Starting phenix.real_space_refine
on Wed Mar  4 14:06:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxe_15009/03_2026/7zxe_15009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxe_15009/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxe_15009/03_2026/7zxe_15009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxe_15009/03_2026/7zxe_15009.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/03_2026/7zxe_15009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxe_15009/03_2026/7zxe_15009.map"
  }
  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-5986/lib/python3.9/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: 2.77, per 1000 atoms: 0.20
  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: 1.20
  Conformation dependent library (CDL) restraints added in 538.9 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: 2.42

  Time building geometry restraints manager: 1.61 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=" N   MET d   1 "
       pdb=" CA  MET d   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" CG  PRO b 308 "
       pdb=" CD  PRO b 308 "
    ideal  model  delta    sigma   weight residual
    1.503  1.547 -0.044 3.40e-02 8.65e+02 1.69e+00
  bond pdb=" C3'  DC T  -6 "
       pdb=" O3'  DC T  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" C1'  DC T  24 "
       pdb=" N1   DC T  24 "
    ideal  model  delta    sigma   weight residual
    1.490  1.521 -0.031 3.00e-02 1.11e+03 1.06e+00
  bond pdb=" C4'  DC T  -6 "
       pdb=" C3'  DC T  -6 "
    ideal  model  delta    sigma   weight residual
    1.523  1.543 -0.020 2.00e-02 2.50e+03 1.03e+00
  ... (remaining 14614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 19372
        1.26 -     2.53: 596
        2.53 -     3.79: 125
        3.79 -     5.06: 16
        5.06 -     6.32: 3
  Bond angle restraints: 20112
  Sorted by residual:
  angle pdb=" N   ILE M 180 "
        pdb=" CA  ILE M 180 "
        pdb=" C   ILE M 180 "
      ideal   model   delta    sigma   weight residual
     111.58  107.59    3.99 1.06e+00 8.90e-01 1.42e+01
  angle pdb=" CA  PRO b 308 "
        pdb=" N   PRO b 308 "
        pdb=" CD  PRO b 308 "
      ideal   model   delta    sigma   weight residual
     112.00  107.85    4.15 1.40e+00 5.10e-01 8.80e+00
  angle pdb=" N   GLU a  31 "
        pdb=" CA  GLU a  31 "
        pdb=" CB  GLU a  31 "
      ideal   model   delta    sigma   weight residual
     110.12  114.27   -4.15 1.47e+00 4.63e-01 7.98e+00
  angle pdb=" C   ARG V  82 "
        pdb=" N   GLU V  83 "
        pdb=" CA  GLU V  83 "
      ideal   model   delta    sigma   weight residual
     122.03  116.91    5.12 2.01e+00 2.48e-01 6.49e+00
  angle pdb=" C   TYR c 141 "
        pdb=" N   MET c 142 "
        pdb=" CA  MET c 142 "
      ideal   model   delta    sigma   weight residual
     120.29  123.88   -3.59 1.42e+00 4.96e-01 6.40e+00
  ... (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: 1739
       0.041 -    0.081: 353
       0.081 -    0.122: 99
       0.122 -    0.162: 14
       0.162 -    0.203: 1
  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=" CA  ILE b 321 "
            pdb=" N   ILE b 321 "
            pdb=" C   ILE b 321 "
            pdb=" CB  ILE b 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.11e-01
  chirality pdb=" CA  ILE b 186 "
            pdb=" N   ILE b 186 "
            pdb=" C   ILE b 186 "
            pdb=" CB  ILE b 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.81e-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:             5.870
  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:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.540
  Find NCS groups from input model:        0.060
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
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      :  0.003   0.047  14627  Z= 0.136
  Angle     :  0.549   6.319  20120  Z= 0.323
  Chirality :  0.037   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
  covalent geometry    : bond        0.00282 (14619)
  covalent geometry    : angle       0.54787 (20112)
  hydrogen bonds       : bond        0.10980 (  750)
  hydrogen bonds       : angle       5.30184 ( 2104)
  metal coordination   : bond        0.00436 (    8)
  metal coordination   : angle       1.96029 (    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  : 0.486 
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: 0.0971
  time to fit residues: 30.7272
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  : 0.481 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
O 166 GLN
