Starting phenix.real_space_refine
on Wed Feb 12 22:07:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w88_37348/02_2025/8w88_37348_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w88_37348/02_2025/8w88_37348.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w88_37348/02_2025/8w88_37348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w88_37348/02_2025/8w88_37348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w88_37348/02_2025/8w88_37348_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w88_37348/02_2025/8w88_37348_neut.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8307
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1957
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 433
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2254
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "R"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 96
          Unusual residues: {'CLR': 3, 'UJL': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.05, per 1000 atoms: 0.61
  Number of scatterers: 8307
  At special positions: 0
  Unit cell: (83.224, 99.704, 135.136, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1519      8.00
     N    1419      7.00
     C    5307      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 954.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      44.6% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 37
      removed outlier: 3.558A  pdb=" N   LYS A  31 " --> pdb=" O   LYS A  27 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.522A  pdb=" N   ASN A 238 " --> pdb=" O   GLN A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 278
      removed outlier: 3.815A  pdb=" N   GLU A 267 " --> pdb=" O   ASN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 302
    Processing helix  chain 'A' and resid 306 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.506A  pdb=" N   PHE A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER A 351 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 390
      removed outlier: 4.494A  pdb=" N   ARG A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 39
      removed outlier: 3.520A  pdb=" N   ARG B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 47
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'G' and resid 5 through 23
    Processing helix  chain 'G' and resid 28 through 43
    Processing helix  chain 'N' and resid 29 through 33
    Processing helix  chain 'N' and resid 75 through 77
      No H-bonds generated for 'chain 'N' and resid 75 through 77'
    Processing helix  chain 'N' and resid 88 through 92
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 52 through 55
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 86
    Processing helix  chain 'R' and resid 92 through 127
      removed outlier: 3.685A  pdb=" N   LYS R  97 " --> pdb=" O   GLU R  93 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 160
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 179
      removed outlier: 3.740A  pdb=" N   HIS R 177 " --> pdb=" O   TYR R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 229
    Processing helix  chain 'R' and resid 248 through 277
      removed outlier: 3.683A  pdb=" N   PHE R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.585A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 316
      removed outlier: 3.514A  pdb=" N   ALA R 314 " --> pdb=" O   TRP R 310 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 213
      removed outlier: 6.407A  pdb=" N   HIS A  40 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   PHE A 221 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A  42 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL A 223 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ALA A 242 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE A 243 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 289 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   PHE A 245 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASN A 291 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64
      removed outlier: 6.308A  pdb=" N   THR B  60 " --> pdb=" O   ASN B 353 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ASN B 353 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS B 330 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 76
      removed outlier: 3.690A  pdb=" N   LYS B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LEU B  92 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ALA B 105 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE B  94 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118
      removed outlier: 6.657A  pdb=" N   GLY B 128 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   CYS B 116 " --> pdb=" O   ALA B 126 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ALA B 126 " --> pdb=" O   CYS B 116 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   TYR B 118 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   TYR B 124 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ASN B 138 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL B 148 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 164
      removed outlier: 3.609A  pdb=" N   CYS B 161 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 170 " --> pdb=" O   TRP B 182 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASP B 183 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLN B 189 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 205
      removed outlier: 6.786A  pdb=" N   GLY B 215 " --> pdb=" O   MET B 201 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU B 203 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL B 213 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   LEU B 205 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU B 211 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA B 221 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   THR B 234 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU B 223 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 247
      removed outlier: 6.579A  pdb=" N   CYS B 263 " --> pdb=" O   THR B 276 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   THR B 276 " --> pdb=" O   CYS B 263 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B 265 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLN B 272 " --> pdb=" O   ASP B 267 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 291
      removed outlier: 3.713A  pdb=" N   SER B 288 " --> pdb=" O   GLY B 301 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ASP B 311 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ARG B 317 " --> pdb=" O   ASP B 311 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8
      removed outlier: 3.522A  pdb=" N   THR N  79 " --> pdb=" O   ASP N  74 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 13
      removed outlier: 6.004A  pdb=" N   GLY N  11 " --> pdb=" O   THR N 126 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   MET N  35 " --> pdb=" O   ASP N  51 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ASP N  51 " --> pdb=" O   MET N  35 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   TRP N  37 " --> pdb=" O   VAL N  49 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 2.68 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:             1.150
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.020
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:13.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.060
-------------------------------------------------------------------------------
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   0.199   8494  Z= 0.402
  Angle     :  0.638  15.729  11518  Z= 0.342
  Chirality :  0.042   0.215   1295
  Planarity :  0.005   0.112   1446
  Dihedral  : 14.725  86.062   3232
  Min Nonbonded Distance : 2.143

