Starting phenix.real_space_refine
on Sat Jun  7 02:49:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w88_37348/06_2025/8w88_37348_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w88_37348/06_2025/8w88_37348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w88_37348/06_2025/8w88_37348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w88_37348/06_2025/8w88_37348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w88_37348/06_2025/8w88_37348_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w88_37348/06_2025/8w88_37348_neut.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.131
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    5307      2.51       5
     N    1419      2.21       5
     O    1519      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8307
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1957
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 433
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2254
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "R"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 96
          Unusual residues: {'CLR': 3, 'UJL': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.10, per 1000 atoms: 0.61
  Number of scatterers: 8307
  At special positions: 0
  Unit cell: (83.224, 99.704, 135.136, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1519      8.00
     N    1419      7.00
     C    5307      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.28

  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: 2.45
  Conformation dependent library (CDL) restraints added in 922.5 milliseconds
  

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      44.6% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 37
      removed outlier: 3.558A  pdb=" N   LYS A  31 " --> pdb=" O   LYS A  27 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.522A  pdb=" N   ASN A 238 " --> pdb=" O   GLN A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 278
      removed outlier: 3.815A  pdb=" N   GLU A 267 " --> pdb=" O   ASN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 302
    Processing helix  chain 'A' and resid 306 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.506A  pdb=" N   PHE A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER A 351 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 390
      removed outlier: 4.494A  pdb=" N   ARG A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 39
      removed outlier: 3.520A  pdb=" N   ARG B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 47
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'G' and resid 5 through 23
    Processing helix  chain 'G' and resid 28 through 43
    Processing helix  chain 'N' and resid 29 through 33
    Processing helix  chain 'N' and resid 75 through 77
      No H-bonds generated for 'chain 'N' and resid 75 through 77'
    Processing helix  chain 'N' and resid 88 through 92
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 52 through 55
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 86
    Processing helix  chain 'R' and resid 92 through 127
      removed outlier: 3.685A  pdb=" N   LYS R  97 " --> pdb=" O   GLU R  93 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 160
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 179
      removed outlier: 3.740A  pdb=" N   HIS R 177 " --> pdb=" O   TYR R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 229
    Processing helix  chain 'R' and resid 248 through 277
      removed outlier: 3.683A  pdb=" N   PHE R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.585A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 316
      removed outlier: 3.514A  pdb=" N   ALA R 314 " --> pdb=" O   TRP R 310 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 213
      removed outlier: 6.407A  pdb=" N   HIS A  40 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   PHE A 221 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A  42 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL A 223 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ALA A 242 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE A 243 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 289 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   PHE A 245 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASN A 291 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64
      removed outlier: 6.308A  pdb=" N   THR B  60 " --> pdb=" O   ASN B 353 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ASN B 353 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS B 330 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 76
      removed outlier: 3.690A  pdb=" N   LYS B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LEU B  92 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ALA B 105 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE B  94 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118
