues processed: 158
  average time/residue: 0.0928
  time to fit residues: 22.8359
Evaluate side-chains
  152 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  317 VAL
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue   46 MET
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  334 LEU
Chi-restraints excluded: chain d residue   22 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 105 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 103 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 106 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 131 optimal weight:    4.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 369 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.084424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.063373 restraints weight = 67361.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.064818 restraints weight = 32442.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.065606 restraints weight = 21140.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.066092 restraints weight = 16991.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.066423 restraints weight = 15163.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
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   0.043  14627  Z= 0.141
  Angle     :  0.660  13.247  20120  Z= 0.350
  Chirality :  0.043   0.302   2206
  Planarity :  0.004   0.060   2263
  Dihedral  : 22.200 146.962   2641
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.91 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.55 (0.22), residues: 1474
  helix:  1.43 (0.19), residues: 766
  sheet:  0.14 (0.48), residues: 107
  loop : -0.99 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG d   9 
 TYR   0.018   0.001   TYR b 340 
 PHE   0.012   0.001   PHE U 351 
 TRP   0.013   0.001   TRP V  72 
 HIS   0.004   0.001   HIS a 227 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.14 (14619)
  covalent geometry    : angle       0.65641 /  0.35 (20112)
  hydrogen bonds       : bond        0.03798 /  2.50 (  750)
  hydrogen bonds       : angle       4.24919 /  3.11 ( 2104)
  metal coordination   : bond        0.00481 /  0.21 (    8)
  metal coordination   : angle       3.26707 /  1.78 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9086 (m110) cc_final: 0.8764 (m110)
REVERT: M  259 TYR cc_start: 0.9278 (t80) cc_final: 0.8846 (t80)
REVERT: M  271 GLN cc_start: 0.9348 (mt0) cc_final: 0.9103 (mt0)
REVERT: V   35 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8326 (mp10)
REVERT: V   83 GLU cc_start: 0.7703 (pp20) cc_final: 0.7303 (pp20)
REVERT: a   11 CYS cc_start: 0.9173 (m) cc_final: 0.8732 (m)
REVERT: a   35 ASN cc_start: 0.9293 (m110) cc_final: 0.9044 (m110)
REVERT: a   46 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6747 (tmm)
REVERT: a   57 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8292 (tt0)
REVERT: a  119 HIS cc_start: 0.8762 (m-70) cc_final: 0.7982 (m90)
REVERT: a  140 MET cc_start: 0.8679 (mmt) cc_final: 0.7609 (mmt)
REVERT: b  143 THR cc_start: 0.8549 (m) cc_final: 0.8206 (p)
REVERT: b  340 TYR cc_start: 0.6899 (t80) cc_final: 0.6613 (t80)
REVERT: c  142 MET cc_start: 0.8043 (tpp) cc_final: 0.7253 (mpp)
REVERT: c  248 LEU cc_start: 0.9102 (tp) cc_final: 0.8792 (tp)
REVERT: d    9 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7829 (tmm160)
  outliers start: 20
  outliers final: 12
  residues processed: 166
  average time/residue: 0.1020
  time to fit residues: 26.7034
Evaluate side-chains
  151 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  144 GLN
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  317 VAL
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue   46 MET
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  334 LEU
Chi-restraints excluded: chain d residue   22 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 148 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   chunk 115 optimal weight:    5.9990
   chunk 143 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0970
   chunk 153 optimal weight:    9.9990
   overall best weight:    2.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M 263 GLN
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.082084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.060800 restraints weight = 67573.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.062246 restraints weight = 33082.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.063083 restraints weight = 21700.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.063542 restraints weight = 17281.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.063760 restraints weight = 15330.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14627  Z= 0.229
  Angle     :  0.722  14.766  20120  Z= 0.384
  Chirality :  0.044   0.284   2206
  Planarity :  0.005   0.101   2263
  Dihedral  : 22.336 146.943   2641
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.51 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.42 (0.22), residues: 1474
  helix:  1.32 (0.19), residues: 767
  sheet:  0.24 (0.50), residues: 107
  loop : -1.07 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG V  51 
 TYR   0.019   0.002   TYR b 340 
 PHE   0.016   0.002   PHE b 410 
 TRP   0.012   0.001   TRP c 317 
 HIS   0.007   0.001   HIS b 313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.23 (14619)
  covalent geometry    : angle       0.71825 /  0.38 (20112)
  hydrogen bonds       : bond        0.04272 /  2.81 (  750)