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 139 HIS
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 144 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.086901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.065855 restraints weight = 67608.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.067316 restraints weight = 32444.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.068210 restraints weight = 21125.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.068621 restraints weight = 16815.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.068878 restraints weight = 15121.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14627  Z= 0.175
  Angle     :  0.623   9.769  20120  Z= 0.335
  Chirality :  0.041   0.214   2206
  Planarity :  0.005   0.068   2263
  Dihedral  : 21.826 149.711   2641
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.87 %
    Favored  : 91.39 %
  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:  0.56 (0.22), residues: 1474
  helix:  1.58 (0.19), residues: 764
  sheet: -0.45 (0.44), residues: 123
  loop : -1.07 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M 217 
 TYR   0.029   0.001   TYR O 237 
 PHE   0.022   0.001   PHE U 351 
 TRP   0.020   0.002   TRP a 226 
 HIS   0.006   0.001   HIS U 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (14619)
  covalent geometry    : angle       0.62000 (20112)
  hydrogen bonds       : bond        0.04122 (  750)
  hydrogen bonds       : angle       4.35747 ( 2104)
  metal coordination   : bond        0.01031 (    8)
  metal coordination   : angle       3.16204 (    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
  182 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  215 MET cc_start: 0.8366 (mpp) cc_final: 0.8105 (mpp)
REVERT: M  267 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: O  237 TYR cc_start: 0.7877 (m-80) cc_final: 0.7638 (m-80)
REVERT: U   24 ASP cc_start: 0.7899 (p0) cc_final: 0.7322 (p0)
REVERT: U   37 GLN cc_start: 0.9094 (mp-120) cc_final: 0.8449 (mp10)
REVERT: U   43 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8796 (ttmt)
REVERT: U   47 GLU cc_start: 0.9091 (mp0) cc_final: 0.8803 (mp0)
REVERT: U  348 LYS cc_start: 0.8962 (mppt) cc_final: 0.8639 (mppt)
REVERT: V   83 GLU cc_start: 0.7743 (pp20) cc_final: 0.7425 (pp20)
REVERT: V   84 VAL cc_start: 0.8738 (t) cc_final: 0.7851 (p)
REVERT: a   35 ASN cc_start: 0.9295 (m110) cc_final: 0.9046 (m110)
REVERT: a   46 MET cc_start: 0.7174 (ptm) cc_final: 0.6948 (ptm)
REVERT: a   57 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8231 (tt0)
REVERT: a  119 HIS cc_start: 0.8819 (m-70) cc_final: 0.7926 (m90)
REVERT: a  226 TRP cc_start: 0.9105 (t60) cc_final: 0.8896 (t60)
REVERT: b  143 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8385 (p)
REVERT: c  214 TYR cc_start: 0.9079 (t80) cc_final: 0.8777 (t80)
REVERT: c  248 LEU cc_start: 0.9104 (tp) cc_final: 0.8819 (tp)
  outliers start: 10
  outliers final: 4
  residues processed: 176
  average time/residue: 0.1062
  time to fit residues: 28.3956
Evaluate side-chains
  143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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 a residue  194 ILE
Chi-restraints excluded: chain b residue  143 THR
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:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 221 ASN
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 256 GLN
a  73 GLN
a 188 GLN
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.082581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.060762 restraints weight = 67586.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.062258 restraints weight = 33074.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.063106 restraints weight = 21629.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.063537 restraints weight = 17418.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.063793 restraints weight = 15668.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14627  Z= 0.218
  Angle     :  0.653   8.831  20120  Z= 0.349
  Chirality :  0.042   0.161   2206
  Planarity :  0.005   0.061   2263
  Dihedral  : 21.954 146.717   2641
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.04 %
    Favored  : 88.16 %
  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:  1.45 (0.19), residues: 767
  sheet: -0.30 (0.45), residues: 118
  loop : -1.17 (0.24), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG a  98 
 TYR   0.019   0.002   TYR c 149 
 PHE   0.016   0.002   PHE U 351 
 TRP   0.016   0.002   TRP a 226 
 HIS   0.011   0.001   HIS a 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (14619)