      removed outlier: 6.657A  pdb=" N   GLY B 128 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   CYS B 116 " --> pdb=" O   ALA B 126 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ALA B 126 " --> pdb=" O   CYS B 116 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   TYR B 118 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   TYR B 124 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ASN B 138 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL B 148 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 164
      removed outlier: 3.609A  pdb=" N   CYS B 161 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 170 " --> pdb=" O   TRP B 182 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASP B 183 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLN B 189 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 205
      removed outlier: 6.786A  pdb=" N   GLY B 215 " --> pdb=" O   MET B 201 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU B 203 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL B 213 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   LEU B 205 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU B 211 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA B 221 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   THR B 234 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU B 223 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 247
      removed outlier: 6.579A  pdb=" N   CYS B 263 " --> pdb=" O   THR B 276 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   THR B 276 " --> pdb=" O   CYS B 263 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B 265 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLN B 272 " --> pdb=" O   ASP B 267 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 291
      removed outlier: 3.713A  pdb=" N   SER B 288 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ASP B 311 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ARG B 317 " --> pdb=" O   ASP B 311 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8
      removed outlier: 3.522A  pdb=" N   THR N  79 " --> pdb=" O   ASP N  74 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 13
      removed outlier: 6.004A  pdb=" N   GLY N  11 " --> pdb=" O   THR N 126 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   MET N  35 " --> pdb=" O   ASP N  51 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ASP N  51 " --> pdb=" O   MET N  35 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   TRP N  37 " --> pdb=" O   VAL N  49 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2655
        1.34 -     1.46: 1381
        1.46 -     1.57: 4369
        1.57 -     1.69: 1
        1.69 -     1.81: 88
  Bond restraints: 8494
  Sorted by residual:
  bond pdb=" C8  UJL R 404 "
       pdb=" S1  UJL R 404 "
    ideal  model  delta    sigma   weight residual
    1.725  1.526  0.199 2.00e-02 2.50e+03 9.94e+01
  bond pdb=" C6  UJL R 404 "
       pdb=" C7  UJL R 404 "
    ideal  model  delta    sigma   weight residual
    1.428  1.613 -0.185 2.00e-02 2.50e+03 8.54e+01
  bond pdb=" C9  UJL R 404 "
       pdb=" S1  UJL R 404 "
    ideal  model  delta    sigma   weight residual
    1.730  1.564  0.166 2.00e-02 2.50e+03 6.90e+01
  bond pdb=" C7  UJL R 404 "
       pdb=" C8  UJL R 404 "
    ideal  model  delta    sigma   weight residual
    1.364  1.428 -0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" C3  UJL R 404 "
       pdb=" C9  UJL R 404 "
    ideal  model  delta    sigma   weight residual
    1.503  1.557 -0.054 2.00e-02 2.50e+03 7.31e+00
  ... (remaining 8489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 11454
        3.15 -     6.29: 60
        6.29 -     9.44: 3
        9.44 -    12.58: 0
       12.58 -    15.73: 1
  Bond angle restraints: 11518
  Sorted by residual:
  angle pdb=" C8  UJL R 404 "
        pdb=" S1  UJL R 404 "
        pdb=" C9  UJL R 404 "
      ideal   model   delta    sigma   weight residual
      91.70  107.43  -15.73 3.00e+00 1.11e-01 2.75e+01
  angle pdb=" N   HIS B 238 "
        pdb=" CA  HIS B 238 "
        pdb=" C   HIS B 238 "
      ideal   model   delta    sigma   weight residual
     110.43  116.41   -5.98 1.31e+00 5.83e-01 2.08e+01
  angle pdb=" CA  PRO N  89 "
        pdb=" N   PRO N  89 "
        pdb=" CD  PRO N  89 "
      ideal   model   delta    sigma   weight residual
     112.00  107.65    4.35 1.40e+00 5.10e-01 9.67e+00
  angle pdb=" C4  UJL R 404 "
        pdb=" C5  UJL R 404 "
        pdb=" C6  UJL R 404 "
      ideal   model   delta    sigma   weight residual
     109.30  118.13   -8.83 3.00e+00 1.11e-01 8.66e+00
  angle pdb=" C3  UJL R 404 "
        pdb=" C9  UJL R 404 "
        pdb=" S1  UJL R 404 "
      ideal   model   delta    sigma   weight residual
     124.67  133.40   -8.73 3.00e+00 1.11e-01 8.47e+00
  ... (remaining 11513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 4652
       17.21 -    34.43: 402
       34.43 -    51.64: 100
       51.64 -    68.85: 22
       68.85 -    86.06: 15
  Dihedral angle restraints: 5191
    sinusoidal: 2165
      harmonic: 3026
  Sorted by residual:
  dihedral pdb=" CA  LYS A 306 "
           pdb=" C   LYS A 306 "
           pdb=" N   ILE A 307 "
           pdb=" CA  ILE A 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  TRP B  95 "
           pdb=" C   TRP B  95 "
