Starting phenix.real_space_refine
on Thu Jun 12 17:18:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxe_15009/06_2025/7zxe_15009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxe_15009/06_2025/7zxe_15009.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/06_2025/7zxe_15009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxe_15009/06_2025/7zxe_15009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxe_15009/06_2025/7zxe_15009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxe_15009/06_2025/7zxe_15009.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.50, per 1000 atoms: 0.67
  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: 3.72
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  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: 5.26
  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: 4.39

  Time building geometry restraints manager: 4.37 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:             5.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     40.740
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.000
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (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
 TRP   0.028   0.001   TRP a 226 
 HIS   0.006   0.001   HIS c 369 
 PHE   0.025   0.001   PHE V  81 
 TYR   0.018   0.001   TYR c 141 
 ARG   0.006   0.000   ARG V  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10980 (  750)
  hydrogen bonds       : angle       5.30184 ( 2104)
  metal coordination   : bond        0.00436 (    8)
  metal coordination   : angle       1.96029 (    8)
  covalent geometry    : bond        0.00282 (14619)
  covalent geometry    : angle       0.54787 (20112)

*********************** 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  : 1.468 
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: 0.2398
  time to fit residues: 75.3228
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  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 116 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 120 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 139 optimal weight:    5.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 256 GLN
a 188 GLN
b 139 HIS
** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.080120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.058804 restraints weight = 68238.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.060201 restraints weight = 33250.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.061027 restraints weight = 21897.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067  14627  Z= 0.365
  Angle     :  0.808  10.262  20120  Z= 0.431
  Chirality :  0.048   0.212   2206
  Planarity :  0.006   0.073   2263
  Dihedral  : 22.418 150.923   2641
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  8.24 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.21), residues: 1474
  helix:  1.09 (0.18), residues: 760
  sheet: -0.58 (0.44), residues: 111
  loop : -1.23 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP a 226 
 HIS   0.014   0.002   HIS U 343 
 PHE   0.025   0.002   PHE U 351 
 TYR   0.026   0.002   TYR O 237 
 ARG   0.015   0.001   ARG d  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05716 (  750)
  hydrogen bonds       : angle       4.78413 ( 2104)
  metal coordination   : bond        0.01700 (    8)
  metal coordination   : angle       5.62222 (    8)
  covalent geometry    : bond        0.00792 (14619)
  covalent geometry    : angle       0.80031 (20112)

*********************** 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
  178 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  304 PHE cc_start: 0.8659 (t80) cc_final: 0.8388 (t80)
REVERT: U   24 ASP cc_start: 0.7997 (p0) cc_final: 0.7788 (p0)
REVERT: U   37 GLN cc_start: 0.9136 (mp-120) cc_final: 0.8501 (mp10)
REVERT: U   40 MET cc_start: 0.8706 (ptt) cc_final: 0.8362 (ptt)
REVERT: V   56 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (t)
REVERT: V   83 GLU cc_start: 0.7857 (pp20) cc_final: 0.7346 (pp20)
REVERT: V   84 VAL cc_start: 0.8933 (t) cc_final: 0.8202 (p)
REVERT: a   35 ASN cc_start: 0.9274 (m110) cc_final: 0.9044 (m110)
REVERT: a  119 HIS cc_start: 0.8912 (m-70) cc_final: 0.8005 (m90)
REVERT: b  143 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8523 (p)
REVERT: b  340 TYR cc_start: 0.7020 (t80) cc_final: 0.6715 (t80)
REVERT: c  248 LEU cc_start: 0.9109 (tp) cc_final: 0.8858 (tp)
  outliers start: 25
  outliers final: 18
  residues processed: 170
  average time/residue: 0.2463
  time to fit residues: 63.0383
Evaluate side-chains
  147 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  116 ASN
Chi-restraints excluded: chain M residue  215 MET
Chi-restraints excluded: chain M residue  283 VAL
Chi-restraints excluded: chain O residue  171 THR
Chi-restraints excluded: chain O residue  221 CYS
Chi-restraints excluded: chain O residue  275 LEU
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   56 VAL
Chi-restraints excluded: chain a residue   88 THR
Chi-restraints excluded: chain a residue   99 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   39 THR
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue   61 LEU
Chi-restraints excluded: chain b residue  143 THR
Chi-restraints excluded: chain b residue  289 GLN
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  197 VAL
Chi-restraints excluded: chain c residue  216 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 145 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
M 116 ASN
M 221 ASN
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 166 GLN
a  73 GLN
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
a 232 ASN
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 144 HIS
c 268 ASN
c 369 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.082292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.061085 restraints weight = 67192.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.062505 restraints weight = 32556.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.063391 restraints weight = 21251.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3389