  covalent geometry    : angle       0.64709 (20112)
  hydrogen bonds       : bond        0.04100 (  750)
  hydrogen bonds       : angle       4.26955 ( 2104)
  metal coordination   : bond        0.01007 (    8)
  metal coordination   : angle       4.40679 (    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
  183 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  259 TYR cc_start: 0.9267 (t80) cc_final: 0.8779 (t80)
REVERT: U   24 ASP cc_start: 0.7928 (p0) cc_final: 0.7706 (p0)
REVERT: U   35 ASP cc_start: 0.7820 (p0) cc_final: 0.6763 (p0)
REVERT: U   37 GLN cc_start: 0.9133 (mp-120) cc_final: 0.8160 (mp10)
REVERT: V   83 GLU cc_start: 0.7756 (pp20) cc_final: 0.7317 (pp20)
REVERT: V   84 VAL cc_start: 0.8799 (t) cc_final: 0.7980 (p)
REVERT: V   91 ASP cc_start: 0.8401 (t0) cc_final: 0.8191 (t0)
REVERT: a   35 ASN cc_start: 0.9294 (m110) cc_final: 0.9051 (m110)
REVERT: a  119 HIS cc_start: 0.8735 (m-70) cc_final: 0.7901 (m90)
REVERT: c  142 MET cc_start: 0.8455 (tpp) cc_final: 0.8053 (tpp)
REVERT: c  149 TYR cc_start: 0.8500 (t80) cc_final: 0.8150 (t80)
REVERT: c  248 LEU cc_start: 0.9123 (tp) cc_final: 0.8829 (tp)
  outliers start: 24
  outliers final: 10
  residues processed: 172
  average time/residue: 0.1041
  time to fit residues: 27.2593
Evaluate side-chains
  143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  251 ILE
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 b residue  289 GLN
Chi-restraints excluded: chain c residue  155 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 151 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0060
   chunk 84 optimal weight:    0.7980
   chunk 140 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    1.0598

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

Flipped N/Q/H residues before XYZ refinement:
M 116 ASN
M 287 GLN
U  48 ASN
a 232 ASN
b 299 ASN
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 369 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.083173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.061520 restraints weight = 67653.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.062923 restraints weight = 32818.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.063781 restraints weight = 21641.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.064190 restraints weight = 17279.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.064494 restraints weight = 15597.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3397

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= 0.150
  Angle     :  0.606  11.505  20120  Z= 0.324
  Chirality :  0.040   0.173   2206
  Planarity :  0.004   0.061   2263
  Dihedral  : 21.911 143.157   2641
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.58 %
    Favored  : 85.77 %
  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:  1.49 (0.19), residues: 765
  sheet: -0.09 (0.46), residues: 111
  loop : -1.04 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG d   9 
 TYR   0.023   0.001   TYR b 340 
 PHE   0.014   0.001   PHE U 351 
 TRP   0.013   0.001   TRP a 226 
 HIS   0.003   0.001   HIS b 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (14619)
  covalent geometry    : angle       0.60172 (20112)
  hydrogen bonds       : bond        0.03605 (  750)
  hydrogen bonds       : angle       4.16889 ( 2104)
  metal coordination   : bond        0.00654 (    8)
  metal coordination   : angle       3.51307 (    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
  180 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9092 (m-40) cc_final: 0.8781 (m110)
REVERT: M  227 GLN cc_start: 0.8888 (pm20) cc_final: 0.8663 (pm20)
REVERT: M  244 LEU cc_start: 0.9094 (mt) cc_final: 0.8641 (tp)
REVERT: M  259 TYR cc_start: 0.9240 (t80) cc_final: 0.8820 (t80)
REVERT: M  271 GLN cc_start: 0.9303 (mt0) cc_final: 0.9098 (mt0)
REVERT: O  237 TYR cc_start: 0.8031 (m-80) cc_final: 0.7807 (m-80)
REVERT: U   24 ASP cc_start: 0.7942 (p0) cc_final: 0.7405 (p0)
REVERT: U   37 GLN cc_start: 0.9181 (mp-120) cc_final: 0.8816 (mp10)
REVERT: V   86 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: a   35 ASN cc_start: 0.9245 (m110) cc_final: 0.9017 (m-40)
REVERT: a  119 HIS cc_start: 0.8734 (m-70) cc_final: 0.7904 (m90)
REVERT: a  140 MET cc_start: 0.8580 (mmt) cc_final: 0.7442 (mmt)
REVERT: b  143 THR cc_start: 0.8854 (m) cc_final: 0.8478 (p)
REVERT: b  204 MET cc_start: 0.8263 (mmm) cc_final: 0.8025 (mmm)
REVERT: b  340 TYR cc_start: 0.6685 (t80) cc_final: 0.6459 (t80)
REVERT: c  149 TYR cc_start: 0.8319 (t80) cc_final: 0.8090 (t80)