           pdb=" N   ASP B  96 "
           pdb=" CA  ASP B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.04   17.96     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ILE A 307 "
           pdb=" C   ILE A 307 "
           pdb=" N   GLU A 308 "
           pdb=" CA  GLU A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.53  -17.47     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 5188 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 966
       0.043 -    0.086: 251
       0.086 -    0.129: 70
       0.129 -    0.172: 6
       0.172 -    0.215: 2
  Chirality restraints: 1295
  Sorted by residual:
  chirality pdb=" CA  ASN R  41 "
            pdb=" N   ASN R  41 "
            pdb=" C   ASN R  41 "
            pdb=" CB  ASN R  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  HIS B 238 "
            pdb=" N   HIS B 238 "
            pdb=" C   HIS B 238 "
            pdb=" CB  HIS B 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.69e-01
  chirality pdb=" CA  ILE R 281 "
            pdb=" N   ILE R 281 "
            pdb=" C   ILE R 281 "
            pdb=" CB  ILE R 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.24e-01
  ... (remaining 1292 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  88 "    0.051 5.00e-02 4.00e+02   7.59e-02 9.21e+00
        pdb=" N   PRO N  89 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO N  89 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO N  89 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 106 "    0.248 9.50e-02 1.11e+02   1.12e-01 8.65e+00
        pdb=" NE  ARG N 106 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 106 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 106 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 106 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 264 "   -0.130 9.50e-02 1.11e+02   5.86e-02 2.20e+00
        pdb=" NE  ARG A 264 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 264 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 264 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 264 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 202
        2.69 -     3.25: 8166
        3.25 -     3.80: 13317
        3.80 -     4.35: 18534
        4.35 -     4.90: 31063
  Nonbonded interactions: 71282
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 326 "
            pdb=" OE1 GLU A 326 "
     model   vdw
     2.143 3.120
  nonbonded pdb=" OG  SER B 294 "
            pdb=" OD2 ASP G  47 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OH  TYR A 317 "
            pdb=" OD2 ASP A 342 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   PHE R 145 "
            pdb=" OG  SER R 149 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ASP B 208 "
            pdb=" OG1 THR B 209 "
     model   vdw
     2.266 3.040
  ... (remaining 71277 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=0.01 max=1.00 mean=0.94
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.550
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.252   8495  Z= 0.305
  Angle     :  0.668  17.434  11520  Z= 0.356
  Chirality :  0.042   0.215   1295
  Planarity :  0.005   0.112   1446
  Dihedral  : 14.725  86.062   3232
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 14.77 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.26), residues: 1023
  helix:  2.06 (0.26), residues: 409
  sheet:  0.04 (0.34), residues: 216
  loop : -0.39 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.004   0.001   HIS B  67 
 PHE   0.014   0.002   PHE R 160 
 TYR   0.013   0.001   TYR R 304 
 ARG   0.018   0.001   ARG N 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15476 (  438)
  hydrogen bonds       : angle       6.35129 ( 1260)
  SS BOND              : bond        0.25175 (    1)
  SS BOND              : angle      15.20198 (    2)
  covalent geometry    : bond        0.00585 ( 8494)
  covalent geometry    : angle       0.63780 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 128
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.6524 (mp0) cc_final: 0.6294 (tp30)
REVERT: B   72 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7863 (m-80)
REVERT: N   47 GLU cc_start: 0.8111 (tt0) cc_final: 0.7891 (tt0)
  outliers start: 3
  outliers final: 2
  residues processed: 130
  average time/residue: 1.3241
  time to fit residues: 182.1804
Evaluate side-chains
  117 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  287 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  13 ASN
A  34 GLN
B 189 GLN
B 238 HIS
B 272 GLN
N   4 GLN
N   6 GLN
R 175 HIS
R 296 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.149298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.109851 restraints weight = 8888.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.93
r_work: 0.3117 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8495  Z= 0.130
  Angle     :  0.540   6.070  11520  Z= 0.292
  Chirality :  0.043   0.159   1295
  Planarity :  0.004   0.052   1446
  Dihedral  :  5.182  58.441   1344
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.87 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.26), residues: 1023