  hydrogen bonds       : angle       4.42862 /  3.24 ( 2104)
  metal coordination   : bond        0.01267 /  0.59 (    8)
  metal coordination   : angle       3.90022 /  2.06 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9210 (m110) cc_final: 0.8894 (m110)
REVERT: M  259 TYR cc_start: 0.9294 (t80) cc_final: 0.8845 (t80)
REVERT: M  271 GLN cc_start: 0.9338 (mt0) cc_final: 0.9078 (mt0)
REVERT: O  237 TYR cc_start: 0.8203 (m-80) cc_final: 0.7877 (m-80)
REVERT: V   35 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8410 (mp10)
REVERT: V   83 GLU cc_start: 0.7753 (pp20) cc_final: 0.7373 (pp20)
REVERT: V   91 ASP cc_start: 0.8488 (t0) cc_final: 0.8253 (t0)
REVERT: a   11 CYS cc_start: 0.9302 (m) cc_final: 0.8815 (m)
REVERT: a   35 ASN cc_start: 0.9317 (m110) cc_final: 0.9058 (m110)
REVERT: a   46 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6728 (tmm)
REVERT: a   57 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8306 (tt0)
REVERT: a  119 HIS cc_start: 0.8879 (m-70) cc_final: 0.8004 (m90)
REVERT: a  140 MET cc_start: 0.8681 (mmt) cc_final: 0.7581 (mmt)
REVERT: b  143 THR cc_start: 0.8629 (m) cc_final: 0.8298 (p)
REVERT: b  340 TYR cc_start: 0.7041 (t80) cc_final: 0.6824 (t80)
REVERT: c  248 LEU cc_start: 0.9130 (tp) cc_final: 0.8836 (tp)
REVERT: c  315 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6086 (tp)
REVERT: d    9 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7956 (tmm160)
  outliers start: 22
  outliers final: 15
  residues processed: 159
  average time/residue: 0.1134
  time to fit residues: 27.6726
Evaluate side-chains
  158 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  206 GLU
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  317 VAL
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   53 ARG
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue   46 MET
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  155 THR
Chi-restraints excluded: chain c residue  315 LEU
Chi-restraints excluded: chain c residue  334 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 77 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 139 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 237 GLN
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.081868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.060209 restraints weight = 67181.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.061570 restraints weight = 32918.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.062331 restraints weight = 21825.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.062826 restraints weight = 17654.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.063089 restraints weight = 15779.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  14627  Z= 0.190
  Angle     :  0.711  15.472  20120  Z= 0.374
  Chirality :  0.043   0.293   2206
  Planarity :  0.004   0.062   2263
  Dihedral  : 22.363 145.240   2641
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.66 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.40 (0.22), residues: 1474
  helix:  1.31 (0.19), residues: 768
  sheet: -0.02 (0.49), residues: 111
  loop : -1.06 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG V  51 
 TYR   0.019   0.001   TYR a  83 
 PHE   0.017   0.001   PHE U 351 
 TRP   0.011   0.001   TRP V  72 
 HIS   0.006   0.001   HIS d  23 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.19 (14619)
  covalent geometry    : angle       0.70686 /  0.37 (20112)
  hydrogen bonds       : bond        0.03938 /  2.61 (  750)
  hydrogen bonds       : angle       4.39854 /  3.22 ( 2104)
  metal coordination   : bond        0.00923 /  0.43 (    8)
  metal coordination   : angle       4.05026 /  2.15 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  179 GLU cc_start: 0.8284 (tt0) cc_final: 0.7822 (tt0)
REVERT: M  259 TYR cc_start: 0.9270 (t80) cc_final: 0.8820 (t80)
REVERT: M  271 GLN cc_start: 0.9296 (mt0) cc_final: 0.9033 (mt0)
REVERT: O  237 TYR cc_start: 0.8195 (m-80) cc_final: 0.7870 (m-80)
REVERT: V   35 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8324 (mp10)
REVERT: V   83 GLU cc_start: 0.7781 (pp20) cc_final: 0.7342 (pp20)
REVERT: a   11 CYS cc_start: 0.9327 (m) cc_final: 0.8824 (m)
REVERT: a   35 ASN cc_start: 0.9282 (m110) cc_final: 0.9042 (m110)
REVERT: a   46 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6712 (tmm)
REVERT: a  119 HIS cc_start: 0.8788 (m-70) cc_final: 0.7950 (m90)
REVERT: b  143 THR cc_start: 0.8620 (m) cc_final: 0.8286 (p)
REVERT: c  142 MET cc_start: 0.8195 (tpp) cc_final: 0.7329 (mpp)
REVERT: c  248 LEU cc_start: 0.9103 (tp) cc_final: 0.8821 (tp)
REVERT: c  315 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6021 (tp)
REVERT: d    9 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7968 (tmm160)
  outliers start: 24
  outliers final: 16
  residues processed: 164
  average time/residue: 0.1125
  time to fit residues: 28.1022
Evaluate side-chains
  156 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  206 GLU
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  317 VAL
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain U residue   47 GLU
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   53 ARG
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue   46 MET
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  155 THR
Chi-restraints excluded: chain c residue  315 LEU
Chi-restraints excluded: chain c residue  334 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0070