REVERT: c  248 LEU cc_start: 0.9095 (tp) cc_final: 0.8811 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 173
  average time/residue: 0.0951
  time to fit residues: 25.7755
Evaluate side-chains
  158 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
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   31 ASP
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   71 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain c residue  155 THR
Chi-restraints excluded: chain c residue  164 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 144 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 136 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0040
   overall best weight:    0.8594

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

Flipped N/Q/H residues before XYZ refinement:
U  48 ASN
V  63 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.083024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.061475 restraints weight = 67410.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.062882 restraints weight = 32711.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.063736 restraints weight = 21594.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.064112 restraints weight = 17306.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.064399 restraints weight = 15670.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14627  Z= 0.144
  Angle     :  0.601  10.076  20120  Z= 0.322
  Chirality :  0.039   0.159   2206
  Planarity :  0.004   0.061   2263
  Dihedral  : 21.871 143.353   2641
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.78 %
    Favored  : 84.27 %
  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:  0.64 (0.22), residues: 1474
  helix:  1.53 (0.19), residues: 765
  sheet:  0.24 (0.46), residues: 107
  loop : -0.99 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 248 
 TYR   0.017   0.001   TYR b 340 
 PHE   0.012   0.001   PHE U 351 
 TRP   0.014   0.001   TRP a 226 
 HIS   0.006   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (14619)
  covalent geometry    : angle       0.59760 (20112)
  hydrogen bonds       : bond        0.03539 (  750)
  hydrogen bonds       : angle       4.10525 ( 2104)
  metal coordination   : bond        0.00545 (    8)
  metal coordination   : angle       3.25050 (    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
  186 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9124 (m-40) cc_final: 0.8757 (m110)
REVERT: M  227 GLN cc_start: 0.8923 (pm20) cc_final: 0.8607 (pm20)
REVERT: M  229 GLN cc_start: 0.9244 (tp40) cc_final: 0.8955 (tp40)
REVERT: M  244 LEU cc_start: 0.9129 (mt) cc_final: 0.8687 (tp)
REVERT: M  259 TYR cc_start: 0.9325 (t80) cc_final: 0.8888 (t80)
REVERT: M  271 GLN cc_start: 0.9353 (mt0) cc_final: 0.9093 (mt0)
REVERT: O  237 TYR cc_start: 0.8062 (m-80) cc_final: 0.7781 (m-80)
REVERT: U   35 ASP cc_start: 0.7816 (p0) cc_final: 0.6425 (p0)
REVERT: U   37 GLN cc_start: 0.9296 (mp-120) cc_final: 0.8531 (mp10)
REVERT: V   86 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8333 (tm-30)
REVERT: a    7 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8582 (tt)
REVERT: a   11 CYS cc_start: 0.9216 (m) cc_final: 0.8759 (m)
REVERT: a   35 ASN cc_start: 0.9295 (m110) cc_final: 0.9052 (m-40)
REVERT: a  119 HIS cc_start: 0.8852 (m-70) cc_final: 0.7940 (m90)
REVERT: a  140 MET cc_start: 0.8655 (mmt) cc_final: 0.7449 (mmt)
REVERT: b  143 THR cc_start: 0.8861 (m) cc_final: 0.8477 (p)
REVERT: b  204 MET cc_start: 0.8297 (mmm) cc_final: 0.8040 (mmm)
REVERT: c  142 MET cc_start: 0.8692 (tpp) cc_final: 0.8474 (tpp)
REVERT: c  149 TYR cc_start: 0.8304 (t80) cc_final: 0.8057 (t80)
REVERT: c  248 LEU cc_start: 0.9129 (tp) cc_final: 0.8831 (tp)
  outliers start: 26
  outliers final: 20
  residues processed: 178
  average time/residue: 0.0965
  time to fit residues: 26.3652
Evaluate side-chains
  164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  144 GLN
Chi-restraints excluded: chain M residue  251 ILE
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  306 VAL
Chi-restraints excluded: chain U residue   31 ASP
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   71 VAL
Chi-restraints excluded: chain a residue    7 LEU
Chi-restraints excluded: chain a residue   74 ILE
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  155 THR
Chi-restraints excluded: chain c residue  164 ASP
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:    0.9990
   chunk 133 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 111 optimal weight:    5.9990