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

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

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

*********************** 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  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.6524 (mp0) cc_final: 0.6294 (tp30)
REVERT: B   72 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7863 (m-80)
REVERT: N   47 GLU cc_start: 0.8111 (tt0) cc_final: 0.7891 (tt0)
  outliers start: 3
  outliers final: 2
  residues processed: 130
  average time/residue: 1.4110
  time to fit residues: 194.1710
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  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  287 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.149298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.109836 restraints weight = 8888.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.93
r_work: 0.3117 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       66 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8494  Z= 0.191
  Angle     :  0.540   6.069  11518  Z= 0.292
  Chirality :  0.043   0.159   1295
  Planarity :  0.004   0.052   1446
  Dihedral  :  5.182  58.441   1344
  Min Nonbonded Distance : 2.506

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

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

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

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

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 LEU cc_start: 0.7344 (mp) cc_final: 0.7119 (tp)
REVERT: A  310 TYR cc_start: 0.6734 (m-80) cc_final: 0.6066 (m-80)
REVERT: A  313 GLU cc_start: 0.7362 (pm20) cc_final: 0.7155 (pm20)
REVERT: A  316 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7048 (ptt90)
REVERT: A  326 GLU cc_start: 0.7066 (mp0) cc_final: 0.6246 (tp30)
REVERT: B   83 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8744 (pp)
REVERT: G   56 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7733 (m)
REVERT: G   57 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6597 (pm20)
REVERT: N   47 GLU cc_start: 0.8476 (tt0) cc_final: 0.8149 (tt0)
REVERT: N  107 ASP cc_start: 0.7932 (p0) cc_final: 0.7432 (p0)
REVERT: R  292 PHE cc_start: 0.7956 (m-80) cc_final: 0.7628 (m-10)
  outliers start: 23
  outliers final: 11
  residues processed: 147
  average time/residue: 1.2615
  time to fit residues: 197.1559
Evaluate side-chains
  134 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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
N  32 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.148532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.110512 restraints weight = 9712.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.94
r_work: 0.3346 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
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:       66 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      102 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8494  Z= 0.296
  Angle     :  0.562   7.313  11518  Z= 0.302
  Chirality :  0.045   0.166   1295
  Planarity :  0.004   0.055   1446
  Dihedral  :  5.430  58.098   1344
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.65 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1023
  helix:  2.24 (0.25), residues: 413
  sheet: -0.11 (0.34), residues: 225
  loop : -0.32 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 291 
 HIS   0.005   0.001   HIS R  63 
 PHE   0.018   0.002   PHE R 160 
 TYR   0.018   0.002   TYR R  79 
 ARG   0.005   0.000   ARG A 264 

*********************** 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
  146 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8751 (tt0)
REVERT: A  310 TYR cc_start: 0.7041 (m-80) cc_final: 0.6325 (m-80)
REVERT: A  316 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6979 (ptt90)
REVERT: A  326 GLU cc_start: 0.7064 (mp0) cc_final: 0.6395 (tp30)
REVERT: B   83 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8799 (pp)
REVERT: B  247 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.7996 (t80)
REVERT: G   56 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7399 (m)
REVERT: G   57 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6297 (pm20)
REVERT: N   47 GLU cc_start: 0.8442 (tt0) cc_final: 0.8180 (tt0)
REVERT: R  292 PHE cc_start: 0.7870 (m-80) cc_final: 0.7548 (m-10)
  outliers start: 33
  outliers final: 16
  residues processed: 136
  average time/residue: 1.3244
  time to fit residues: 191.1561
Evaluate side-chains
  127 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  116 CYS
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue  209 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0570
   chunk 76 optimal weight:    0.0770
   chunk 29 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.4656