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= 0.154
  Angle     :  0.616  10.057  20120  Z= 0.331
  Chirality :  0.040   0.158   2206
  Planarity :  0.004   0.064   2263
  Dihedral  : 22.114 147.393   2641
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.69 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.22), residues: 1474
  helix:  1.50 (0.19), residues: 758
  sheet: -0.61 (0.43), residues: 118
  loop : -1.13 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP a 226 
 HIS   0.008   0.001   HIS a 227 
 PHE   0.014   0.001   PHE U 351 
 TYR   0.016   0.001   TYR b 340 
 ARG   0.005   0.000   ARG M 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  750)
  hydrogen bonds       : angle       4.24461 ( 2104)
  metal coordination   : bond        0.00625 (    8)
  metal coordination   : angle       3.90539 (    8)
  covalent geometry    : bond        0.00329 (14619)
  covalent geometry    : angle       0.61095 (20112)

*********************** 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: 15
    poor density    : 168
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  229 GLN cc_start: 0.9066 (tp40) cc_final: 0.8460 (tp40)
REVERT: M  259 TYR cc_start: 0.9249 (t80) cc_final: 0.8887 (t80)
REVERT: M  271 GLN cc_start: 0.9284 (mt0) cc_final: 0.8992 (mt0)
REVERT: O  237 TYR cc_start: 0.8140 (m-80) cc_final: 0.7760 (m-80)
REVERT: U   24 ASP cc_start: 0.8040 (p0) cc_final: 0.7486 (p0)
REVERT: U   35 ASP cc_start: 0.7767 (p0) cc_final: 0.6604 (p0)
REVERT: U   37 GLN cc_start: 0.9245 (mp-120) cc_final: 0.8425 (mp10)
REVERT: U   40 MET cc_start: 0.8704 (ptt) cc_final: 0.8424 (ptt)
REVERT: U  348 LYS cc_start: 0.9056 (mppt) cc_final: 0.8841 (mmtm)
REVERT: V   83 GLU cc_start: 0.7820 (pp20) cc_final: 0.7346 (pp20)
REVERT: V   84 VAL cc_start: 0.8871 (t) cc_final: 0.8072 (p)
REVERT: a   35 ASN cc_start: 0.9328 (m110) cc_final: 0.9070 (m110)
REVERT: a  119 HIS cc_start: 0.8807 (m-70) cc_final: 0.7893 (m90)
REVERT: b  204 MET cc_start: 0.8193 (mmm) cc_final: 0.7903 (mmm)
REVERT: b  293 MET cc_start: 0.7719 (ttt) cc_final: 0.7464 (ttt)
REVERT: c  248 LEU cc_start: 0.9126 (tp) cc_final: 0.8847 (tp)
  outliers start: 15
  outliers final: 7
  residues processed: 176
  average time/residue: 0.2405
  time to fit residues: 65.2303
Evaluate side-chains
  146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  183 VAL
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 V residue   15 LEU
Chi-restraints excluded: chain c residue  164 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0060
   chunk 42 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 102 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 237 GLN
b 299 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 = 0.3961 r_free = 0.3961 target = 0.082089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.060886 restraints weight = 67522.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.062323 restraints weight = 33073.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.063202 restraints weight = 21539.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3649

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= 0.149
  Angle     :  0.603  10.747  20120  Z= 0.320
  Chirality :  0.040   0.174   2206
  Planarity :  0.004   0.062   2263
  Dihedral  : 22.038 148.156   2641
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.41 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.22), residues: 1474
  helix:  1.43 (0.19), residues: 766
  sheet: -0.41 (0.44), residues: 118
  loop : -1.09 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP a 226 
 HIS   0.024   0.001   HIS a 227 
 PHE   0.013   0.001   PHE U 351 
 TYR   0.022   0.001   TYR b 340 
 ARG   0.005   0.000   ARG d   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  750)
  hydrogen bonds       : angle       4.11918 ( 2104)
  metal coordination   : bond        0.00538 (    8)
  metal coordination   : angle       3.42574 (    8)
  covalent geometry    : bond        0.00327 (14619)
  covalent geometry    : angle       0.59922 (20112)