   chunk 115 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.080932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.059314 restraints weight = 67504.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.060739 restraints weight = 33190.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.061547 restraints weight = 21885.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.061933 restraints weight = 17541.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.062191 restraints weight = 15820.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14627  Z= 0.188
  Angle     :  0.634   9.134  20120  Z= 0.340
  Chirality :  0.041   0.169   2206
  Planarity :  0.004   0.059   2263
  Dihedral  : 21.934 144.875   2641
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.36 %
    Favored  : 82.47 %
  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:  0.63 (0.22), residues: 1474
  helix:  1.53 (0.19), residues: 766
  sheet:  0.17 (0.47), residues: 111
  loop : -1.00 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG d  17 
 TYR   0.021   0.001   TYR a  83 
 PHE   0.013   0.001   PHE O 325 
 TRP   0.019   0.001   TRP a 226 
 HIS   0.013   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (14619)
  covalent geometry    : angle       0.62888 (20112)
  hydrogen bonds       : bond        0.03771 (  750)
  hydrogen bonds       : angle       4.14750 ( 2104)
  metal coordination   : bond        0.00900 (    8)
  metal coordination   : angle       3.92484 (    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
  186 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9142 (m-40) cc_final: 0.8773 (m110)
REVERT: M  227 GLN cc_start: 0.8982 (pm20) cc_final: 0.8718 (pm20)
REVERT: M  229 GLN cc_start: 0.9257 (tp40) cc_final: 0.8626 (tp40)
REVERT: M  259 TYR cc_start: 0.9334 (t80) cc_final: 0.8889 (t80)
REVERT: M  271 GLN cc_start: 0.9348 (mt0) cc_final: 0.9043 (mt0)
REVERT: O  237 TYR cc_start: 0.8194 (m-80) cc_final: 0.7917 (m-80)
REVERT: U   24 ASP cc_start: 0.8072 (p0) cc_final: 0.7805 (p0)
REVERT: U   35 ASP cc_start: 0.7978 (p0) cc_final: 0.6986 (p0)
REVERT: U   37 GLN cc_start: 0.9374 (mp-120) cc_final: 0.8604 (mp10)
REVERT: V   89 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8618 (tptt)
REVERT: a   11 CYS cc_start: 0.9318 (m) cc_final: 0.8859 (m)
REVERT: a   35 ASN cc_start: 0.9302 (m110) cc_final: 0.9062 (m110)
REVERT: a  119 HIS cc_start: 0.8860 (m-70) cc_final: 0.8494 (m90)
REVERT: b  143 THR cc_start: 0.8919 (m) cc_final: 0.8527 (p)
REVERT: b  204 MET cc_start: 0.8338 (mmm) cc_final: 0.8006 (mmm)
REVERT: c  149 TYR cc_start: 0.8654 (t80) cc_final: 0.8331 (t80)
REVERT: c  248 LEU cc_start: 0.9148 (tp) cc_final: 0.8858 (tp)
REVERT: c  315 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6125 (tp)
  outliers start: 29
  outliers final: 19
  residues processed: 177
  average time/residue: 0.1065
  time to fit residues: 28.8061
Evaluate side-chains
  166 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  251 ILE
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   31 ASP
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   71 VAL
Chi-restraints excluded: chain a residue   74 ILE
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  155 THR
Chi-restraints excluded: chain c residue  216 HIS
Chi-restraints excluded: chain c residue  315 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:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 131 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
V  39 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.081229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.060228 restraints weight = 67306.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.061670 restraints weight = 32888.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.062446 restraints weight = 21489.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.062929 restraints weight = 17104.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.063235 restraints weight = 15193.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14627  Z= 0.154
  Angle     :  0.636  10.584  20120  Z= 0.337
  Chirality :  0.041   0.382   2206
  Planarity :  0.004   0.070   2263
  Dihedral  : 21.890 144.987   2641
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.73 %
    Favored  : 82.25 %
  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:  0.66 (0.22), residues: 1474
  helix:  1.53 (0.19), residues: 767
  sheet:  0.22 (0.47), residues: 111
  loop : -0.96 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG V  51 
 TYR   0.011   0.001   TYR a 146 
 PHE   0.016   0.001   PHE U 351 
 TRP   0.013   0.001   TRP a 226 
 HIS   0.008   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14619)