-------------------------------------------------------------------------------
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**
B 272 GLN
N   4 GLN
N   6 GLN
N  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.153685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.117463 restraints weight = 9629.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.86
r_work: 0.3424 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      102 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      111 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8494  Z= 0.138
  Angle     :  0.463   5.164  11518  Z= 0.250
  Chirality :  0.041   0.138   1295
  Planarity :  0.004   0.057   1446
  Dihedral  :  4.841  59.164   1344
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 15.10 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1023
  helix:  2.48 (0.25), residues: 414
  sheet: -0.12 (0.33), residues: 223
  loop : -0.26 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 291 
 HIS   0.002   0.001   HIS R 113 
 PHE   0.010   0.001   PHE B 164 
 TYR   0.011   0.001   TYR R  79 
 ARG   0.005   0.000   ARG A 264 

*********************** 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
  158 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7326 (tp40) cc_final: 0.6743 (mt0)
REVERT: A   58 GLN cc_start: 0.7541 (mm110) cc_final: 0.5922 (tt0)
REVERT: A  212 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8637 (tt0)
REVERT: A  310 TYR cc_start: 0.7048 (m-80) cc_final: 0.6223 (m-80)
REVERT: A  316 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6842 (ptt90)
REVERT: A  326 GLU cc_start: 0.7017 (mp0) cc_final: 0.6351 (tp30)
REVERT: B  247 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8094 (t80)
REVERT: G   28 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7504 (mttp)
REVERT: G   56 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7390 (m)
REVERT: G   57 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6329 (pm20)
REVERT: N   44 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7024 (mttp)
REVERT: N   47 GLU cc_start: 0.8303 (tt0) cc_final: 0.7970 (tt0)
REVERT: N   61 TYR cc_start: 0.8452 (m-80) cc_final: 0.8175 (m-80)
REVERT: N  107 ASP cc_start: 0.7844 (p0) cc_final: 0.7616 (p0)
REVERT: R   53 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7818 (pm20)
REVERT: R   77 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7472 (mtt)
REVERT: R  292 PHE cc_start: 0.7765 (m-80) cc_final: 0.7446 (m-10)
  outliers start: 28
  outliers final: 11
  residues processed: 147
  average time/residue: 1.2720
  time to fit residues: 198.5513
Evaluate side-chains
  141 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue   54 GLN
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   77 MET
Chi-restraints excluded: chain R residue  209 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0870
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 25 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6758

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.116258 restraints weight = 9577.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.85
r_work: 0.3410 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      111 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      112 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8494  Z= 0.158
  Angle     :  0.478   8.598  11518  Z= 0.254
  Chirality :  0.041   0.131   1295
  Planarity :  0.004   0.055   1446
  Dihedral  :  4.669  58.423   1342
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 15.88 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1023
  helix:  2.59 (0.25), residues: 414
  sheet: -0.17 (0.32), residues: 223
  loop : -0.21 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.012   0.001   TYR R  79 
 ARG   0.006   0.000   ARG N  20 

*********************** 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
  154 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7191 (tt0)
REVERT: A   34 GLN cc_start: 0.7379 (tp40) cc_final: 0.6948 (mt0)
REVERT: A   58 GLN cc_start: 0.7567 (mm110) cc_final: 0.5902 (tm-30)
REVERT: A  212 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8615 (tt0)
REVERT: A  310 TYR cc_start: 0.7267 (m-80) cc_final: 0.6223 (m-80)
REVERT: A  316 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6797 (ptt90)
REVERT: A  326 GLU cc_start: 0.7060 (mp0) cc_final: 0.6385 (tp30)
REVERT: B   83 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8713 (pp)
REVERT: B  230 MET cc_start: 0.8583 (pmm) cc_final: 0.8356 (ppp)
REVERT: B  247 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8094 (t80)
REVERT: G   28 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7459 (mttp)
REVERT: G   57 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6372 (pm20)
REVERT: N   44 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6998 (mttp)
REVERT: N   47 GLU cc_start: 0.8303 (tt0) cc_final: 0.8028 (tt0)
REVERT: N   61 TYR cc_start: 0.8487 (m-80) cc_final: 0.8237 (m-80)
REVERT: R   53 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7851 (pm20)
REVERT: R  193 LEU cc_start: 0.7984 (mm) cc_final: 0.7578 (mm)
REVERT: R  280 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8199 (mp)
REVERT: R  292 PHE cc_start: 0.7802 (m-80) cc_final: 0.7481 (m-10)
  outliers start: 32
  outliers final: 13
  residues processed: 141
  average time/residue: 1.2774
  time to fit residues: 191.2273
Evaluate side-chains
  138 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue  212 GLN
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  316 ARG
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue   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   28 LYS
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  280 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0270
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.153450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.117008 restraints weight = 9562.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.86
r_work: 0.3420 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      112 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      122 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8494  Z= 0.152
  Angle     :  0.476   8.808  11518  Z= 0.252
  Chirality :  0.041   0.129   1295
  Planarity :  0.004   0.053   1446
  Dihedral  :  4.552  58.167   1342
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.33 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1023
  helix:  2.65 (0.25), residues: 414
  sheet: -0.26 (0.32), residues: 229
  loop : -0.01 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 291 
 HIS   0.002   0.001   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.011   0.001   TYR N  96 
 ARG   0.006   0.000   ARG A 264 