*********************** 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
  174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  229 GLN cc_start: 0.9053 (tp40) cc_final: 0.8585 (tp40)
REVERT: M  259 TYR cc_start: 0.9223 (t80) cc_final: 0.8790 (t80)
REVERT: O  237 TYR cc_start: 0.8141 (m-80) cc_final: 0.7830 (m-80)
REVERT: U   24 ASP cc_start: 0.7960 (p0) cc_final: 0.7748 (p0)
REVERT: U   36 GLU cc_start: 0.8503 (tp30) cc_final: 0.6926 (tp30)
REVERT: U   37 GLN cc_start: 0.9237 (mp-120) cc_final: 0.8634 (mm-40)
REVERT: U  348 LYS cc_start: 0.9063 (mppt) cc_final: 0.8843 (mmtm)
REVERT: V   83 GLU cc_start: 0.7814 (pp20) cc_final: 0.7376 (pp20)
REVERT: V   84 VAL cc_start: 0.8842 (t) cc_final: 0.7963 (p)
REVERT: a   35 ASN cc_start: 0.9289 (m110) cc_final: 0.9044 (m-40)
REVERT: a  119 HIS cc_start: 0.8837 (m-70) cc_final: 0.8502 (m90)
REVERT: a  140 MET cc_start: 0.8589 (mmt) cc_final: 0.7414 (mmt)
REVERT: b  143 THR cc_start: 0.8864 (m) cc_final: 0.8472 (p)
REVERT: b  340 TYR cc_start: 0.6855 (t80) cc_final: 0.6641 (t80)
REVERT: c  142 MET cc_start: 0.8574 (tpp) cc_final: 0.8209 (tpp)
REVERT: c  248 LEU cc_start: 0.9106 (tp) cc_final: 0.8831 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 166
  average time/residue: 0.2383
  time to fit residues: 59.6033
Evaluate side-chains
  158 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
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 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   36 VAL
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  186 ILE
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain d residue   29 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0000
   chunk 79 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 145 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
M 271 GLN
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3930 r_free = 0.3930 target = 0.080635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.059255 restraints weight = 67477.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.060661 restraints weight = 33052.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.061383 restraints weight = 21744.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14627  Z= 0.192
  Angle     :  0.637  10.995  20120  Z= 0.338
  Chirality :  0.041   0.173   2206
  Planarity :  0.004   0.061   2263
  Dihedral  : 22.099 151.198   2641
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.61 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.22), residues: 1474
  helix:  1.50 (0.19), residues: 766
  sheet: -0.35 (0.45), residues: 118
  loop : -1.04 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP a 226 
 HIS   0.004   0.001   HIS a 227 
 PHE   0.013   0.001   PHE O 325 
 TYR   0.020   0.001   TYR a  83 
 ARG   0.008   0.000   ARG d   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03834 (  750)
  hydrogen bonds       : angle       4.13772 ( 2104)
  metal coordination   : bond        0.00947 (    8)
  metal coordination   : angle       3.89525 (    8)
  covalent geometry    : bond        0.00425 (14619)
  covalent geometry    : angle       0.63194 (20112)