  covalent geometry    : angle       0.63242 (20112)
  hydrogen bonds       : bond        0.03573 (  750)
  hydrogen bonds       : angle       4.17564 ( 2104)
  metal coordination   : bond        0.00606 (    8)
  metal coordination   : angle       3.61551 (    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
  183 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9177 (m-40) cc_final: 0.8764 (m110)
REVERT: M  227 GLN cc_start: 0.8901 (pm20) cc_final: 0.8668 (pm20)
REVERT: M  229 GLN cc_start: 0.9273 (tp40) cc_final: 0.9009 (tp40)
REVERT: M  259 TYR cc_start: 0.9323 (t80) cc_final: 0.8897 (t80)
REVERT: O  237 TYR cc_start: 0.8156 (m-80) cc_final: 0.7912 (m-80)
REVERT: U   35 ASP cc_start: 0.7845 (p0) cc_final: 0.6863 (p0)
REVERT: U   36 GLU cc_start: 0.8687 (tp30) cc_final: 0.7761 (tp30)
REVERT: U   37 GLN cc_start: 0.9366 (mp-120) cc_final: 0.8092 (mp10)
REVERT: V   89 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8599 (tptt)
REVERT: a   11 CYS cc_start: 0.9318 (m) cc_final: 0.8863 (m)
REVERT: a   35 ASN cc_start: 0.9307 (m110) cc_final: 0.9068 (m110)
REVERT: a  119 HIS cc_start: 0.8818 (m-70) cc_final: 0.8456 (m90)
REVERT: b  143 THR cc_start: 0.8886 (m) cc_final: 0.8497 (p)
REVERT: c  149 TYR cc_start: 0.8555 (t80) cc_final: 0.8208 (t80)
REVERT: c  248 LEU cc_start: 0.9157 (tp) cc_final: 0.8879 (tp)
REVERT: c  315 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6137 (tp)
  outliers start: 27
  outliers final: 20
  residues processed: 176
  average time/residue: 0.1064
  time to fit residues: 28.6220
Evaluate side-chains
  165 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  251 ILE
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   31 ASP
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain U residue   47 GLU
Chi-restraints excluded: chain U residue  338 GLN
Chi-restraints excluded: chain U residue  351 PHE
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   74 ILE
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 148 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 115 optimal weight:    3.9990
   chunk 143 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0870
   chunk 153 optimal weight:    8.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 271 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**
** 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 = 0.3961 r_free = 0.3961 target = 0.081781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.060822 restraints weight = 67211.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.062260 restraints weight = 32579.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.063077 restraints weight = 21426.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.063445 restraints weight = 17006.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.063738 restraints weight = 15246.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14627  Z= 0.144
  Angle     :  0.659  16.245  20120  Z= 0.345
  Chirality :  0.040   0.240   2206
  Planarity :  0.004   0.061   2263
  Dihedral  : 21.847 145.581   2641
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.73 %
    Favored  : 82.32 %
  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:  0.69 (0.22), residues: 1474
  helix:  1.51 (0.19), residues: 767
  sheet:  0.56 (0.49), residues: 107
  loop : -0.94 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG V  51 
 TYR   0.034   0.001   TYR a  83 
 PHE   0.014   0.001   PHE U 351 
 TRP   0.014   0.001   TRP a 226 
 HIS   0.007   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14619)
  covalent geometry    : angle       0.65532 (20112)
  hydrogen bonds       : bond        0.03633 (  750)
  hydrogen bonds       : angle       4.17795 ( 2104)
  metal coordination   : bond        0.00465 (    8)
  metal coordination   : angle       3.31781 (    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
  179 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9087 (m-40) cc_final: 0.8729 (m110)
REVERT: M  227 GLN cc_start: 0.8837 (pm20) cc_final: 0.8573 (pm20)
REVERT: M  229 GLN cc_start: 0.9220 (tp40) cc_final: 0.8976 (tp40)
REVERT: M  259 TYR cc_start: 0.9270 (t80) cc_final: 0.8853 (t80)
REVERT: O  237 TYR cc_start: 0.8139 (m-80) cc_final: 0.7925 (m-80)
REVERT: U   35 ASP cc_start: 0.7731 (p0) cc_final: 0.7094 (p0)
REVERT: U   37 GLN cc_start: 0.9038 (mp-120) cc_final: 0.8543 (mp10)
REVERT: V   89 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8606 (tptt)
REVERT: a   35 ASN cc_start: 0.9247 (m110) cc_final: 0.9011 (m-40)
REVERT: a   83 TYR cc_start: 0.8406 (t80) cc_final: 0.8167 (t80)
