Starting phenix.real_space_refine
on Fri Aug 22 22:43:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w88_37348/08_2025/8w88_37348_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w88_37348/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w88_37348/08_2025/8w88_37348_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w88_37348/08_2025/8w88_37348_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w88_37348/08_2025/8w88_37348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w88_37348/08_2025/8w88_37348.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.131
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'HIS:plan': 1, 'ARG: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: 1.56, per 1000 atoms: 0.19
  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: 0.53
  Conformation dependent library (CDL) restraints added in 282.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.28
  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: 1.11

  Time building geometry restraints manager: 0.74 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:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.120
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.170
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (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
 ARG   0.018   0.001   ARG N 106 
 TYR   0.013   0.001   TYR R 304 
 PHE   0.014   0.002   PHE R 160 
 TRP   0.018   0.002   TRP R 291 
 HIS   0.004   0.001   HIS B  67 

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

*********************** 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  : 0.216 
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: 0.5273
  time to fit residues: 72.4165
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  : 0.207 
-------------------------------------------------------------------------------
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 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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
N  32 ASN
R 175 HIS
R 296 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.105319 restraints weight = 9043.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.97
r_work: 0.3053 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       58 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8495  Z= 0.218
  Angle     :  0.615   7.675  11520  Z= 0.331
  Chirality :  0.046   0.190   1295
  Planarity :  0.005   0.054   1446
  Dihedral  :  5.481  56.996   1344
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 13.76 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.26), residues: 1023
  helix:  2.02 (0.25), residues: 413
  sheet:  0.08 (0.34), residues: 228
  loop : -0.29 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  73 
 TYR   0.016   0.002   TYR R  79 
 PHE   0.020   0.002   PHE R 160 
 TRP   0.022   0.003   TRP R 291 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 8494)
  covalent geometry    : angle       0.61411 (11518)
  SS BOND              : bond        0.00339 (    1)
  SS BOND              : angle       2.42948 (    2)
  hydrogen bonds       : bond        0.05249 (  438)
  hydrogen bonds       : angle       5.26243 ( 1260)

*********************** 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
  144 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.6240 (mmpt) cc_final: 0.5902 (ttpp)
REVERT: A  222 ASP cc_start: 0.8982 (t0) cc_final: 0.8594 (t0)
REVERT: A  310 TYR cc_start: 0.6751 (m-80) cc_final: 0.6253 (m-80)
REVERT: A  316 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7059 (ptt90)
REVERT: A  326 GLU cc_start: 0.7127 (mp0) cc_final: 0.6304 (tp30)
REVERT: B   72 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8816 (m-80)
REVERT: B   83 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8872 (pp)
REVERT: G   56 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7819 (m)
REVERT: G   57 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6405 (pm20)
REVERT: N   47 GLU cc_start: 0.8587 (tt0) cc_final: 0.8333 (tt0)
  outliers start: 26
  outliers final: 14
  residues processed: 135
  average time/residue: 0.4962
  time to fit residues: 71.0676
Evaluate side-chains
  126 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 THR
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  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   56 SER
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 86 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 42 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.151591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.115446 restraints weight = 9554.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.84
r_work: 0.3405 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       58 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       88 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8495  Z= 0.116
  Angle     :  0.494   5.191  11520  Z= 0.267
  Chirality :  0.041   0.142   1295
  Planarity :  0.004   0.055   1446
  Dihedral  :  5.086  59.447   1344
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.88 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1023
  helix:  2.38 (0.25), residues: 413
  sheet: -0.04 (0.33), residues: 226
  loop : -0.29 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.015   0.001   TYR R  79 
 PHE   0.011   0.001   PHE B 164 
 TRP   0.020   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8494)
  covalent geometry    : angle       0.49323 (11518)
  SS BOND              : bond        0.00147 (    1)
  SS BOND              : angle       1.40536 (    2)
  hydrogen bonds       : bond        0.03938 (  438)
  hydrogen bonds       : angle       4.83538 ( 1260)