*********************** 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
  175 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  259 TYR cc_start: 0.9218 (t80) cc_final: 0.8800 (t80)
REVERT: O  237 TYR cc_start: 0.8188 (m-80) cc_final: 0.7854 (m-80)
REVERT: U   35 ASP cc_start: 0.8031 (p0) cc_final: 0.6551 (p0)
REVERT: U   37 GLN cc_start: 0.8998 (mp-120) cc_final: 0.8434 (mp10)
REVERT: U  348 LYS cc_start: 0.9138 (mppt) cc_final: 0.8892 (mmtm)
REVERT: V   91 ASP cc_start: 0.8510 (t0) cc_final: 0.8285 (t0)
REVERT: a   35 ASN cc_start: 0.9270 (m110) cc_final: 0.9022 (m110)
REVERT: a  119 HIS cc_start: 0.8818 (m-70) cc_final: 0.8469 (m90)
REVERT: c  248 LEU cc_start: 0.9145 (tp) cc_final: 0.8873 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 166
  average time/residue: 0.2557
  time to fit residues: 64.0354
Evaluate side-chains
  157 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 1.604 
-------------------------------------------------------------------------------
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  338 GLN
Chi-restraints excluded: chain U residue  351 PHE
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   71 VAL
Chi-restraints excluded: chain V residue   80 GLU
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  186 ILE
Chi-restraints excluded: chain c residue  164 ASP
Chi-restraints excluded: chain c residue  216 HIS
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 18 optimal weight:    9.9990
   chunk 73 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 116 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 120 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.080552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.058964 restraints weight = 67077.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.060353 restraints weight = 32836.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.061059 restraints weight = 21704.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14627  Z= 0.173
  Angle     :  0.637  10.352  20120  Z= 0.337
  Chirality :  0.040   0.163   2206
  Planarity :  0.004   0.062   2263
  Dihedral  : 22.055 153.416   2641
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.36 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.22), residues: 1474
  helix:  1.46 (0.19), residues: 767
  sheet: -0.19 (0.46), residues: 111
  loop : -1.02 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP a 226 
 HIS   0.027   0.001   HIS a 227 
 PHE   0.017   0.001   PHE U 351 
 TYR   0.014   0.001   TYR a  65 
 ARG   0.006   0.000   ARG d   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  750)
  hydrogen bonds       : angle       4.18260 ( 2104)
  metal coordination   : bond        0.00781 (    8)
  metal coordination   : angle       3.87302 (    8)
  covalent geometry    : bond        0.00385 (14619)
  covalent geometry    : angle       0.63206 (20112)

*********************** 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
  178 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 1.453 
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: 0.9205 (m-40) cc_final: 0.8819 (m110)
REVERT: M  229 GLN cc_start: 0.9178 (tp40) cc_final: 0.8937 (tp40)
REVERT: M  259 TYR cc_start: 0.9245 (t80) cc_final: 0.8788 (t80)
REVERT: O  237 TYR cc_start: 0.8187 (m-80) cc_final: 0.7879 (m-80)
REVERT: U   35 ASP cc_start: 0.8166 (p0) cc_final: 0.7395 (p0)
REVERT: U   37 GLN cc_start: 0.9054 (mp-120) cc_final: 0.8514 (mp10)
REVERT: U  348 LYS cc_start: 0.9166 (mppt) cc_final: 0.8930 (mmtm)
REVERT: V   35 GLN cc_start: 0.8657 (mp10) cc_final: 0.8318 (mp10)
REVERT: V   89 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8688 (tptt)
REVERT: a   35 ASN cc_start: 0.9301 (m110) cc_final: 0.9062 (m-40)
REVERT: a  119 HIS cc_start: 0.8847 (m-70) cc_final: 0.8519 (m90)
REVERT: c  142 MET cc_start: 0.8574 (tpp) cc_final: 0.8333 (tpp)
REVERT: c  248 LEU cc_start: 0.9176 (tp) cc_final: 0.8901 (tp)
REVERT: c  315 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6297 (tp)
REVERT: c  356 MET cc_start: 0.8934 (tpp) cc_final: 0.8339 (tpp)
  outliers start: 28
  outliers final: 17
  residues processed: 169
  average time/residue: 0.2553
  time to fit residues: 64.8684
Evaluate side-chains
  161 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
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  338 GLN
Chi-restraints excluded: chain U residue  351 PHE
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  186 ILE
Chi-restraints excluded: chain b residue  365 VAL
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 148 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 16 optimal weight:    0.3980
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 140 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.8584

-------------------------------------------------------------------------------
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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  39 GLN
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 237 GLN
** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 219 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.079339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.057733 restraints weight = 67560.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.059148 restraints weight = 33160.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.059965 restraints weight = 21880.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  14627  Z= 0.204
  Angle     :  0.660   9.714  20120  Z= 0.348
  Chirality :  0.041   0.190   2206
  Planarity :  0.004   0.060   2263
  Dihedral  : 22.138 156.947   2641
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.25 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.22), residues: 1474
  helix:  1.48 (0.19), residues: 766
  sheet: -0.09 (0.47), residues: 106
  loop : -1.05 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP a 226 
 HIS   0.004   0.001   HIS a 227 
 PHE   0.017   0.001   PHE U 351 
 TYR   0.020   0.001   TYR a  83 
 ARG   0.005   0.000   ARG d   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03877 (  750)
  hydrogen bonds       : angle       4.22335 ( 2104)
  metal coordination   : bond        0.01053 (    8)
  metal coordination   : angle       4.22462 (    8)
  covalent geometry    : bond        0.00455 (14619)
  covalent geometry    : angle       0.65512 (20112)