*********************** 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
  159 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7219 (tt0)
REVERT: A   34 GLN cc_start: 0.7254 (tp40) cc_final: 0.6781 (mt0)
REVERT: A   58 GLN cc_start: 0.7509 (mm110) cc_final: 0.5850 (tm-30)
REVERT: A  212 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8573 (tt0)
REVERT: A  310 TYR cc_start: 0.7451 (m-80) cc_final: 0.6453 (m-80)
REVERT: A  316 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6794 (ptt90)
REVERT: A  326 GLU cc_start: 0.7057 (mp0) cc_final: 0.6399 (tp30)
REVERT: B   83 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8690 (pp)
REVERT: B  208 ASP cc_start: 0.8235 (p0) cc_final: 0.7936 (p0)
REVERT: B  230 MET cc_start: 0.8620 (pmm) cc_final: 0.8379 (ppp)
REVERT: B  247 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8096 (t80)
REVERT: G   28 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7152 (mmtt)
REVERT: G   56 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7443 (m)
REVERT: G   57 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6327 (pm20)
REVERT: N   44 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7010 (mttp)
REVERT: N   47 GLU cc_start: 0.8305 (tt0) cc_final: 0.7975 (tt0)
REVERT: N   61 TYR cc_start: 0.8506 (m-80) cc_final: 0.8248 (m-80)
REVERT: R   53 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7868 (pm20)
REVERT: R  193 LEU cc_start: 0.8013 (mm) cc_final: 0.7614 (mm)
REVERT: R  292 PHE cc_start: 0.7843 (m-80) cc_final: 0.7521 (m-10)
  outliers start: 34
  outliers final: 14
  residues processed: 144
  average time/residue: 1.2195
  time to fit residues: 187.2530
Evaluate side-chains
  148 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
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  191 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  209 VAL
Chi-restraints excluded: chain R residue  229 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.8784

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.148797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111547 restraints weight = 9763.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.86
r_work: 0.3357 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      122 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      120 |
|-----------------------------------------------------------------------------|
r_final: 0.3322
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8494  Z= 0.301
  Angle     :  0.559   7.984  11518  Z= 0.298
  Chirality :  0.044   0.169   1295
  Planarity :  0.004   0.051   1446
  Dihedral  :  4.990  58.296   1342
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.44 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1023
  helix:  2.48 (0.25), residues: 413
  sheet: -0.24 (0.33), residues: 225
  loop : -0.11 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 291 
 HIS   0.006   0.001   HIS R  63 
 PHE   0.015   0.002   PHE R 160 
 TYR   0.015   0.001   TYR N  96 
 ARG   0.006   0.001   ARG A 264 