*********************** 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
  149 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8689 (tt0)
REVERT: A  310 TYR cc_start: 0.6940 (m-80) cc_final: 0.6176 (m-80)
REVERT: A  316 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6895 (ptt90)
REVERT: A  326 GLU cc_start: 0.7045 (mp0) cc_final: 0.6346 (tp30)
REVERT: B   83 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8687 (pp)
REVERT: B  247 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: G   56 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7456 (m)
REVERT: G   57 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6288 (pm20)
REVERT: N   47 GLU cc_start: 0.8342 (tt0) cc_final: 0.8044 (tt0)
REVERT: N  107 ASP cc_start: 0.7958 (p0) cc_final: 0.7696 (p0)
REVERT: R  149 SER cc_start: 0.8565 (m) cc_final: 0.8316 (p)
REVERT: R  302 MET cc_start: 0.8132 (mtp) cc_final: 0.7899 (mtt)
  outliers start: 28
  outliers final: 11
  residues processed: 139
  average time/residue: 0.4803
  time to fit residues: 70.9951
Evaluate side-chains
  130 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
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  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 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
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 75 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 47 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 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 = 0.3845 r_free = 0.3845 target = 0.148621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.112170 restraints weight = 9819.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.83
r_work: 0.3357 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       88 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      107 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8495  Z= 0.171
  Angle     :  0.541   6.870  11520  Z= 0.290
  Chirality :  0.044   0.170   1295
  Planarity :  0.004   0.057   1446
  Dihedral  :  5.141  58.175   1342
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 14.99 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.26), residues: 1023
  helix:  2.32 (0.25), residues: 413
  sheet: -0.17 (0.33), residues: 225
  loop : -0.29 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.017   0.001   TYR R  79 
 PHE   0.016   0.002   PHE R 160 
 TRP   0.020   0.002   TRP R 291 
 HIS   0.005   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8494)
  covalent geometry    : angle       0.54068 (11518)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       1.47559 (    2)
  hydrogen bonds       : bond        0.04420 (  438)
  hydrogen bonds       : angle       4.92223 ( 1260)

*********************** 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
  151 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 114
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8689 (tt0)
REVERT: A  310 TYR cc_start: 0.7106 (m-80) cc_final: 0.6309 (m-80)
REVERT: A  316 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6885 (ptt90)
REVERT: A  326 GLU cc_start: 0.7109 (mp0) cc_final: 0.6451 (tp30)
REVERT: B   83 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8808 (pp)
REVERT: B  247 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8027 (t80)
REVERT: G   56 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7429 (m)
REVERT: G   57 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6286 (pm20)
REVERT: N   44 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7179 (mttp)
REVERT: N   47 GLU cc_start: 0.8407 (tt0) cc_final: 0.8134 (tt0)
REVERT: R   53 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7870 (pm20)
REVERT: R  292 PHE cc_start: 0.7894 (m-80) cc_final: 0.7577 (m-10)
  outliers start: 37
  outliers final: 20
  residues processed: 138
  average time/residue: 0.4695
  time to fit residues: 68.7242
Evaluate side-chains
  139 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  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 B residue  330 CYS
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   60 SER
Chi-restraints excluded: chain N residue   84 MET
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  114 THR
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 79 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.152631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.116235 restraints weight = 9720.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.84
r_work: 0.3373 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      107 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      115 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8495  Z= 0.137
  Angle     :  0.513   9.120  11520  Z= 0.273
  Chirality :  0.042   0.150   1295
  Planarity :  0.004   0.054   1446
  Dihedral  :  4.951  58.752   1342
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 15.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.26), residues: 1023
  helix:  2.40 (0.25), residues: 413
  sheet: -0.27 (0.33), residues: 223
  loop : -0.27 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 264 
 TYR   0.014   0.001   TYR R  79 
 PHE   0.012   0.001   PHE R 160 
 TRP   0.019   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8494)
  covalent geometry    : angle       0.51292 (11518)
  SS BOND              : bond        0.00147 (    1)
  SS BOND              : angle       1.13160 (    2)
  hydrogen bonds       : bond        0.04021 (  438)
  hydrogen bonds       : angle       4.75401 ( 1260)