*********************** 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
  170 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  221 ASN cc_start: 0.9191 (m-40) cc_final: 0.8807 (m110)
REVERT: M  229 GLN cc_start: 0.9190 (tp40) cc_final: 0.8918 (tp40)
REVERT: M  259 TYR cc_start: 0.9234 (t80) cc_final: 0.8764 (t80)
REVERT: O  237 TYR cc_start: 0.8214 (m-80) cc_final: 0.8000 (m-80)
REVERT: U   35 ASP cc_start: 0.7984 (p0) cc_final: 0.7055 (p0)
REVERT: U   37 GLN cc_start: 0.9087 (mp-120) cc_final: 0.8511 (mp10)
REVERT: U   40 MET cc_start: 0.8564 (mmm) cc_final: 0.7883 (mmm)
REVERT: U  348 LYS cc_start: 0.9170 (mppt) cc_final: 0.8933 (mmtm)
REVERT: a   35 ASN cc_start: 0.9277 (m110) cc_final: 0.9043 (m110)
REVERT: a  119 HIS cc_start: 0.8863 (m-70) cc_final: 0.8556 (m90)
REVERT: b  386 MET cc_start: 0.8928 (mmm) cc_final: 0.8680 (mmm)
REVERT: c  248 LEU cc_start: 0.9152 (tp) cc_final: 0.8891 (tp)
REVERT: c  315 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6430 (tp)
REVERT: c  356 MET cc_start: 0.8858 (tpp) cc_final: 0.8290 (tpp)
  outliers start: 25
  outliers final: 18
  residues processed: 163
  average time/residue: 0.2404
  time to fit residues: 59.9354
Evaluate side-chains
  159 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
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  338 GLN
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  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  174 MET
Chi-restraints excluded: chain b residue  186 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 153 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 99 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3924 r_free = 0.3924 target = 0.080115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.059042 restraints weight = 67468.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.060461 restraints weight = 32718.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.061291 restraints weight = 21472.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4879

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= 0.152
  Angle     :  0.651  10.784  20120  Z= 0.339
  Chirality :  0.040   0.185   2206
  Planarity :  0.004   0.071   2263
  Dihedral  : 22.082 157.448   2641
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.22), residues: 1474
  helix:  1.49 (0.19), residues: 769
  sheet: -0.17 (0.46), residues: 111
  loop : -0.99 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP a 226 
 HIS   0.017   0.001   HIS a 227 
 PHE   0.016   0.001   PHE U 367 
 TYR   0.012   0.001   TYR a  83 
 ARG   0.016   0.000   ARG V  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  750)
  hydrogen bonds       : angle       4.12185 ( 2104)
  metal coordination   : bond        0.00599 (    8)
  metal coordination   : angle       3.80421 (    8)
  covalent geometry    : bond        0.00336 (14619)
  covalent geometry    : angle       0.64646 (20112)