*********************** 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
  149 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7428 (tp40) cc_final: 0.7023 (mt0)
REVERT: A  212 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8639 (tt0)
REVERT: A  316 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6876 (ptt90)
REVERT: A  326 GLU cc_start: 0.7049 (mp0) cc_final: 0.6411 (tp30)
REVERT: B   83 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8826 (pp)
REVERT: B  230 MET cc_start: 0.8570 (pmm) cc_final: 0.8344 (ppp)
REVERT: B  247 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.7997 (t80)
REVERT: G   28 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7530 (mttp)
REVERT: G   56 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7508 (m)
REVERT: G   57 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6277 (pm20)
REVERT: N   44 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7187 (mttp)
REVERT: N   47 GLU cc_start: 0.8435 (tt0) cc_final: 0.8198 (tt0)
REVERT: N   61 TYR cc_start: 0.8526 (m-80) cc_final: 0.8258 (m-80)
REVERT: R   53 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7841 (pm20)
REVERT: R  193 LEU cc_start: 0.8035 (mm) cc_final: 0.7624 (mm)
REVERT: R  292 PHE cc_start: 0.7911 (m-80) cc_final: 0.7606 (m-10)
  outliers start: 35
  outliers final: 18
  residues processed: 135
  average time/residue: 1.2510
  time to fit residues: 179.8500
Evaluate side-chains
  134 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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  287 THR
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
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 2 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 76 optimal weight:    0.2980
   chunk 42 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.1782

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.150228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113571 restraints weight = 9766.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.87
r_work: 0.3376 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      120 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      126 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8494  Z= 0.213
  Angle     :  0.513   7.841  11518  Z= 0.274
  Chirality :  0.042   0.130   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  4.807  59.164   1342
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.78 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1023
  helix:  2.50 (0.25), residues: 413
  sheet: -0.22 (0.33), residues: 223
  loop : -0.11 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.012   0.001   PHE B 164 
 TYR   0.017   0.001   TYR R  79 
 ARG   0.007   0.000   ARG A 264 

*********************** 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
  146 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7394 (tp40) cc_final: 0.6977 (mt0)
REVERT: A   58 GLN cc_start: 0.7552 (mm110) cc_final: 0.5960 (tm-30)
REVERT: A  212 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8620 (tt0)
REVERT: A  222 ASP cc_start: 0.8877 (t0) cc_final: 0.8467 (t0)
REVERT: A  316 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6819 (ptt90)
REVERT: A  326 GLU cc_start: 0.7082 (mp0) cc_final: 0.6409 (tp30)
REVERT: B   83 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8770 (pp)
REVERT: B  230 MET cc_start: 0.8511 (pmm) cc_final: 0.8280 (ppp)
REVERT: B  247 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.7981 (t80)
REVERT: G   28 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7195 (mmtt)
REVERT: G   56 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7554 (m)
REVERT: G   57 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6338 (pm20)
REVERT: N   44 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7183 (mttp)
REVERT: N   47 GLU cc_start: 0.8382 (tt0) cc_final: 0.8103 (tt0)
REVERT: N   61 TYR cc_start: 0.8476 (m-80) cc_final: 0.8225 (m-80)
REVERT: N  107 ASP cc_start: 0.8118 (p0) cc_final: 0.7404 (p0)
REVERT: R   53 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7848 (pm20)
REVERT: R  193 LEU cc_start: 0.7992 (mm) cc_final: 0.7575 (mm)
REVERT: R  292 PHE cc_start: 0.7866 (m-80) cc_final: 0.7545 (m-10)
  outliers start: 32
  outliers final: 19
  residues processed: 135
  average time/residue: 1.2748
  time to fit residues: 182.6731
Evaluate side-chains
  141 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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  287 THR
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue    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  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 78 optimal weight:    4.9990
   chunk 66 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.151014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.114380 restraints weight = 9816.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.87
r_work: 0.3385 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      126 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      128 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8494  Z= 0.180
  Angle     :  0.498   7.671  11518  Z= 0.265
  Chirality :  0.041   0.130   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  4.729  59.933   1342
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.78 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1023
  helix:  2.57 (0.25), residues: 413
  sheet: -0.22 (0.32), residues: 221
  loop : -0.11 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE R  95 
 TYR   0.017   0.001   TYR R  79 
 ARG   0.007   0.000   ARG A 264 