*********************** 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
  150 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7464 (tp40) cc_final: 0.6856 (mt0)
REVERT: A   58 GLN cc_start: 0.7613 (mm110) cc_final: 0.5943 (tm-30)
REVERT: A  212 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8670 (tt0)
REVERT: A  310 TYR cc_start: 0.7337 (m-80) cc_final: 0.6329 (m-80)
REVERT: A  316 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6899 (ptt90)
REVERT: A  326 GLU cc_start: 0.7081 (mp0) cc_final: 0.6440 (tp30)
REVERT: B   83 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8742 (pp)
REVERT: B  230 MET cc_start: 0.8663 (pmm) cc_final: 0.8427 (ppp)
REVERT: B  247 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8001 (t80)
REVERT: G   36 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7397 (mp)
REVERT: G   56 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7426 (m)
REVERT: G   57 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6261 (pm20)
REVERT: N   44 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7173 (mttp)
REVERT: N   47 GLU cc_start: 0.8374 (tt0) cc_final: 0.8127 (tt0)
REVERT: R   53 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7863 (pm20)
REVERT: R  132 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8346 (mttp)
REVERT: R  292 PHE cc_start: 0.7856 (m-80) cc_final: 0.7535 (m-10)
  outliers start: 35
  outliers final: 18
  residues processed: 138
  average time/residue: 0.4655
  time to fit residues: 68.3624
Evaluate side-chains
  135 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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  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   36 LEU
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   84 MET
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  132 LYS
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 83 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 84 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0970
   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 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 = 0.3873 r_free = 0.3873 target = 0.151217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.114563 restraints weight = 9625.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.84
r_work: 0.3390 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      115 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      123 |
|-----------------------------------------------------------------------------|
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8495  Z= 0.121
  Angle     :  0.492   8.769  11520  Z= 0.262
  Chirality :  0.041   0.130   1295
  Planarity :  0.004   0.053   1446
  Dihedral  :  4.803  59.854   1342
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.44 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1023
  helix:  2.49 (0.25), residues: 413
  sheet: -0.25 (0.32), residues: 223
  loop : -0.26 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 264 
 TYR   0.013   0.001   TYR R  79 
 PHE   0.011   0.001   PHE R  95 
 TRP   0.019   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8494)
  covalent geometry    : angle       0.49228 (11518)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.88481 (    2)
  hydrogen bonds       : bond        0.03765 (  438)
  hydrogen bonds       : angle       4.64046 ( 1260)

*********************** 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
  152 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7491 (tp40) cc_final: 0.6918 (mt0)
REVERT: A   58 GLN cc_start: 0.7582 (mm110) cc_final: 0.5969 (tm-30)
REVERT: A  212 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8605 (tt0)
REVERT: A  316 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6862 (ptt90)
REVERT: A  326 GLU cc_start: 0.7096 (mp0) cc_final: 0.6447 (tp30)
REVERT: B   83 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8736 (pp)
REVERT: B  230 MET cc_start: 0.8655 (pmm) cc_final: 0.8413 (ppp)
REVERT: B  247 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8089 (t80)
REVERT: G   56 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7471 (m)
REVERT: G   57 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6260 (pm20)
REVERT: N   44 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7196 (mttp)
REVERT: N   47 GLU cc_start: 0.8359 (tt0) cc_final: 0.8088 (tt0)
REVERT: N   61 TYR cc_start: 0.8512 (m-80) cc_final: 0.8279 (m-80)
REVERT: R   53 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7852 (pm20)
REVERT: R  193 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7592 (mm)
REVERT: R  292 PHE cc_start: 0.7849 (m-80) cc_final: 0.7525 (m-10)
  outliers start: 34
  outliers final: 19
  residues processed: 139
  average time/residue: 0.4229
  time to fit residues: 62.7142
Evaluate side-chains
  140 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  236 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   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue   84 MET
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.151931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.115473 restraints weight = 9750.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.86
r_work: 0.3400 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      123 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      133 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8495  Z= 0.109
  Angle     :  0.478   8.149  11520  Z= 0.254
  Chirality :  0.041   0.129   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  4.655  59.083   1342
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.22 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.26), residues: 1023
  helix:  2.65 (0.25), residues: 413
  sheet: -0.28 (0.32), residues: 229
  loop : -0.08 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.015   0.001   TYR R  79 
 PHE   0.011   0.001   PHE R  95 
 TRP   0.019   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8494)
  covalent geometry    : angle       0.47823 (11518)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.76918 (    2)
  hydrogen bonds       : bond        0.03574 (  438)
  hydrogen bonds       : angle       4.53474 ( 1260)