  helix:  2.24 (0.25), residues: 413
  sheet:  0.05 (0.34), residues: 228
  loop : -0.26 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R 113 
 PHE   0.013   0.001   PHE R 160 
 TYR   0.015   0.001   TYR R  79 
 ARG   0.005   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  438)
  hydrogen bonds       : angle       5.07007 ( 1260)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       1.61347 (    2)
  covalent geometry    : bond        0.00293 ( 8494)
  covalent geometry    : angle       0.53980 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 LEU cc_start: 0.7353 (mp) cc_final: 0.7126 (tp)
REVERT: A  310 TYR cc_start: 0.6736 (m-80) cc_final: 0.6068 (m-80)
REVERT: A  313 GLU cc_start: 0.7370 (pm20) cc_final: 0.7166 (pm20)
REVERT: A  316 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7055 (ptt90)
REVERT: A  326 GLU cc_start: 0.7066 (mp0) cc_final: 0.6250 (tp30)
REVERT: B   83 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8744 (pp)
REVERT: G   56 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7732 (m)
REVERT: G   57 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6595 (pm20)
REVERT: N   47 GLU cc_start: 0.8474 (tt0) cc_final: 0.8145 (tt0)
REVERT: N  107 ASP cc_start: 0.7947 (p0) cc_final: 0.7454 (p0)
REVERT: R  292 PHE cc_start: 0.7955 (m-80) cc_final: 0.7626 (m-10)
  outliers start: 23
  outliers final: 11
  residues processed: 147
  average time/residue: 1.2401
  time to fit residues: 193.8348
Evaluate side-chains
  134 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 ASN
B 233 GLN
B 272 GLN
N   4 GLN
N   6 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.148981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112581 restraints weight = 9753.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.85
r_work: 0.3366 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8495  Z= 0.172
  Angle     :  0.547   6.856  11520  Z= 0.294
  Chirality :  0.044   0.153   1295
  Planarity :  0.004   0.055   1446
  Dihedral  :  5.340  58.301   1344
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.43 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1023
  helix:  2.29 (0.25), residues: 413
  sheet: -0.04 (0.34), residues: 228
  loop : -0.29 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.017   0.002   PHE R 160 
 TYR   0.017   0.001   TYR R  79 
 ARG   0.005   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04551 (  438)
  hydrogen bonds       : angle       4.99691 ( 1260)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       1.77220 (    2)
  covalent geometry    : bond        0.00410 ( 8494)
  covalent geometry    : angle       0.54692 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8702 (tt0)
REVERT: A  222 ASP cc_start: 0.8929 (t0) cc_final: 0.8491 (t0)
REVERT: A  310 TYR cc_start: 0.6932 (m-80) cc_final: 0.6257 (m-80)
REVERT: A  313 GLU cc_start: 0.7334 (pm20) cc_final: 0.7126 (pm20)
REVERT: A  316 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6936 (ptt90)
REVERT: A  326 GLU cc_start: 0.7029 (mp0) cc_final: 0.6346 (tp30)
REVERT: B   83 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8800 (pp)
REVERT: B  247 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.7966 (t80)
REVERT: G   56 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7460 (m)
REVERT: G   57 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6330 (pm20)
REVERT: N   47 GLU cc_start: 0.8427 (tt0) cc_final: 0.8133 (tt0)
REVERT: R  292 PHE cc_start: 0.7830 (m-80) cc_final: 0.7495 (m-10)
  outliers start: 34
  outliers final: 17
  residues processed: 138
  average time/residue: 1.2667
  time to fit residues: 185.5180
Evaluate side-chains
  132 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  116 CYS
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue  209 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
B 272 GLN
N   4 GLN
N   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.151058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.114483 restraints weight = 9638.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.86
r_work: 0.3388 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      104 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8495  Z= 0.122
  Angle     :  0.489   5.240  11520  Z= 0.264
  Chirality :  0.042   0.143   1295
  Planarity :  0.004   0.057   1446
  Dihedral  :  5.048  59.297   1344
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.77 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1023
  helix:  2.43 (0.25), residues: 413
  sheet: -0.16 (0.33), residues: 223
  loop : -0.27 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE B 164 
 TYR   0.014   0.001   TYR R  79 
 ARG   0.007   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  438)
  hydrogen bonds       : angle       4.75863 ( 1260)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       1.15409 (    2)
  covalent geometry    : bond        0.00277 ( 8494)
  covalent geometry    : angle       0.48917 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7383 (tp40) cc_final: 0.6806 (mt0)
REVERT: A  212 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8682 (tt0)