   chunk 151 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** 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 = 0.3980 r_free = 0.3980 target = 0.082937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.061174 restraints weight = 66724.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.062589 restraints weight = 32606.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.063425 restraints weight = 21513.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.063853 restraints weight = 17357.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.064071 restraints weight = 15484.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14627  Z= 0.145
  Angle     :  0.721  15.993  20120  Z= 0.377
  Chirality :  0.043   0.298   2206
  Planarity :  0.004   0.065   2263
  Dihedral  : 22.289 144.691   2641
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 16.25 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.44 (0.22), residues: 1474
  helix:  1.28 (0.19), residues: 768
  sheet:  0.31 (0.50), residues: 107
  loop : -1.00 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG V  51 
 TYR   0.013   0.001   TYR V  65 
 PHE   0.019   0.001   PHE U 351 
 TRP   0.014   0.001   TRP V  72 
 HIS   0.006   0.001   HIS b 139 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 (14619)
  covalent geometry    : angle       0.71699 /  0.38 (20112)
  hydrogen bonds       : bond        0.03835 /  2.52 (  750)
  hydrogen bonds       : angle       4.34475 /  3.17 ( 2104)
  metal coordination   : bond        0.00473 /  0.21 (    8)
  metal coordination   : angle       3.63611 /  1.94 (    8)

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

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

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2948 Ramachandran restraints generated.
    1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  259 TYR cc_start: 0.9260 (t80) cc_final: 0.8814 (t80)
REVERT: M  271 GLN cc_start: 0.9289 (mt0) cc_final: 0.9012 (mt0)
REVERT: O  237 TYR cc_start: 0.8177 (m-80) cc_final: 0.7864 (m-80)
REVERT: V   35 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8312 (mp10)
REVERT: V   83 GLU cc_start: 0.7794 (pp20) cc_final: 0.7434 (pp20)
REVERT: a   11 CYS cc_start: 0.9309 (m) cc_final: 0.8809 (m)
REVERT: a   35 ASN cc_start: 0.9266 (m110) cc_final: 0.9034 (m110)
REVERT: a   46 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6672 (tmm)
REVERT: a  119 HIS cc_start: 0.8756 (m-70) cc_final: 0.7859 (m90)
REVERT: b  143 THR cc_start: 0.8656 (m) cc_final: 0.8338 (p)
REVERT: c  142 MET cc_start: 0.8164 (tpp) cc_final: 0.7322 (mpp)
REVERT: c  248 LEU cc_start: 0.9097 (tp) cc_final: 0.8812 (tp)
REVERT: c  315 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6010 (tp)
  outliers start: 21
  outliers final: 15
  residues processed: 168
  average time/residue: 0.1133
  time to fit residues: 29.2801
Evaluate side-chains
  157 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  206 GLU
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  317 VAL
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   35 GLN
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   53 ARG
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue   46 MET
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  197 GLU
Chi-restraints excluded: chain c residue  155 THR
Chi-restraints excluded: chain c residue  315 LEU
Chi-restraints excluded: chain c residue  334 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 135 optimal weight:    0.0170
   chunk 66 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 138 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.6420

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** 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 = 0.3979 r_free = 0.3979 target = 0.082904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.061287 restraints weight = 66598.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.062692 restraints weight = 32518.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.063478 restraints weight = 21479.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.063895 restraints weight = 17198.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.064175 restraints weight = 15436.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14627  Z= 0.149
  Angle     :  0.740  16.200  20120  Z= 0.389
  Chirality :  0.043   0.286   2206
  Planarity :  0.004   0.061   2263
  Dihedral  : 22.276 144.934   2641
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 17.08 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 are not related in a simple way.
  whole:  0.43 (0.22), residues: 1474
  helix:  1.26 (0.19), residues: 768
  sheet:  0.41 (0.50), residues: 107
  loop : -1.01 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG V  51 
 TYR   0.019   0.001   TYR b 340 
 PHE   0.018   0.001   PHE U 351 
 TRP   0.013   0.001   TRP V  72 
 HIS   0.006   0.001   HIS b 139 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 (14619)
  covalent geometry    : angle       0.73675 /  0.39 (20112)
  hydrogen bonds       : bond        0.03892 /  2.58 (  750)
  hydrogen bonds       : angle       4.41039 /  3.23 ( 2104)
  metal coordination   : bond        0.00487 /  0.21 (    8)
  metal coordination   : angle       3.46465 /  1.85 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3244.82 seconds
wall clock time: 56 minutes 39.21 seconds (3399.21 seconds total)