*********************** 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
  175 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.595 
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: 0.9193 (m-40) cc_final: 0.8782 (m110)
REVERT: M  227 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8657 (pm20)
REVERT: M  229 GLN cc_start: 0.9186 (tp40) cc_final: 0.8906 (tp40)
REVERT: M  259 TYR cc_start: 0.9241 (t80) cc_final: 0.8777 (t80)
REVERT: U   35 ASP cc_start: 0.8070 (p0) cc_final: 0.7159 (p0)
REVERT: U   36 GLU cc_start: 0.8172 (tp30) cc_final: 0.7867 (tp30)
REVERT: U   37 GLN cc_start: 0.9106 (mp-120) cc_final: 0.8560 (mp10)
REVERT: U   40 MET cc_start: 0.8411 (mmm) cc_final: 0.7898 (mmm)
REVERT: U  346 LYS cc_start: 0.8073 (tptt) cc_final: 0.7621 (tptp)
REVERT: U  348 LYS cc_start: 0.9184 (mppt) cc_final: 0.8959 (mmtm)
REVERT: U  355 ASP cc_start: 0.8475 (p0) cc_final: 0.8091 (p0)
REVERT: V   35 GLN cc_start: 0.8646 (mp10) cc_final: 0.8344 (mp10)
REVERT: V   91 ASP cc_start: 0.8528 (t0) cc_final: 0.8326 (t0)
REVERT: a   35 ASN cc_start: 0.9309 (m110) cc_final: 0.9092 (m110)
REVERT: a  140 MET cc_start: 0.8635 (mmt) cc_final: 0.7513 (mmt)
REVERT: b  386 MET cc_start: 0.9000 (mmm) cc_final: 0.8738 (mmm)
REVERT: c  315 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6339 (tp)
REVERT: c  356 MET cc_start: 0.8894 (tpp) cc_final: 0.8330 (tpp)
  outliers start: 22
  outliers final: 19
  residues processed: 169
  average time/residue: 0.2501
  time to fit residues: 64.5464
Evaluate side-chains
  160 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 1.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  227 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  317 VAL
Chi-restraints excluded: chain U residue   31 ASP
Chi-restraints excluded: chain U residue   39 LEU
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   36 VAL
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  175 ILE
Chi-restraints excluded: chain b residue  186 ILE
Chi-restraints excluded: chain b residue  354 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 146 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   chunk 112 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 50 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3937 r_free = 0.3937 target = 0.080666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.059466 restraints weight = 66722.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.060840 restraints weight = 32409.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.061638 restraints weight = 21364.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
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      :  0.003   0.040  14627  Z= 0.142
  Angle     :  0.665  11.732  20120  Z= 0.346
  Chirality :  0.041   0.370   2206
  Planarity :  0.004   0.060   2263
  Dihedral  : 22.024 157.874   2641
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.38 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.22), residues: 1474
  helix:  1.50 (0.19), residues: 768
  sheet: -0.08 (0.47), residues: 111
  loop : -0.86 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP a 226 
 HIS   0.006   0.001   HIS a 227 
 PHE   0.018   0.001   PHE M 304 
 TYR   0.018   0.001   TYR b 340 
 ARG   0.012   0.000   ARG V  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  750)
  hydrogen bonds       : angle       4.11420 ( 2104)
  metal coordination   : bond        0.00478 (    8)
  metal coordination   : angle       3.47056 (    8)
  covalent geometry    : bond        0.00314 (14619)
  covalent geometry    : angle       0.66135 (20112)

*********************** 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
  178 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 1.529 
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: 0.9132 (m-40) cc_final: 0.8771 (m110)
REVERT: M  227 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (pm20)
REVERT: M  229 GLN cc_start: 0.9127 (tp40) cc_final: 0.8914 (tp40)
REVERT: M  259 TYR cc_start: 0.9189 (t80) cc_final: 0.8731 (t80)
REVERT: U   37 GLN cc_start: 0.9098 (mp-120) cc_final: 0.8711 (mp10)
REVERT: U   40 MET cc_start: 0.8367 (mmm) cc_final: 0.8049 (mmm)
REVERT: U  346 LYS cc_start: 0.7935 (tptt) cc_final: 0.7573 (tptp)
REVERT: U  348 LYS cc_start: 0.9130 (mppt) cc_final: 0.8921 (mppt)
REVERT: U  355 ASP cc_start: 0.8381 (p0) cc_final: 0.7955 (p0)
REVERT: V   35 GLN cc_start: 0.8554 (mp10) cc_final: 0.8217 (mp10)
REVERT: a   35 ASN cc_start: 0.9257 (m110) cc_final: 0.9055 (m-40)
REVERT: a  140 MET cc_start: 0.8558 (mmt) cc_final: 0.7425 (mmt)
REVERT: b  386 MET cc_start: 0.8870 (mmm) cc_final: 0.8651 (mmm)
REVERT: c  315 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6358 (tp)
REVERT: c  356 MET cc_start: 0.8819 (tpp) cc_final: 0.8315 (tpp)
REVERT: d    9 ARG cc_start: 0.8137 (tmm160) cc_final: 0.7722 (ptm-80)
  outliers start: 23
  outliers final: 17
  residues processed: 171
  average time/residue: 0.2459
  time to fit residues: 64.4192
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  : 1.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  227 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  317 VAL
Chi-restraints excluded: chain U residue   31 ASP
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain U residue  351 PHE
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   36 VAL
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  175 ILE
Chi-restraints excluded: chain b residue  186 ILE
Chi-restraints excluded: chain b residue  354 CYS
Chi-restraints excluded: chain b residue  365 VAL
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 22 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 95 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 145 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  50 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 = 0.3921 r_free = 0.3921 target = 0.079931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.058538 restraints weight = 66989.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.059914 restraints weight = 32797.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.060738 restraints weight = 21687.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.5163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  14627  Z= 0.171
  Angle     :  0.709  14.811  20120  Z= 0.364
  Chirality :  0.041   0.329   2206
  Planarity :  0.004   0.059   2263
  Dihedral  : 22.050 159.693   2641
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.90 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.22), residues: 1474
  helix:  1.49 (0.19), residues: 769
  sheet: -0.06 (0.47), residues: 111
  loop : -0.94 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP a 226 
 HIS   0.013   0.001   HIS a 227 
 PHE   0.017   0.001   PHE O 325 
 TYR   0.019   0.001   TYR b 340 
 ARG   0.015   0.000   ARG V  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  750)
  hydrogen bonds       : angle       4.16968 ( 2104)
  metal coordination   : bond        0.00787 (    8)
  metal coordination   : angle       3.74589 (    8)
  covalent geometry    : bond        0.00384 (14619)
  covalent geometry    : angle       0.70505 (20112)