*********************** 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
  157 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7468 (tp40) cc_final: 0.6922 (mt0)
REVERT: A  212 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8560 (tt0)
REVERT: A  316 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6827 (ptt90)
REVERT: A  326 GLU cc_start: 0.7121 (mp0) cc_final: 0.6438 (tp30)
REVERT: B   83 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8671 (pp)
REVERT: B  230 MET cc_start: 0.8640 (pmm) cc_final: 0.8395 (ppp)
REVERT: B  247 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8107 (t80)
REVERT: G   57 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6372 (pm20)
REVERT: N   44 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7100 (mttp)
REVERT: N   47 GLU cc_start: 0.8313 (tt0) cc_final: 0.8049 (tt0)
REVERT: N   61 TYR cc_start: 0.8521 (m-80) cc_final: 0.8274 (m-80)
REVERT: N  107 ASP cc_start: 0.8041 (p0) cc_final: 0.7320 (p0)
REVERT: R   53 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7824 (pm20)
REVERT: R  193 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7572 (mm)
REVERT: R  292 PHE cc_start: 0.7840 (m-80) cc_final: 0.7532 (m-10)
  outliers start: 34
  outliers final: 17
  residues processed: 145
  average time/residue: 0.4520
  time to fit residues: 69.6878
Evaluate side-chains
  143 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
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  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   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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0170
   chunk 15 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6820

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.152234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115898 restraints weight = 9646.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.85
r_work: 0.3405 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      133 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      133 |
|-----------------------------------------------------------------------------|
r_final: 0.3375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2046

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     :  0.484   7.809  11520  Z= 0.257
  Chirality :  0.041   0.128   1295
  Planarity :  0.004   0.051   1446
  Dihedral  :  4.570  58.537   1342
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1023
  helix:  2.64 (0.25), residues: 414
  sheet: -0.27 (0.32), residues: 229
  loop : -0.06 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 147 
 TYR   0.013   0.001   TYR R  79 
 PHE   0.011   0.001   PHE R  95 
 TRP   0.018   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8494)
  covalent geometry    : angle       0.48442 (11518)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.73459 (    2)
  hydrogen bonds       : bond        0.03523 (  438)
  hydrogen bonds       : angle       4.49745 ( 1260)

*********************** 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
  148 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7466 (tp40) cc_final: 0.6948 (mt0)
REVERT: A   58 GLN cc_start: 0.7534 (mm110) cc_final: 0.5961 (tm-30)
REVERT: A  212 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8528 (tt0)
REVERT: A  316 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6807 (ptt90)
REVERT: A  326 GLU cc_start: 0.7087 (mp0) cc_final: 0.6391 (tp30)
REVERT: B   83 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8704 (pp)
REVERT: B  230 MET cc_start: 0.8594 (pmm) cc_final: 0.8354 (ppp)
REVERT: B  247 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8105 (t80)
REVERT: G   57 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6737 (pm20)
REVERT: N   44 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7055 (mttp)
REVERT: N   47 GLU cc_start: 0.8295 (tt0) cc_final: 0.8004 (tt0)
REVERT: N   61 TYR cc_start: 0.8554 (m-80) cc_final: 0.8310 (m-80)
REVERT: N  107 ASP cc_start: 0.8028 (p0) cc_final: 0.7272 (p0)
REVERT: R   53 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7830 (pm20)
REVERT: R  193 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7556 (mm)
REVERT: R  292 PHE cc_start: 0.7841 (m-80) cc_final: 0.7534 (m-10)
  outliers start: 28
  outliers final: 17
  residues processed: 136
  average time/residue: 0.4565
  time to fit residues: 65.9228
Evaluate side-chains
  146 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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 B residue  330 CYS
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue    6 GLN
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.151134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.114598 restraints weight = 9693.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.85
r_work: 0.3388 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      133 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      136 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2002

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= 0.131
  Angle     :  0.504   7.557  11520  Z= 0.267
  Chirality :  0.042   0.127   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  4.658  59.082   1342
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.79 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1023
  helix:  2.65 (0.25), residues: 413
  sheet: -0.26 (0.32), residues: 229
  loop : -0.07 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 147 
 TYR   0.015   0.001   TYR R  79 
 PHE   0.012   0.001   PHE A 211 
 TRP   0.018   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8494)
  covalent geometry    : angle       0.50359 (11518)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.83556 (    2)
  hydrogen bonds       : bond        0.03741 (  438)
  hydrogen bonds       : angle       4.55817 ( 1260)