REVERT: A  310 TYR cc_start: 0.7084 (m-80) cc_final: 0.6264 (m-80)
REVERT: A  313 GLU cc_start: 0.7322 (pm20) cc_final: 0.7103 (pm20)
REVERT: A  316 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6853 (ptt90)
REVERT: A  326 GLU cc_start: 0.7034 (mp0) cc_final: 0.6365 (tp30)
REVERT: B   83 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8730 (pp)
REVERT: B  247 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8080 (t80)
REVERT: G   28 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7570 (mttp)
REVERT: G   56 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7486 (m)
REVERT: G   57 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6357 (pm20)
REVERT: N   44 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7117 (mttp)
REVERT: N   47 GLU cc_start: 0.8355 (tt0) cc_final: 0.8064 (tt0)
REVERT: N   61 TYR cc_start: 0.8473 (m-80) cc_final: 0.8204 (m-80)
REVERT: N  107 ASP cc_start: 0.8009 (p0) cc_final: 0.7794 (p0)
REVERT: R   53 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7837 (pm20)
REVERT: R  292 PHE cc_start: 0.7829 (m-80) cc_final: 0.7488 (m-10)
  outliers start: 34
  outliers final: 14
  residues processed: 144
  average time/residue: 1.1779
  time to fit residues: 180.3611
Evaluate side-chains
  141 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0470
   chunk 79 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.8882

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.153711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.117479 restraints weight = 9565.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.84
r_work: 0.3389 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      104 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      112 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8495  Z= 0.119
  Angle     :  0.490   8.967  11520  Z= 0.260
  Chirality :  0.041   0.131   1295
  Planarity :  0.004   0.056   1446
  Dihedral  :  4.933  59.630   1344
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.99 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1023
  helix:  2.50 (0.25), residues: 413
  sheet: -0.23 (0.33), residues: 223
  loop : -0.25 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.016   0.001   TYR R  79 
 ARG   0.007   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  438)
  hydrogen bonds       : angle       4.66092 ( 1260)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       1.00732 (    2)
  covalent geometry    : bond        0.00272 ( 8494)
  covalent geometry    : angle       0.48991 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7435 (tp40) cc_final: 0.6870 (mt0)
REVERT: A   58 GLN cc_start: 0.7590 (mm110) cc_final: 0.5943 (tm-30)
REVERT: A  212 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8634 (tt0)
REVERT: A  222 ASP cc_start: 0.8900 (t0) cc_final: 0.8509 (t0)
REVERT: A  310 TYR cc_start: 0.7335 (m-80) cc_final: 0.6316 (m-80)
REVERT: A  313 GLU cc_start: 0.7323 (pm20) cc_final: 0.7100 (pm20)
REVERT: A  316 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6902 (ptt90)
REVERT: A  326 GLU cc_start: 0.7069 (mp0) cc_final: 0.6406 (tp30)
REVERT: B   83 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8744 (pp)
REVERT: B  230 MET cc_start: 0.8640 (pmm) cc_final: 0.8416 (ppp)
REVERT: B  247 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8116 (t80)
REVERT: G   28 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7521 (mttp)
REVERT: G   57 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6287 (pm20)
REVERT: N   47 GLU cc_start: 0.8335 (tt0) cc_final: 0.8070 (tt0)
REVERT: N   61 TYR cc_start: 0.8531 (m-80) cc_final: 0.8263 (m-80)
REVERT: R   53 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7864 (pm20)
REVERT: R  193 LEU cc_start: 0.8022 (mm) cc_final: 0.7607 (mm)
REVERT: R  292 PHE cc_start: 0.7829 (m-80) cc_final: 0.7497 (m-10)
  outliers start: 34
  outliers final: 17
  residues processed: 141
  average time/residue: 1.1882
  time to fit residues: 178.2759
Evaluate side-chains
  139 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0000
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.152046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.115505 restraints weight = 9577.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.85
r_work: 0.3402 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      112 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      120 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8495  Z= 0.113
  Angle     :  0.478   8.605  11520  Z= 0.254
  Chirality :  0.041   0.131   1295
  Planarity :  0.004   0.054   1446
  Dihedral  :  4.702  59.165   1342
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.22 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1023
  helix:  2.60 (0.25), residues: 413
  sheet: -0.26 (0.32), residues: 223
  loop : -0.12 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.014   0.001   TYR R  79 
 ARG   0.005   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03654 (  438)
  hydrogen bonds       : angle       4.56879 ( 1260)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.88514 (    2)
  covalent geometry    : bond        0.00254 ( 8494)