*********************** 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: 32
    poor density    : 116
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7393 (tp40) cc_final: 0.6976 (mt0)
REVERT: A  212 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8620 (tt0)
REVERT: A  222 ASP cc_start: 0.8845 (t0) cc_final: 0.8437 (t0)
REVERT: A  316 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6799 (ptt90)
REVERT: A  326 GLU cc_start: 0.7068 (mp0) cc_final: 0.6403 (tp30)
REVERT: B   83 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8750 (pp)
REVERT: B  230 MET cc_start: 0.8519 (pmm) cc_final: 0.8286 (ppp)
REVERT: B  247 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8076 (t80)
REVERT: G   28 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7190 (mmtt)
REVERT: G   56 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7532 (m)
REVERT: G   57 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6388 (pm20)
REVERT: N   44 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7178 (mttp)
REVERT: N   47 GLU cc_start: 0.8354 (tt0) cc_final: 0.8076 (tt0)
REVERT: N   61 TYR cc_start: 0.8480 (m-80) cc_final: 0.8235 (m-80)
REVERT: N  107 ASP cc_start: 0.8062 (p0) cc_final: 0.7258 (p0)
REVERT: R   53 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7830 (pm20)
REVERT: R  193 LEU cc_start: 0.8015 (mm) cc_final: 0.7593 (mm)
REVERT: R  292 PHE cc_start: 0.7824 (m-80) cc_final: 0.7499 (m-10)
  outliers start: 32
  outliers final: 17
  residues processed: 138
  average time/residue: 1.2459
  time to fit residues: 182.6997
Evaluate side-chains
  140 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
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  287 THR
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
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 67 optimal weight:    0.0570
   chunk 60 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    2.1704

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
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 = 0.3875 r_free = 0.3875 target = 0.150260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113355 restraints weight = 9681.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.85
r_work: 0.3347 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      128 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      130 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8494  Z= 0.341
  Angle     :  0.582   7.652  11518  Z= 0.307
  Chirality :  0.045   0.165   1295
  Planarity :  0.004   0.050   1446
  Dihedral  :  5.068  57.963   1342
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.45 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.26), residues: 1023
  helix:  2.34 (0.25), residues: 413
  sheet: -0.24 (0.33), residues: 225
  loop : -0.12 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.006   0.001   HIS R  63 
 PHE   0.015   0.002   PHE A 211 
 TYR   0.020   0.002   TYR N  96 
 ARG   0.007   0.001   ARG B 147 

********************** 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
  139 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.7455 (tp40) cc_final: 0.7060 (mt0)
REVERT: A   58 GLN cc_start: 0.7553 (mm110) cc_final: 0.5975 (tm-30)
REVERT: A  212 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8665 (tt0)
REVERT: A  316 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6859 (ptt90)
REVERT: A  326 GLU cc_start: 0.7089 (mp0) cc_final: 0.6445 (tp30)
REVERT: B   83 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8829 (pp)
REVERT: B  230 MET cc_start: 0.8532 (pmm) cc_final: 0.8303 (ppp)
REVERT: B  247 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.7992 (t80)
REVERT: G   28 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7197 (mmtt)
REVERT: G   56 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7559 (m)
REVERT: G   57 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6344 (pm20)
REVERT: N   44 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7227 (mttp)
REVERT: N   47 GLU cc_start: 0.8451 (tt0) cc_final: 0.8227 (tt0)
REVERT: N   61 TYR cc_start: 0.8523 (m-80) cc_final: 0.8276 (m-80)
REVERT: R   53 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7872 (pm20)
REVERT: R  292 PHE cc_start: 0.7921 (m-80) cc_final: 0.7603 (m-10)
  outliers start: 29
  outliers final: 19
  residues processed: 130
  average time/residue: 1.3284
  time to fit residues: 183.7797
Evaluate side-chains
  138 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
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  287 THR
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  330 CYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain N residue   44 LYS
Chi-restraints excluded: chain N residue  105 THR
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue   53 GLN
Chi-restraints excluded: chain R residue  149 SER
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 97 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
B 145 ASN
B 272 GLN
N   4 GLN
N  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.150565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.113991 restraints weight = 9816.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.87
r_work: 0.3379 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      130 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      132 |
|-----------------------------------------------------------------------------|
r_final: 0.3353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8494  Z= 0.193
  Angle     :  0.510   7.491  11518  Z= 0.271
  Chirality :  0.042   0.130   1295
  Planarity :  0.004   0.049   1446
  Dihedral  :  4.777  59.360   1342
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1023
  helix:  2.51 (0.25), residues: 413
  sheet: -0.21 (0.33), residues: 221
  loop : -0.09 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 291 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.012   0.001   PHE R  95 
 TYR   0.016   0.001   TYR R  79 
 ARG   0.007   0.000   ARG A 264 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7334.28 seconds
wall clock time: 129 minutes 50.31 seconds (7790.31 seconds total)