*********************** 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
  148 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7448 (tp40) cc_final: 0.6934 (mt0)
REVERT: A   58 GLN cc_start: 0.7512 (mm110) cc_final: 0.5969 (tm-30)
REVERT: A  212 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8562 (tt0)
REVERT: A  316 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6802 (ptt90)
REVERT: A  326 GLU cc_start: 0.7084 (mp0) cc_final: 0.6385 (tp30)
REVERT: B   83 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8720 (pp)
REVERT: B  230 MET cc_start: 0.8591 (pmm) cc_final: 0.8354 (ppp)
REVERT: B  247 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8091 (t80)
REVERT: G   57 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6760 (pm20)
REVERT: N   44 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7045 (mttp)
REVERT: N   47 GLU cc_start: 0.8340 (tt0) cc_final: 0.8040 (tt0)
REVERT: N   61 TYR cc_start: 0.8562 (m-80) cc_final: 0.8323 (m-80)
REVERT: N  107 ASP cc_start: 0.8036 (p0) cc_final: 0.7315 (p0)
REVERT: R   53 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7826 (pm20)
REVERT: R  193 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7555 (mm)
REVERT: R  292 PHE cc_start: 0.7866 (m-80) cc_final: 0.7559 (m-10)
  outliers start: 28
  outliers final: 16
  residues processed: 137
  average time/residue: 0.4211
  time to fit residues: 61.4360
Evaluate side-chains
  142 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  116 CYS
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  287 THR
Chi-restraints excluded: chain B residue  330 CYS
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 69 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 145 ASN
B 272 GLN
N   4 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 = 0.3879 r_free = 0.3879 target = 0.151670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115109 restraints weight = 9728.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.86
r_work: 0.3395 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      136 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      137 |
|-----------------------------------------------------------------------------|
r_final: 0.3365
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8495  Z= 0.117
  Angle     :  0.497   7.513  11520  Z= 0.263
  Chirality :  0.041   0.127   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  4.611  58.960   1342
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.26), residues: 1023
  helix:  2.63 (0.25), residues: 414
  sheet: -0.26 (0.31), residues: 229
  loop : -0.05 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 264 
 TYR   0.014   0.001   TYR R  79 
 PHE   0.013   0.001   PHE R 165 
 TRP   0.018   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8494)
  covalent geometry    : angle       0.49689 (11518)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.72197 (    2)
  hydrogen bonds       : bond        0.03629 (  438)
  hydrogen bonds       : angle       4.52848 ( 1260)

********************** 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
  149 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7433 (tp40) cc_final: 0.6952 (mt0)
REVERT: A   58 GLN cc_start: 0.7420 (mm110) cc_final: 0.5850 (tm-30)
REVERT: A  212 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8580 (tt0)
REVERT: A  316 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6774 (ptt90)
REVERT: A  326 GLU cc_start: 0.7071 (mp0) cc_final: 0.6380 (tp30)
REVERT: B   83 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8717 (pp)
REVERT: B  230 MET cc_start: 0.8571 (pmm) cc_final: 0.8347 (ppp)
REVERT: B  247 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8096 (t80)
REVERT: G   57 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6783 (pm20)
REVERT: N   44 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7049 (mttp)
REVERT: N   47 GLU cc_start: 0.8334 (tt0) cc_final: 0.8049 (tt0)
REVERT: N   61 TYR cc_start: 0.8532 (m-80) cc_final: 0.8303 (m-80)
REVERT: N  107 ASP cc_start: 0.8014 (p0) cc_final: 0.7216 (p0)
REVERT: R   53 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7823 (pm20)
REVERT: R  193 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7562 (mm)
REVERT: R  292 PHE cc_start: 0.7860 (m-80) cc_final: 0.7555 (m-10)
  outliers start: 27
  outliers final: 16
  residues processed: 137
  average time/residue: 0.4394
  time to fit residues: 64.2187
Evaluate side-chains
  146 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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  116 CYS
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  330 CYS
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  193 LEU
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0050
   chunk 24 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4772

-------------------------------------------------------------------------------
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  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.153616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.117285 restraints weight = 9627.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.86
r_work: 0.3424 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| 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:      137 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      140 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8495  Z= 0.098
  Angle     :  0.476   7.445  11520  Z= 0.252
  Chirality :  0.040   0.127   1295
  Planarity :  0.003   0.049   1446
  Dihedral  :  4.428  57.671   1341
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.02 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.26), residues: 1023
  helix:  2.74 (0.25), residues: 414
  sheet: -0.22 (0.31), residues: 229
  loop : -0.03 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 264 
 TYR   0.013   0.001   TYR N  96 
 PHE   0.011   0.001   PHE R  95 
 TRP   0.019   0.002   TRP R 291 
 HIS   0.002   0.000   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8494)
  covalent geometry    : angle       0.47541 (11518)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       1.59357 (    2)
  hydrogen bonds       : bond        0.03310 (  438)
  hydrogen bonds       : angle       4.41890 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2995.17 seconds
wall clock time: 51 minutes 31.69 seconds (3091.69 seconds total)