  covalent geometry    : angle       0.47744 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7423 (tp40) cc_final: 0.6878 (mt0)
REVERT: A   58 GLN cc_start: 0.7588 (mm110) cc_final: 0.5961 (tm-30)
REVERT: A  212 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8615 (tt0)
REVERT: A  310 TYR cc_start: 0.7505 (m-80) cc_final: 0.6506 (m-80)
REVERT: A  313 GLU cc_start: 0.7311 (pm20) cc_final: 0.7094 (pm20)
REVERT: A  316 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6865 (ptt90)
REVERT: A  326 GLU cc_start: 0.7071 (mp0) cc_final: 0.6419 (tp30)
REVERT: B   83 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8711 (pp)
REVERT: B  230 MET cc_start: 0.8631 (pmm) cc_final: 0.8403 (ppp)
REVERT: B  247 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8098 (t80)
REVERT: G   28 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7492 (mttp)
REVERT: G   56 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7438 (m)
REVERT: G   57 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6276 (pm20)
REVERT: N   44 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7121 (mttp)
REVERT: N   47 GLU cc_start: 0.8329 (tt0) cc_final: 0.8022 (tt0)
REVERT: N   61 TYR cc_start: 0.8509 (m-80) cc_final: 0.8234 (m-80)
REVERT: R   53 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7820 (pm20)
REVERT: R  193 LEU cc_start: 0.8040 (mm) cc_final: 0.7617 (mm)
REVERT: R  292 PHE cc_start: 0.7852 (m-80) cc_final: 0.7525 (m-10)
  outliers start: 31
  outliers final: 17
  residues processed: 141
  average time/residue: 1.1894
  time to fit residues: 178.8242
Evaluate side-chains
  144 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 63 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 72 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.152784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.116187 restraints weight = 9656.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.86
r_work: 0.3410 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      120 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      125 |
|-----------------------------------------------------------------------------|
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8495  Z= 0.105
  Angle     :  0.470   8.227  11520  Z= 0.250
  Chirality :  0.041   0.130   1295
  Planarity :  0.004   0.051   1446
  Dihedral  :  4.573  58.297   1342
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.00 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1023
  helix:  2.68 (0.25), residues: 414
  sheet: -0.31 (0.32), residues: 229
  loop : -0.03 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.013   0.001   TYR R  79 
 ARG   0.005   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  438)
  hydrogen bonds       : angle       4.48772 ( 1260)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.72534 (    2)
  covalent geometry    : bond        0.00232 ( 8494)
  covalent geometry    : angle       0.46963 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7441 (tp40) cc_final: 0.6890 (mt0)
REVERT: A  212 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (tt0)
REVERT: A  222 ASP cc_start: 0.8869 (t0) cc_final: 0.8481 (t0)
REVERT: A  313 GLU cc_start: 0.7339 (pm20) cc_final: 0.7111 (pm20)
REVERT: A  316 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6819 (ptt90)
REVERT: A  326 GLU cc_start: 0.7027 (mp0) cc_final: 0.6363 (tp30)
REVERT: B   83 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8696 (pp)
REVERT: B  230 MET cc_start: 0.8574 (pmm) cc_final: 0.8357 (ppp)
REVERT: B  247 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8091 (t80)
REVERT: G   28 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7145 (mmtt)
REVERT: G   56 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7481 (m)
REVERT: G   57 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6348 (pm20)
REVERT: N   44 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7047 (mttp)
REVERT: N   47 GLU cc_start: 0.8296 (tt0) cc_final: 0.7998 (tt0)
REVERT: N   61 TYR cc_start: 0.8508 (m-80) cc_final: 0.8250 (m-80)
REVERT: N  107 ASP cc_start: 0.8075 (p0) cc_final: 0.7149 (p0)
REVERT: R   53 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7859 (pm20)
REVERT: R  193 LEU cc_start: 0.8028 (mm) cc_final: 0.7594 (mm)
REVERT: R  292 PHE cc_start: 0.7845 (m-80) cc_final: 0.7524 (m-10)
  outliers start: 33
  outliers final: 17
  residues processed: 147
  average time/residue: 1.2648
  time to fit residues: 197.6366
Evaluate side-chains
  144 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Chi-restraints excluded: chain R residue  280 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0070
   chunk 42 optimal weight:    2.9990
   chunk 90 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.154130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.117806 restraints weight = 9711.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.88
r_work: 0.3428 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      125 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      129 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8495  Z= 0.097