REVERT: a   87 ASN cc_start: 0.9225 (m-40) cc_final: 0.8923 (m110)
REVERT: b  143 THR cc_start: 0.8909 (m) cc_final: 0.8527 (p)
REVERT: c  149 TYR cc_start: 0.8467 (t80) cc_final: 0.8138 (t80)
REVERT: c  248 LEU cc_start: 0.9125 (tp) cc_final: 0.8858 (tp)
REVERT: c  315 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6113 (tp)
REVERT: d    9 ARG cc_start: 0.8067 (tmm160) cc_final: 0.7867 (tmm160)
  outliers start: 26
  outliers final: 21
  residues processed: 171
  average time/residue: 0.1003
  time to fit residues: 26.7626
Evaluate side-chains
  165 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  251 ILE
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   31 ASP
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain U residue   47 GLU
Chi-restraints excluded: chain U residue  351 PHE
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  194 ILE
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  175 ILE
Chi-restraints excluded: chain b residue  234 THR
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  155 THR
Chi-restraints excluded: chain c residue  216 HIS
Chi-restraints excluded: chain c residue  315 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0980
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0970
   chunk 46 optimal weight:    0.9990
   chunk 139 optimal weight:    4.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 271 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.081003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.059976 restraints weight = 67800.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.061365 restraints weight = 33021.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.062195 restraints weight = 21700.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.062598 restraints weight = 17264.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.063050 restraints weight = 15463.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.4691

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= 0.164
  Angle     :  0.684  15.155  20120  Z= 0.356
  Chirality :  0.041   0.208   2206
  Planarity :  0.004   0.067   2263
  Dihedral  : 21.859 146.931   2641
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 16.40 %
    Favored  : 82.02 %
  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:  0.68 (0.22), residues: 1474
  helix:  1.49 (0.19), residues: 767
  sheet:  0.15 (0.49), residues: 116
  loop : -0.87 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG V  51 
 TYR   0.035   0.001   TYR a  83 
 PHE   0.015   0.001   PHE U 351 
 TRP   0.021   0.001   TRP a 226 
 HIS   0.008   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (14619)
  covalent geometry    : angle       0.68016 (20112)
  hydrogen bonds       : bond        0.03618 (  750)
  hydrogen bonds       : angle       4.23483 ( 2104)
  metal coordination   : bond        0.00687 (    8)
  metal coordination   : angle       3.47619 (    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: 21
    poor density    : 151
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9143 (m-40) cc_final: 0.8770 (m110)
REVERT: M  229 GLN cc_start: 0.9232 (tp40) cc_final: 0.8993 (tp40)
REVERT: M  259 TYR cc_start: 0.9293 (t80) cc_final: 0.8873 (t80)
REVERT: U   35 ASP cc_start: 0.7822 (p0) cc_final: 0.7065 (p0)
REVERT: U   37 GLN cc_start: 0.9296 (mp-120) cc_final: 0.8198 (mp10)
REVERT: a   35 ASN cc_start: 0.9300 (m110) cc_final: 0.9081 (m110)
REVERT: b  143 THR cc_start: 0.8892 (m) cc_final: 0.8508 (p)
REVERT: c  149 TYR cc_start: 0.8548 (t80) cc_final: 0.8173 (t80)
REVERT: c  248 LEU cc_start: 0.9179 (tp) cc_final: 0.8903 (tp)
REVERT: c  315 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6116 (tp)
  outliers start: 21
  outliers final: 19
  residues processed: 164
  average time/residue: 0.1022
  time to fit residues: 25.7338
Evaluate side-chains
  164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  251 ILE
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   31 ASP
Chi-restraints excluded: chain U residue   47 GLU
Chi-restraints excluded: chain U residue  351 PHE
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  194 ILE
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  175 ILE
Chi-restraints excluded: chain b residue  234 THR
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  216 HIS
Chi-restraints excluded: chain c residue  315 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:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 55 optimal weight:    0.1980
   chunk 151 optimal weight:    8.9990