********************** 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
  169 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 1.444 
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: 0.9136 (m-40) cc_final: 0.8763 (m110)
REVERT: M  227 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8697 (pm20)
REVERT: M  229 GLN cc_start: 0.9128 (tp40) cc_final: 0.8921 (tp40)
REVERT: M  259 TYR cc_start: 0.9205 (t80) cc_final: 0.8740 (t80)
REVERT: U   37 GLN cc_start: 0.9089 (mp-120) cc_final: 0.8721 (mp10)
REVERT: U  346 LYS cc_start: 0.7965 (tptt) cc_final: 0.7577 (tptp)
REVERT: U  348 LYS cc_start: 0.9141 (mppt) cc_final: 0.8941 (mppt)
REVERT: V   35 GLN cc_start: 0.8551 (mp10) cc_final: 0.8236 (mp10)
REVERT: c  315 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6343 (tp)
REVERT: c  356 MET cc_start: 0.8848 (tpp) cc_final: 0.8348 (tpp)
  outliers start: 21
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2381
  time to fit residues: 58.9534
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  : 1.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  134 ILE
Chi-restraints excluded: chain M residue  227 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  317 VAL
Chi-restraints excluded: chain U residue   31 ASP
Chi-restraints excluded: chain U residue   39 LEU
Chi-restraints excluded: chain U residue  351 PHE
Chi-restraints excluded: chain V residue   15 LEU
Chi-restraints excluded: chain V residue   36 VAL
Chi-restraints excluded: chain V residue   84 VAL
Chi-restraints excluded: chain a residue  194 ILE
Chi-restraints excluded: chain b residue   60 ASP
Chi-restraints excluded: chain b residue  175 ILE
Chi-restraints excluded: chain b residue  186 ILE
Chi-restraints excluded: chain b residue  354 CYS
Chi-restraints excluded: chain b residue  365 VAL
Chi-restraints excluded: chain c residue  164 ASP
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 92 optimal weight:    8.9990
   chunk 113 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:   20.0000
   chunk 146 optimal weight:    0.9990
   chunk 133 optimal weight:    7.9990
   chunk 117 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b 195 HIS
** 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 = 0.3894 r_free = 0.3894 target = 0.078692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.057179 restraints weight = 67825.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.058549 restraints weight = 33209.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.059309 restraints weight = 21980.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.5447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  14627  Z= 0.216
  Angle     :  0.743  14.839  20120  Z= 0.381
  Chirality :  0.044   0.448   2206
  Planarity :  0.005   0.059   2263
  Dihedral  : 22.145 162.591   2641
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.73 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.22), residues: 1474
  helix:  1.34 (0.19), residues: 771
  sheet: -0.12 (0.48), residues: 111
  loop : -1.00 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP a 226 
 HIS   0.029   0.001   HIS a 227 
 PHE   0.020   0.001   PHE O 325 
 TYR   0.020   0.001   TYR b 340 
 ARG   0.012   0.001   ARG V  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  750)
  hydrogen bonds       : angle       4.33302 ( 2104)
  metal coordination   : bond        0.01100 (    8)
  metal coordination   : angle       4.41720 (    8)
  covalent geometry    : bond        0.00481 (14619)
  covalent geometry    : angle       0.73744 (20112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6515.66 seconds
wall clock time: 114 minutes 48.02 seconds (6888.02 seconds total)