  Angle     :  0.467   7.902  11520  Z= 0.248
  Chirality :  0.040   0.129   1295
  Planarity :  0.003   0.052   1446
  Dihedral  :  4.459  57.203   1342
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.78 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1023
  helix:  2.72 (0.25), residues: 414
  sheet: -0.22 (0.32), residues: 227
  loop : -0.02 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.002   0.000   HIS R  63 
 PHE   0.010   0.001   PHE R  95 
 TYR   0.012   0.001   TYR R  79 
 ARG   0.006   0.000   ARG B 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  438)
  hydrogen bonds       : angle       4.39949 ( 1260)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.63984 (    2)
  covalent geometry    : bond        0.00210 ( 8494)
  covalent geometry    : angle       0.46715 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 1.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7432 (tp40) cc_final: 0.6931 (mt0)
REVERT: A   58 GLN cc_start: 0.7434 (mm110) cc_final: 0.5865 (tm-30)
REVERT: A  212 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8546 (tt0)
REVERT: A  222 ASP cc_start: 0.8803 (t0) cc_final: 0.8410 (t0)
REVERT: A  313 GLU cc_start: 0.7365 (pm20) cc_final: 0.7101 (pm20)
REVERT: A  316 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6791 (ptt90)
REVERT: A  326 GLU cc_start: 0.7035 (mp0) cc_final: 0.6347 (tp30)
REVERT: B  208 ASP cc_start: 0.8274 (p0) cc_final: 0.7991 (p0)
REVERT: B  230 MET cc_start: 0.8582 (pmm) cc_final: 0.8317 (ppp)
REVERT: B  247 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8077 (t80)
REVERT: G   28 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7075 (mmtt)
REVERT: G   56 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7496 (m)
REVERT: G   57 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6456 (pm20)
REVERT: N   44 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7047 (mttp)
REVERT: N   47 GLU cc_start: 0.8269 (tt0) cc_final: 0.7966 (tt0)
REVERT: N   61 TYR cc_start: 0.8522 (m-80) cc_final: 0.8266 (m-80)
REVERT: N  107 ASP cc_start: 0.7995 (p0) cc_final: 0.6968 (p0)
REVERT: R   53 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7807 (pm20)
REVERT: R  193 LEU cc_start: 0.8013 (mm) cc_final: 0.7587 (mm)
REVERT: R  292 PHE cc_start: 0.7813 (m-80) cc_final: 0.7495 (m-10)
  outliers start: 30
  outliers final: 15
  residues processed: 151
  average time/residue: 1.2412
  time to fit residues: 200.3902
Evaluate side-chains
  149 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain B residue  352 TRP
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  280 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 87 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
B 233 GLN
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.153211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.116716 restraints weight = 9780.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.87
r_work: 0.3415 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      129 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      130 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8495  Z= 0.108
  Angle     :  0.479   7.674  11520  Z= 0.254
  Chirality :  0.041   0.128   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  4.464  57.697   1341
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.45 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1023
  helix:  2.71 (0.25), residues: 414
  sheet: -0.21 (0.32), residues: 227
  loop : -0.02 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.013   0.001   PHE R  95 
 TYR   0.013   0.001   TYR R  79 
 ARG   0.008   0.000   ARG B 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  438)
  hydrogen bonds       : angle       4.44355 ( 1260)
  SS BOND              : bond        0.00476 (    1)
  SS BOND              : angle       1.40313 (    2)
  covalent geometry    : bond        0.00243 ( 8494)
  covalent geometry    : angle       0.47819 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7445 (tp40) cc_final: 0.6950 (mt0)
REVERT: A  212 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8577 (tt0)
REVERT: A  219 HIS cc_start: 0.8596 (t-170) cc_final: 0.8387 (t-90)
REVERT: A  313 GLU cc_start: 0.7401 (pm20) cc_final: 0.7130 (pm20)
REVERT: A  316 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6771 (ptt90)
REVERT: A  326 GLU cc_start: 0.7026 (mp0) cc_final: 0.6344 (tp30)
REVERT: B  208 ASP cc_start: 0.8315 (p0) cc_final: 0.8028 (p0)
REVERT: B  230 MET cc_start: 0.8554 (pmm) cc_final: 0.8305 (ppp)
REVERT: B  247 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8084 (t80)
REVERT: B  271 ASP cc_start: 0.7324 (t0) cc_final: 0.7068 (t0)
REVERT: G   28 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7101 (mmtt)
REVERT: G   56 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7525 (m)
REVERT: G   57 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6452 (pm20)
REVERT: N   44 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7024 (mttp)
REVERT: N   47 GLU cc_start: 0.8275 (tt0) cc_final: 0.7974 (tt0)
REVERT: N   61 TYR cc_start: 0.8538 (m-80) cc_final: 0.8295 (m-80)
REVERT: N  107 ASP cc_start: 0.8007 (p0) cc_final: 0.6994 (p0)