   chunk 100 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 271 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.080115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.058617 restraints weight = 67583.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.060010 restraints weight = 33191.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.060763 restraints weight = 21881.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.061279 restraints weight = 17666.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.061541 restraints weight = 15626.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14627  Z= 0.189
  Angle     :  0.714  15.549  20120  Z= 0.372
  Chirality :  0.041   0.205   2206
  Planarity :  0.004   0.059   2263
  Dihedral  : 21.905 148.704   2641
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.78 %
    Favored  : 81.42 %
  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:  0.59 (0.22), residues: 1474
  helix:  1.41 (0.19), residues: 773
  sheet:  0.02 (0.48), residues: 116
  loop : -0.90 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG V  51 
 TYR   0.016   0.001   TYR a  83 
 PHE   0.014   0.001   PHE U 351 
 TRP   0.016   0.001   TRP a 226 
 HIS   0.007   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (14619)
  covalent geometry    : angle       0.70996 (20112)
  hydrogen bonds       : bond        0.03738 (  750)
  hydrogen bonds       : angle       4.31343 ( 2104)
  metal coordination   : bond        0.00873 (    8)
  metal coordination   : angle       4.00247 (    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
  172 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9132 (m-40) cc_final: 0.8767 (m110)
REVERT: M  259 TYR cc_start: 0.9269 (t80) cc_final: 0.8841 (t80)
REVERT: U   35 ASP cc_start: 0.7713 (p0) cc_final: 0.7207 (p0)
REVERT: U   37 GLN cc_start: 0.9027 (mp-120) cc_final: 0.8440 (mp10)
REVERT: a  185 ASP cc_start: 0.8716 (t0) cc_final: 0.8378 (p0)
REVERT: c  149 TYR cc_start: 0.8678 (t80) cc_final: 0.8298 (t80)
REVERT: c  315 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6092 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 163
  average time/residue: 0.1062
  time to fit residues: 26.4508
Evaluate side-chains
  160 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  251 ILE
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   31 ASP
Chi-restraints excluded: chain U residue   47 GLU
Chi-restraints excluded: chain U residue  351 PHE
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue   74 ILE
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  175 ILE
Chi-restraints excluded: chain b residue  234 THR
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  216 HIS
Chi-restraints excluded: chain c residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 129 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 135 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 138 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 119 HIS
** 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 = 0.3950 r_free = 0.3950 target = 0.081116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.059652 restraints weight = 67234.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.061034 restraints weight = 33069.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.061886 restraints weight = 21846.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.062279 restraints weight = 17487.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.062551 restraints weight = 15741.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.5074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  14627  Z= 0.149
  Angle     :  0.701  16.020  20120  Z= 0.367
  Chirality :  0.041   0.198   2206
  Planarity :  0.004   0.060   2263
  Dihedral  : 21.808 149.825   2641
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.53 %
    Favored  : 81.05 %
  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:  0.63 (0.23), residues: 1474
  helix:  1.43 (0.19), residues: 771
  sheet:  0.12 (0.48), residues: 116
  loop : -0.86 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG V  51 
 TYR   0.020   0.001   TYR a  83 
 PHE   0.015   0.001   PHE U 351 
 TRP   0.015   0.001   TRP a 226 
 HIS   0.008   0.001   HIS a 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (14619)
  covalent geometry    : angle       0.69816 (20112)
  hydrogen bonds       : bond        0.03610 (  750)
  hydrogen bonds       : angle       4.32411 ( 2104)
  metal coordination   : bond        0.00447 (    8)
  metal coordination   : angle       3.42199 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3182.56 seconds
wall clock time: 55 minutes 19.58 seconds (3319.58 seconds total)