REVERT: R   53 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7808 (pm20)
REVERT: R  193 LEU cc_start: 0.8013 (mm) cc_final: 0.7592 (mm)
REVERT: R  292 PHE cc_start: 0.7827 (m-80) cc_final: 0.7512 (m-10)
  outliers start: 28
  outliers final: 17
  residues processed: 146
  average time/residue: 1.3682
  time to fit residues: 213.4874
Evaluate side-chains
  152 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain B residue  352 TRP
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Chi-restraints excluded: chain R residue  280 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 92 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 145 ASN
B 233 GLN
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.116163 restraints weight = 9709.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.86
r_work: 0.3409 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      130 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      136 |
|-----------------------------------------------------------------------------|
r_final: 0.3377
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8495  Z= 0.116
  Angle     :  0.492   7.571  11520  Z= 0.261
  Chirality :  0.041   0.170   1295
  Planarity :  0.003   0.049   1446
  Dihedral  :  4.518  58.036   1341
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.01 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1023
  helix:  2.66 (0.25), residues: 414
  sheet: -0.11 (0.32), residues: 227
  loop : -0.03 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.013   0.001   PHE R  95 
 TYR   0.015   0.001   TYR N  96 
 ARG   0.005   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  438)
  hydrogen bonds       : angle       4.48884 ( 1260)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       1.34413 (    2)
  covalent geometry    : bond        0.00264 ( 8494)
  covalent geometry    : angle       0.49134 (11518)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7446 (tp40) cc_final: 0.6980 (mt0)
REVERT: A   58 GLN cc_start: 0.7390 (mm110) cc_final: 0.5834 (tm-30)
REVERT: A  212 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8603 (tt0)
REVERT: A  313 GLU cc_start: 0.7424 (pm20) cc_final: 0.7154 (pm20)
REVERT: A  316 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6759 (ptt90)
REVERT: A  326 GLU cc_start: 0.7022 (mp0) cc_final: 0.6343 (tp30)
REVERT: B  208 ASP cc_start: 0.8319 (p0) cc_final: 0.8031 (p0)
REVERT: B  230 MET cc_start: 0.8594 (pmm) cc_final: 0.8338 (ppp)
REVERT: B  247 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: G   28 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7107 (mmtt)
REVERT: G   56 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7536 (m)
REVERT: G   57 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6475 (pm20)
REVERT: N   44 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7022 (mttp)
REVERT: N   47 GLU cc_start: 0.8302 (tt0) cc_final: 0.7991 (tt0)
REVERT: N   61 TYR cc_start: 0.8529 (m-80) cc_final: 0.8281 (m-80)
REVERT: N  107 ASP cc_start: 0.8018 (p0) cc_final: 0.7004 (p0)
REVERT: R   53 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7821 (pm20)
REVERT: R  193 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7602 (mm)
REVERT: R  292 PHE cc_start: 0.7861 (m-80) cc_final: 0.7553 (m-10)
  outliers start: 28
  outliers final: 17
  residues processed: 142
  average time/residue: 1.2161
  time to fit residues: 183.7352
Evaluate side-chains
  147 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain B residue  352 TRP
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Chi-restraints excluded: chain R residue  280 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0010
   chunk 9 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 233 GLN
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.154330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.117837 restraints weight = 9755.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 1.90
r_work: 0.3435 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      136 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      140 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8495  Z= 0.099
  Angle     :  0.469   7.519  11520  Z= 0.249
  Chirality :  0.040   0.160   1295
  Planarity :  0.003   0.049   1446
  Dihedral  :  4.380  56.931   1341
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.90 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1023
  helix:  2.74 (0.25), residues: 414
  sheet: -0.14 (0.32), residues: 227
  loop :  0.01 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 291 
 HIS   0.002   0.000   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.013   0.001   TYR N  96 
 ARG   0.005   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (  438)
  hydrogen bonds       : angle       4.38126 ( 1260)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.81153 (    2)
  covalent geometry    : bond        0.00215 ( 8494)
  covalent geometry    : angle       0.46862 (11518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8092.97 seconds
wall clock time: 140 minutes 15.06 seconds (8415.06 seconds total)